RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9949
(383 letters)
>gnl|CDD|176210 cd08248, RTN4I1, Human Reticulon 4 Interacting Protein 1. Human
Reticulon 4 Interacting Protein 1 is a member of the
medium chain dehydrogenase/ reductase (MDR) family.
Riticulons are endoplasmic reticulum associated proteins
involved in membrane trafficking and neuroendocrine
secretion. The MDR/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES.
Length = 350
Score = 425 bits (1094), Expect = e-149
Identities = 172/355 (48%), Positives = 216/355 (60%), Gaps = 8/355 (2%)
Query: 29 AWQISSYGGADELQFNDNVKTP-ILKSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQ 87
AWQI SYGG D L +N + P I K VL+++ A SVNPIDV M GYG +LN R+
Sbjct: 3 AWQIHSYGGIDSLLLLENARIPVIRKPNQVLIKVHAASVNPIDVLMRSGYGRTLLNKKRK 62
Query: 88 LETCSVEPVLEFPLTLGRDFCGKIVAKGPRVTDLNIDDVVYGVIQPHKQGSFSKLILADS 147
++C + EFPLTLGRD G +V G V I D V+G + P QG+ ++ ++
Sbjct: 63 PQSCKYSGI-EFPLTLGRDCSGVVVDIGSGVKSFEIGDEVWGAVPPWSQGTHAEYVVVPE 121
Query: 148 ALVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRVLVLGASGGVGTMAVQ 207
V KKP N+S EEAA + Y GLTAWSAL L KRVL+LG SGGVGT A+Q
Sbjct: 122 NEVSKKPKNLSHEEAASLPYAGLTAWSALVNVGGLNPKNAAGKRVLILGGSGGVGTFAIQ 181
Query: 208 LLKAWDIEVVTTCSGDAKDLVTSLNPNLVIDYNEPEAMHSIAGAGPYDVILDAAGIPLDQ 267
LLKAW V TTCS DA LV SL + VIDYN + + G +DVILD G ++
Sbjct: 182 LLKAWGAHVTTTCSTDAIPLVKSLGADDVIDYNNEDFEEELTERGKFDVILDTVGGDTEK 241
Query: 268 INSYLPFLKTGKFSKFVTLRSPFLKNTDSLGLVPGLVKNAFDLLKSNFESGELCKTNTIR 327
L LK K +VTL SP LKNTD LGLV G++K+A DLLK N +S L K + R
Sbjct: 242 --WALKLLK--KGGTYVTLVSPLLKNTDKLGLVGGMLKSAVDLLKKNVKS--LLKGSHYR 295
Query: 328 WGFFMPIPYAVKEINKFIERGQIKPVIDSKYNFCELPTAFEKVQQGHLRGKIILN 382
WGFF P A+ E+ K +E G+IKPVID + F E+P A+EKV+ GH RGK ++
Sbjct: 296 WGFFSPSGSALDELAKLVEDGKIKPVIDKVFPFEEVPEAYEKVESGHARGKTVIK 350
>gnl|CDD|176191 cd05289, MDR_like_2, alcohol dehydrogenase and quinone
reductase-like medium chain degydrogenases/reductases.
Members identified as zinc-dependent alcohol
dehydrogenases and quinone oxidoreductase. QOR catalyzes
the conversion of a quinone + NAD(P)H to a hydroquinone
+ NAD(P)+. Quinones are cyclic diones derived from
aromatic compounds. Membrane bound QOR actin the
respiratory chains of bacteria and mitochondria, while
soluble QOR acts to protect from toxic quinones (e.g.
DT-diaphorase) or as a soluble eye-lens protein in some
vertebrates (e.g. zeta-crystalin). QOR reduces quinones
through a semi-quinone intermediate via a
NAD(P)H-dependent single electron transfer. QOR is a
member of the medium chain dehydrogenase/reductase
family, but lacks the zinc-binding sites of the
prototypical alcohol dehydrogenases of this group.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding domains
at the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 309
Score = 238 bits (611), Expect = 1e-76
Identities = 103/353 (29%), Positives = 162/353 (45%), Gaps = 46/353 (13%)
Query: 29 AWQISSYGGADELQFNDNVKTPILKSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQL 88
A +I YGG + L+ D V TP +VLV++ A VNP+D+ + G
Sbjct: 3 AVRIHEYGGPEVLELAD-VPTPEPGPGEVLVKVHAAGVNPVDLKIREGLLKAAFP----- 56
Query: 89 ETCSVEPVLEFPLTLGRDFCGKIVAKGPRVTDLNIDDVVYGVIQPHKQGSFSKLILADSA 148
L PL G D G +VA GP VT + D V+G+ + G++++ ++ +
Sbjct: 57 --------LTLPLIPGHDVAGVVVAVGPGVTGFKVGDEVFGMTPFTRGGAYAEYVVVPAD 108
Query: 149 LVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRVLVLGASGGVGTMAVQL 208
+ KP+N+S EEAA + GLTAW AL L + VL+ GA+GGVG+ AVQL
Sbjct: 109 ELALKPANLSFEEAAALPLAGLTAWQALFELGGLK----AGQTVLIHGAAGGVGSFAVQL 164
Query: 209 LKAWDIEVVTTCSGDAKDLVTSLNPNLVIDYNEPEAMHSIAGAGPYDVILDAAGIPLDQI 268
KA V+ T S D + SL + VIDY + + + A G D +LD G + +
Sbjct: 165 AKARGARVIATASAANADFLRSLGADEVIDYTKGDFERAAAP-GGVDAVLDTVGG--ETL 221
Query: 269 NSYLPFLKTGKFSKFVTLRSPFLKNTDSLGLVPGLVKNAFDLLKSNFESGELCKTNTIRW 328
L +K G + V++ P E + +
Sbjct: 222 ARSLALVKPG--GRLVSIAGP-----------------------PPAEQAAKRRGVRAGF 256
Query: 329 GFFMPIPYAVKEINKFIERGQIKPVIDSKYNFCELPTAFEKVQQGHLRGKIIL 381
F P + E+ + +E G+++PV+D + + A E+++ GH RGK++L
Sbjct: 257 VFVEPDGEQLAELAELVEAGKLRPVVDRVFPLEDAAEAHERLESGHARGKVVL 309
>gnl|CDD|176228 cd08267, MDR1, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 319
Score = 232 bits (594), Expect = 5e-74
Identities = 116/355 (32%), Positives = 171/355 (48%), Gaps = 39/355 (10%)
Query: 30 WQISSYGGADELQ-FNDNVKTPILKSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQL 88
+ YG + L V P K +VLV++ A SVNP+D + G ++L
Sbjct: 1 VVYTRYGSPEVLLLLEVEVPIPTPKPGEVLVKVHAASVNPVDWKLRRGPPKLLL------ 54
Query: 89 ETCSVEPVLEFPLTLGRDFCGKIVAKGPRVTDLNIDDVVYGVIQPHKQGSFSKLILADSA 148
FP G DF G++VA G VT + D V+G + P G+ ++ ++A +
Sbjct: 55 -------GRPFPPIPGMDFAGEVVAVGSGVTRFKVGDEVFGRLPPKGGGALAEYVVAPES 107
Query: 149 LVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRVLVLGASGGVGTMAVQL 208
+ KKP +S EEAA + GLTA AL+ G V P +RVL+ GASGGVGT AVQ+
Sbjct: 108 GLAKKPEGVSFEEAAALPVAGLTALQALR---DAGKVKP-GQRVLINGASGGVGTFAVQI 163
Query: 209 LKAWDIEVVTTCSGDAKDLVTSLNPNLVIDYNEPEAMHSIAGAGPYDVILDAAGIPLDQI 268
KA V CS +LV SL + VIDY + + AG YDVI DA G +
Sbjct: 164 AKALGAHVTGVCSTRNAELVRSLGADEVIDYTTEDFVALTAGGEKYDVIFDAVGNSPFSL 223
Query: 269 NSYLPFLKTGKFSKFVTLRSPFLKNTDSLGLVPGLVKNAFDLLKSNFESGELCKTNTIRW 328
LK G ++V++ G GL+ L + G R
Sbjct: 224 YRASLALKPGG--RYVSV----------GGGPSGLLLVLLLLPLTLGGGGR-------RL 264
Query: 329 GFFMPIPYA--VKEINKFIERGQIKPVIDSKYNFCELPTAFEKVQQGHLRGKIIL 381
FF+ P A ++++ + +E G++KPVIDS Y + P A+ +++ G RGK+++
Sbjct: 265 KFFLAKPNAEDLEQLAELVEEGKLKPVIDSVYPLEDAPEAYRRLKSGRARGKVVI 319
>gnl|CDD|223677 COG0604, Qor, NADPH:quinone reductase and related Zn-dependent
oxidoreductases [Energy production and conversion /
General function prediction only].
Length = 326
Score = 182 bits (463), Expect = 2e-54
Identities = 99/363 (27%), Positives = 147/363 (40%), Gaps = 51/363 (14%)
Query: 29 AWQISSYGGADELQFNDNVKTPILKSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQL 88
A + +GG + L+ + V P +VLV +KA VNPIDV + G
Sbjct: 3 AVVVEEFGGPEVLKVVE-VPEPEPGPGEVLVRVKAAGVNPIDVLVRQGLAP--------- 52
Query: 89 ETCSVEPVLEFPLTLGRDFCGKIVAKGPRVTDLNIDDVVYGVIQPHKQGSFSKLILADSA 148
PV P G + G +VA G VT + D V + + G +++ ++ +
Sbjct: 53 ------PVRPLPFIPGSEAAGVVVAVGSGVTGFKVGDRVAALGGVGRDGGYAEYVVVPAD 106
Query: 149 LVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRVLVLGASGGVGTMAVQL 208
+ P +S EEAA + GLTAW AL A L + VLV GA+GGVG+ A+QL
Sbjct: 107 WLVPLPDGLSFEEAAALPLAGLTAWLALFDRAGLKP----GETVLVHGAAGGVGSAAIQL 162
Query: 209 LKAWDIEVV-TTCSGDAKDLVTSLNPNLVIDYNEP---EAMHSIAGAGPYDVILDAAGIP 264
KA VV S + +L+ L + VI+Y E E + + G DV+LD G
Sbjct: 163 AKALGATVVAVVSSSEKLELLKELGADHVINYREEDFVEQVRELTGGKGVDVVLDTVGG- 221
Query: 265 LDQINSYLPFLKT-GKFSKFVTLRSPFLKNTDSLGLVPGLVKNAFDLLKSNFESGELCKT 323
D + L L G+ L + L L+ +
Sbjct: 222 -DTFAASLAALAPGGRLVSIGALSGGPPVPLNLLPLLGKRLT------------------ 262
Query: 324 NTIRWGFFMPIPYAV----KEINKFIERGQIKPVIDSKYNFCELPTAFEKV-QQGHLRGK 378
P A+ E+ + G++KPVID Y E P A + + GK
Sbjct: 263 -LRGVTLGSRDPEALAEALAELFDLLASGKLKPVIDRVYPLAEAPAAAAHLLLERRTTGK 321
Query: 379 IIL 381
++L
Sbjct: 322 VVL 324
>gnl|CDD|176233 cd08272, MDR6, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 326
Score = 157 bits (399), Expect = 6e-45
Identities = 101/363 (27%), Positives = 150/363 (41%), Gaps = 57/363 (15%)
Query: 32 ISSYGGADELQFNDNVKTPILKSKDVLVEMKAVSVNPIDVAM-LGGYGNVVLNSLRQLET 90
+ S+GG + + + V P VLV + A VNP+D + GG
Sbjct: 6 LESFGGPEVFELRE-VPRPQPGPGQVLVRVHASGVNPLDTKIRRGGAAARP--------- 55
Query: 91 CSVEPVLEFPLTLGRDFCGKIVAKGPRVTDLNIDDVVYGVIQPHK--QGSFSKLILADSA 148
P LG D G + A G VT + D VYG QGS ++ + D+
Sbjct: 56 -------PLPAILGCDVAGVVEAVGEGVTRFRVGDEVYGCAGGLGGLQGSLAEYAVVDAR 108
Query: 149 LVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRVLVLGASGGVGTMAVQL 208
L+ KP+N+S EAA + G+TAW L AA+ + VL+ G +GGVG +AVQL
Sbjct: 109 LLALKPANLSMREAAALPLVGITAWEGLVDRAAVQA----GQTVLIHGGAGGVGHVAVQL 164
Query: 209 LKAWDIEVVTTCSGDAKDLVTSLNPNLVIDYNEP---EAMHSIAGAGPYDVILDAAGIP- 264
KA V T S + SL + +I Y E G G +DV+ D G
Sbjct: 165 AKAAGARVYATASSEKAAFARSLGADPIIYYRETVVEYVAEHTGGRG-FDVVFDTVGGET 223
Query: 265 LDQINSYLPFLKTGKFSKFVTLRSPFLKNTDSLGLVPGLVKNA-----FDLLKSNFESGE 319
LD F + + V++ + L P +NA F LL G
Sbjct: 224 LDA-----SFEAVALYGRVVSILGG-----ATHDLAPLSFRNATYSGVFTLLPLLTGEGR 273
Query: 320 LCKTNTIRWGFFMPIPYAVKEINKFIERGQIKPVIDSK-YNFCELPTAFEKVQQGHLRGK 378
+R E + +ERGQ++P++D + + E A +++ G RGK
Sbjct: 274 AHHGEILR------------EAARLVERGQLRPLLDPRTFPLEEAAAAHARLESGSARGK 321
Query: 379 IIL 381
I++
Sbjct: 322 IVI 324
>gnl|CDD|176209 cd08247, AST1_like, AST1 is a cytoplasmic protein associated with
the periplasmic membrane in yeast. This group contains
members identified in targeting of yeast membrane
proteins ATPase. AST1 is a cytoplasmic protein
associated with the periplasmic membrane in yeast,
identified as a multicopy suppressor of pma1 mutants
which cause temperature sensitive growth arrest due to
the inability of ATPase to target to the cell surface.
This family is homologous to the medium chain family of
dehydrogenases and reductases. Medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of an
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES.
Length = 352
Score = 149 bits (379), Expect = 8e-42
Identities = 103/362 (28%), Positives = 157/362 (43%), Gaps = 54/362 (14%)
Query: 47 VKTPI---LKSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQLETCSVEPVLEFPLTL 103
+K P+ K +++V++ A ++NP+D+ + Y L
Sbjct: 18 IKLPLPNCYKDNEIVVKVHAAALNPVDLKLYNSYTFHFKVK---------------EKGL 62
Query: 104 GRDFCGKIVAKGPRV-TDLNIDDVVYGVIQPH---KQGSFSKLILADSALVHK----KPS 155
GRD+ G IV G V ++ + D V G I PH QG+ S+ +L D K KP
Sbjct: 63 GRDYSGVIVKVGSNVASEWKVGDEVCG-IYPHPYGGQGTLSQYLLVDPKKDKKSITRKPE 121
Query: 156 NISDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRVLVLGASGGVGTMAVQLLK-AWDI 214
NIS EEAA TA+ L + P D +VLVLG S VG A+QL K ++I
Sbjct: 122 NISLEEAAAWPLVLGTAYQIL--EDLGQKLGP-DSKVLVLGGSTSVGRFAIQLAKNHYNI 178
Query: 215 -EVVTTCSGDAKDLVTSLNPNLVIDYNEP-------EAMHSIAGAGPYDVILDAAGIP-- 264
VV TCS + +L L + IDY+ + ++ G G +D+ILD G
Sbjct: 179 GTVVGTCSSRSAELNKKLGADHFIDYDAHSGVKLLKPVLENVKGQGKFDLILDCVGGYDL 238
Query: 265 LDQINSYLPFLKTGKFSKFVTL--RSPFLKNTDSLGLVPGLVKNAFDLLKSNFESGELCK 322
INS L +VT+ D+ NA L S
Sbjct: 239 FPHINSILKPKSKN--GHYVTIVGDYKANYKKDTFNSWDNPSANARKLFGS-------LG 289
Query: 323 TNTIRWGFFMPIPYA--VKEINKFIERGQIKPVIDSKYNFCELPTAFEKVQQGHLRGKII 380
+ + FF+ P A +++ + I G++KP IDS Y F + AFE+++ +GK++
Sbjct: 290 LWSYNYQFFLLDPNADWIEKCAELIADGKVKPPIDSVYPFEDYKEAFERLKSNRAKGKVV 349
Query: 381 LN 382
+
Sbjct: 350 IK 351
>gnl|CDD|176215 cd08253, zeta_crystallin, Zeta-crystallin with NADP-dependent
quinone reductase activity (QOR). Zeta-crystallin is a
eye lens protein with NADP-dependent quinone reductase
activity (QOR). It has been cited as a structural
component in mammalian eyes, but also has homology to
quinone reductases in unrelated species. QOR catalyzes
the conversion of a quinone and NAD(P)H to a
hydroquinone and NAD(P+. Quinones are cyclic diones
derived from aromatic compounds. Membrane bound QOR acts
in the respiratory chains of bacteria and mitochondria,
while soluble QOR acts to protect from toxic quinones
(e.g. DT-diaphorase) or as a soluble eye-lens protein in
some vertebrates (e.g. zeta-crystalin). QOR reduces
quinones through a semi-quinone intermediate via a
NAD(P)H-dependent single electron transfer. QOR is a
member of the medium chain dehydrogenase/reductase
family, but lacks the zinc-binding sites of the
prototypical alcohol dehydrogenases of this group.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation. ADH
is a member of the medium chain alcohol dehydrogenase
family (MDR), which has a NAD(P)(H)-binding domain in a
Rossmann fold of a beta-alpha form. The NAD(H)-binding
region is comprised of 2 structurally similar halves,
each of which contacts a mononucleotide. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site, and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the
cleft between the catalytic and coenzyme-binding domains
at the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 325
Score = 144 bits (365), Expect = 4e-40
Identities = 86/366 (23%), Positives = 138/366 (37%), Gaps = 57/366 (15%)
Query: 28 AAWQISSYGGADELQFNDNVKTPILKSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQ 87
A +G D L+ D + P +VLV + A VNP+D + G
Sbjct: 3 AIR-YHEFGAPDVLRLGD-LPVPTPGPGEVLVRVHASGVNPVDTYIRAG----------- 49
Query: 88 LETCSVEPVLEFPLTLGRDFCGKIVAKGPRVTDLNIDDVVY--GVIQPHKQGSFSKLILA 145
+ + P G D G + A G V L + D V+ + +QG+ ++ ++
Sbjct: 50 ----AYPGLPPLPYVPGSDGAGVVEAVGEGVDGLKVGDRVWLTNLGWGRRQGTAAEYVVV 105
Query: 146 DSALVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRVLVLGASGGVGTMA 205
+ + P +S E+ A + LTA+ AL A G + VLV G SG VG A
Sbjct: 106 PADQLVPLPDGVSFEQGAALGIPALTAYRAL-FHRA-GAK--AGETVLVHGGSGAVGHAA 161
Query: 206 VQLLKAWDIEVVTTCSGDAK-DLVTSLNPNLVIDYNEP---EAMHSIAGAGPYDVILDAA 261
VQL + V+ T S +LV + V +Y + + + DVI++
Sbjct: 162 VQLARWAGARVIATASSAEGAELVRQAGADAVFNYRAEDLADRILAATAGQGVDVIIEVL 221
Query: 262 GIPLDQINSYLPFLKTGKFSKFVTLRSPFLKNTDSLGLVPGLVKNAFDLLKSNFESGELC 321
+ L L G + V S ++ + P + K A
Sbjct: 222 AN--VNLAKDLDVLAPG--GRIVVYGSG--GLRGTIPINPLMAKEA-------------- 261
Query: 322 KTNTIRWGFFMPIPY------AVKEINKFIERGQIKPVIDSKYNFCELPTAFEKVQQGHL 375
+IR G + A + I + G ++PVI +Y E A E V+ G
Sbjct: 262 ---SIR-GVLLYTATPEERAAAAEAIAAGLADGALRPVIAREYPLEEAAAAHEAVESGGA 317
Query: 376 RGKIIL 381
GK++L
Sbjct: 318 IGKVVL 323
>gnl|CDD|176211 cd08249, enoyl_reductase_like, enoyl_reductase_like. Member
identified as possible enoyl reductase of the MDR
family. 2-enoyl thioester reductase (ETR) catalyzes the
NADPH-dependent dependent conversion of trans-2-enoyl
acyl carrier protein/coenzyme A (ACP/CoA) to
acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl
thioester reductase activity has been linked in Candida
tropicalis as essential in maintaining mitiochondrial
respiratory function. This ETR family is a part of the
medium chain dehydrogenase/reductase family, but lack
the zinc coordination sites characteristic of the
alcohol dehydrogenases in this family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. The N-terminal catalytic domain has a
distant homology to GroES. These proteins typically
form dimers (typically higher plants, mammals) or
tetramers (yeast, bacteria), and have 2 tightly bound
zinc atoms per subunit, a catalytic zinc at the active
site, and a structural zinc in a lobe of the catalytic
domain. NAD(H)-binding occurs in the cleft between the
catalytic and coenzyme-binding domains at the active
site, and coenzyme binding induces a conformational
closing of this cleft. Coenzyme binding typically
precedes and contributes to substrate binding. Candida
tropicalis enoyl thioester reductase (Etr1p) catalyzes
the NADPH-dependent reduction of trans-2-enoyl
thioesters in mitochondrial fatty acid synthesis. Etr1p
forms homodimers with each subunit containing a
nucleotide-binding Rossmann fold domain and a catalytic
domain.
Length = 339
Score = 142 bits (361), Expect = 2e-39
Identities = 80/251 (31%), Positives = 112/251 (44%), Gaps = 33/251 (13%)
Query: 27 TAAWQISSYGGADELQFNDNVKTPILKSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLR 86
AA GG + +V P +VLV++KAV++NP+D
Sbjct: 2 KAAVLTGPGGGLLVVV---DVPVPKPGPDEVLVKVKAVALNPVDWKHQDYG--------- 49
Query: 87 QLETCSVEPVLEFPLTLGRDFCGKIVAKGPRVTDLNIDDVVYGVIQ-----PHKQGSFSK 141
+ +P LG DF G +V G VT + D V G + + G+F +
Sbjct: 50 --------FIPSYPAILGCDFAGTVVEVGSGVTRFKVGDRVAGFVHGGNPNDPRNGAFQE 101
Query: 142 LILADSALVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYP------RDKRVLVL 195
++AD+ L K P NIS EEAA + +TA AL L L P + K VL+
Sbjct: 102 YVVADADLTAKIPDNISFEEAATLPVGLVTAALALFQKLGLPLPPPKPSPASKGKPVLIW 161
Query: 196 GASGGVGTMAVQLLKAWDIEVVTTCSGDAKDLVTSLNPNLVIDYNEPEAMHSIAGA--GP 253
G S VGT+A+QL K +V+TT S DLV SL + V DY++P+ + I A G
Sbjct: 162 GGSSSVGTLAIQLAKLAGYKVITTASPKNFDLVKSLGADAVFDYHDPDVVEDIRAATGGK 221
Query: 254 YDVILDAAGIP 264
LD P
Sbjct: 222 LRYALDCISTP 232
>gnl|CDD|176203 cd08241, QOR1, Quinone oxidoreductase (QOR). QOR catalyzes the
conversion of a quinone + NAD(P)H to a hydroquinone +
NAD(P)+. Quinones are cyclic diones derived from
aromatic compounds. Membrane bound QOR acts in the
respiratory chains of bacteria and mitochondria, while
soluble QOR acts to protect from toxic quinones (e.g.
DT-diaphorase) or as a soluble eye-lens protein in some
vertebrates (e.g. zeta-crystalin). QOR reduces quinones
through a semi-quinone intermediate via a
NAD(P)H-dependent single electron transfer. QOR is a
member of the medium chain dehydrogenase/reductase
family, but lacks the zinc-binding sites of the
prototypical alcohol dehydrogenases of this group.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site, and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the
cleft between the catalytic and coenzyme-binding domains
at the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 323
Score = 134 bits (341), Expect = 1e-36
Identities = 95/377 (25%), Positives = 146/377 (38%), Gaps = 81/377 (21%)
Query: 29 AWQISSYGGADELQFNDNVKTPILKSKDVLVEMKAVSVNPIDVAMLGG-YGNVVLNSLRQ 87
A GG ++L + P + V + ++A VN D+ M+ G Y
Sbjct: 3 AVVCKELGGPEDLVLEEVPPEPGAPGE-VRIRVEAAGVNFPDLLMIQGKYQVKP------ 55
Query: 88 LETCSVEPVLEFPLTLGRDFCGKIVAKGPRVTDLNIDDVVYGVIQPHKQGSFSKLILADS 147
P G + G + A G VT + D V + QG F++ ++ +
Sbjct: 56 ----------PLPFVPGSEVAGVVEAVGEGVTGFKVGDRVVALTG---QGGFAEEVVVPA 102
Query: 148 ALVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRVLVLGASGGVGTMAVQ 207
A V P +S EEAA + T TA+ AL A L P + VLVLGA+GGVG AVQ
Sbjct: 103 AAVFPLPDGLSFEEAAALPVTYGTAYHALVRRARLQ---PGET-VLVLGAAGGVGLAAVQ 158
Query: 208 LLKAWDIEVVTTCSGDAK-DLVTSLNPNLVIDYNEP---EAMHSIAGAGPYDVILDAAGI 263
L KA V+ S + K L +L + VIDY +P E + ++ G DV+ D G
Sbjct: 159 LAKALGARVIAAASSEEKLALARALGADHVIDYRDPDLRERVKALTGGRGVDVVYDPVG- 217
Query: 264 PLDQINSYLPFLKTGKFSKFVTLRSPFLKNTDSLGLVPGLVKNAFD--LLKSNFESGE-- 319
G + SL + A+ LL F SGE
Sbjct: 218 --------------GDVFE------------ASLRSL------AWGGRLLVIGFASGEIP 245
Query: 320 -------LCKTNTI---RWGFFM-----PIPYAVKEINKFIERGQIKPVIDSKYNFCELP 364
L K ++ WG + + + E+ + G+I+P + + + +
Sbjct: 246 QIPANLLLLKNISVVGVYWGAYARREPELLRANLAELFDLLAEGKIRPHVSAVFPLEQAA 305
Query: 365 TAFEKVQQGHLRGKIIL 381
A + GK++L
Sbjct: 306 EALRALADRKATGKVVL 322
>gnl|CDD|176214 cd08252, AL_MDR, Arginate lyase and other MDR family members. This
group contains a structure identified as an arginate
lyase. Other members are identified quinone reductases,
alginate lyases, and other proteins related to the
zinc-dependent dehydrogenases/reductases. QOR catalyzes
the conversion of a quinone and NAD(P)H to a
hydroquinone and NAD(P+. Quinones are cyclic diones
derived from aromatic compounds. Membrane bound QOR acts
in the respiratory chains of bacteria and mitochondria,
while soluble QOR acts to protect from toxic quinones
(e.g. DT-diaphorase) or as a soluble eye-lens protein in
some vertebrates (e.g. zeta-crystalin). QOR reduces
quinones through a semi-quinone intermediate via a
NAD(P)H-dependent single electron transfer. QOR is a
member of the medium chain dehydrogenase/reductase
family, but lacks the zinc-binding sites of the
prototypical alcohol dehydrogenases of this group.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation. ADH
is a member of the medium chain alcohol dehydrogenase
family (MDR), which has a NAD(P)(H)-binding domain in a
Rossmann fold of a beta-alpha form. The NAD(H)-binding
region is comprised of 2 structurally similar halves,
each of which contacts a mononucleotide. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H) binding occurs in the cleft
between the catalytic and coenzyme-binding domains at
the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 336
Score = 131 bits (332), Expect = 3e-35
Identities = 93/357 (26%), Positives = 151/357 (42%), Gaps = 62/357 (17%)
Query: 46 NVKTPILKSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQLETCSVEPVLEFPLTLGR 105
+ P+ +D+LV ++AVSVNP+D + G PV P LG
Sbjct: 22 ELPKPVPGGRDLLVRVEAVSVNPVDTKVRAGGA----------------PVPGQPKILGW 65
Query: 106 DFCGKIVAKGPRVTDLNIDDVVY--GVIQPHKQGSFSKLILADSALVHKKPSNISDEEAA 163
D G + A G VT + D VY G I + GS ++ L D +V KP ++S EAA
Sbjct: 66 DASGVVEAVGSEVTLFKVGDEVYYAGDIT--RPGSNAEYQLVDERIVGHKPKSLSFAEAA 123
Query: 164 GVLYTGLTAWSAL----QITAALGLVYPRDKRVLVLGASGGVGTMAVQLLKAW-DIEVVT 218
+ T LTAW AL I+ K +L++G +GGVG++A+QL K + V+
Sbjct: 124 ALPLTSLTAWEALFDRLGISEDAE---NEGKTLLIIGGAGGVGSIAIQLAKQLTGLTVIA 180
Query: 219 TCS-GDAKDLVTSLNPNLVIDYNEP--EAMHSIAGAGPYDVILDAAGIP--LDQINSYL- 272
T S ++ V L + VI++++ E + ++ G P D I D + +
Sbjct: 181 TASRPESIAWVKELGADHVINHHQDLAEQLEAL-GIEPVDYIFCLTDTDQHWDAMAELIA 239
Query: 273 PFLKTGKFSKFVTLRSPF----LKNTDSLGLVPGLVKNAFDLLKSNFESGELCKTNTIRW 328
P G V + P LK+ S F +S F++ ++ + + I
Sbjct: 240 PQ---GHICLIVDPQEPLDLGPLKSK-SASFH-----WEFMFTRSMFQTPDMIEQHEI-- 288
Query: 329 GFFMPIPYAVKEINKFIERGQIKPVIDSKY---NFCELPTAFEKVQQGHLRGKIILN 382
+ E+ ++ G++K + N L A ++ G GKI+L
Sbjct: 289 ---------LNEVADLLDAGKLKTTLTETLGPINAENLREAHALLESGKTIGKIVLE 336
>gnl|CDD|176232 cd08271, MDR5, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 325
Score = 130 bits (328), Expect = 1e-34
Identities = 75/243 (30%), Positives = 114/243 (46%), Gaps = 34/243 (13%)
Query: 28 AAWQISSYGGADELQFNDNVKTPILKSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQ 87
AW + G A +L + ++ P + +VLV++ A +NP+D ++ G
Sbjct: 2 KAWVLPKPGAALQLTLEE-IEIPGPGAGEVLVKVHAAGLNPVDWKVIAW-GP-------- 51
Query: 88 LETCSVEPVLEFPLTLGRDFCGKIVAKGPRVTDLNIDD-VVYGVIQPH----KQGSFSKL 142
P +P G D G +VA G +VT + D V Y H + GSF++
Sbjct: 52 -------PAWSYPHVPGVDGAGVVVAVGAKVTGWKVGDRVAY-----HASLARGGSFAEY 99
Query: 143 ILADSALVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRVLVLGASGGVG 202
+ D+ V P ++S EEAA + GLTA+ AL + + +L+ G +GGVG
Sbjct: 100 TVVDARAVLPLPDSLSFEEAAALPCAGLTAYQALFKKLRI----EAGRTILITGGAGGVG 155
Query: 203 TMAVQLLKAWDIEVVTTCSGDAKDLVTSLNPNLVIDYNEPEAMHSIAGA-GPY--DVILD 259
+ AVQL K + V+TTCS + V SL + VIDYN+ + I G D +LD
Sbjct: 156 SFAVQLAKRAGLRVITTCSKRNFEYVKSLGADHVIDYNDEDVCERIKEITGGRGVDAVLD 215
Query: 260 AAG 262
G
Sbjct: 216 TVG 218
>gnl|CDD|176178 cd05188, MDR, Medium chain reductase/dehydrogenase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
The medium chain reductase/dehydrogenases
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH) , quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. ADH-like proteins
typically form dimers (typically higher plants, mammals)
or tetramers (yeast, bacteria), and generally have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. The active site zinc is
coordinated by a histidine, two cysteines, and a water
molecule. The second zinc seems to play a structural
role, affects subunit interactions, and is typically
coordinated by 4 cysteines. Other MDR members have only
a catalytic zinc, and some contain no coordinated zinc.
Length = 271
Score = 127 bits (322), Expect = 2e-34
Identities = 71/246 (28%), Positives = 105/246 (42%), Gaps = 44/246 (17%)
Query: 56 DVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQLETCSVEPVLEFPLTLGRDFCGKIVAKG 115
+VLV ++A + D+ + G P + PL LG + G +V G
Sbjct: 1 EVLVRVEAAGLCGTDLHIRRGGY---------------PPPPKLPLILGHEGAGVVVEVG 45
Query: 116 PRVTDLNI-DDVVY-------------------GVIQPHKQGSFSKLILADSALVHKKPS 155
P VT + + D VV G++ G F++ ++ + + P
Sbjct: 46 PGVTGVKVGDRVVVLPNLGCGTCELCRELCPGGGILGEGLDGGFAEYVVVPADNLVPLPD 105
Query: 156 NISDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRVLVLGASGGVGTMAVQLLKAWDIE 215
+S EEAA + TA+ AL+ V VLVLGA GGVG +A QL KA
Sbjct: 106 GLSLEEAALLPEPLATAYHALRRAG----VLKPGDTVLVLGA-GGVGLLAAQLAKAAGAR 160
Query: 216 VVTTCSGDAK-DLVTSLNPNLVIDY--NEPEAMHSIAGAGPYDVILDAAGIPLDQINSYL 272
V+ T D K +L L + VIDY + E + G G DV++DA G P + + L
Sbjct: 161 VIVTDRSDEKLELAKELGADHVIDYKEEDLEEELRLTGGGGADVVIDAVGGP-ETLAQAL 219
Query: 273 PFLKTG 278
L+ G
Sbjct: 220 RLLRPG 225
>gnl|CDD|176179 cd05195, enoyl_red, enoyl reductase of polyketide synthase.
Putative enoyl reductase of polyketide synthase.
Polyketide synthases produce polyketides in step by step
mechanism that is similar to fatty acid synthesis. Enoyl
reductase reduces a double to single bond. Erythromycin
is one example of a polyketide generated by 3 complex
enzymes (megasynthases). 2-enoyl thioester reductase
(ETR) catalyzes the NADPH-dependent dependent conversion
of trans-2-enoyl acyl carrier protein/coenzyme A
(ACP/CoA) to acyl-(ACP/CoA) in fatty acid synthesis.
2-enoyl thioester reductase activity has been linked in
Candida tropicalis as essential in maintaining
mitiochondrial respiratory function. This ETR family is
a part of the medium chain dehydrogenase/reductase
family, but lack the zinc coordination sites
characteristic of the alcohol dehydrogenases in this
family. NAD(P)(H)-dependent oxidoreductases are the
major enzymes in the interconversion of alcohols and
aldehydes or ketones. Alcohol dehydrogenase in the liver
converts ethanol and NAD+ to acetaldehyde and NADH,
while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. The N-terminal catalytic domain has a
distant homology to GroES. These proteins typically
form dimers (typically higher plants, mammals) or
tetramers (yeast, bacteria), and have 2 tightly bound
zinc atoms per subunit, a catalytic zinc at the active
site, and a structural zinc in a lobe of the catalytic
domain. NAD(H) binding occurs in the cleft between the
catalytic and coenzyme-binding domains, at the active
site, and coenzyme binding induces a conformational
closing of this cleft. Coenzyme binding typically
precedes and contributes to substrate binding.
Length = 293
Score = 126 bits (318), Expect = 1e-33
Identities = 86/343 (25%), Positives = 140/343 (40%), Gaps = 68/343 (19%)
Query: 56 DVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQLETCSVEPVLEFPLTLGRDFCGKIVAKG 115
+V VE+KA +N DV + G + LG + G + G
Sbjct: 2 EVEVEVKAAGLNFRDVLVALG------------------LLPGDETPLGLECSGIVTRVG 43
Query: 116 PRVTDLNIDDVVYGVIQPHKQGSFSKLILADSALVHKKPSNISDEEAAGVLYTGLTAWSA 175
VT L + D V G+ G+F+ + D+ LV K P ++S EEAA + LTA+ A
Sbjct: 44 SGVTGLKVGDRVMGLAP----GAFATHVRVDARLVVKIPDSLSFEEAATLPVAYLTAYYA 99
Query: 176 LQITAALGLVYPRDKRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAK-DLVTSL--- 231
L A L + + VL+ A+GGVG A+QL + EV T + K + + L
Sbjct: 100 LVDLARLQ----KGESVLIHAAAGGVGQAAIQLAQHLGAEVFATVGSEEKREFLRELGGP 155
Query: 232 --------NPNLVIDYNEPEAMHSIAGAGPYDVILDA-AGIPLDQINSYLPFLKTGKFSK 282
+ + + + G G DV+L++ +G L L F +
Sbjct: 156 VDHIFSSRDLSFA-----DGILRATGGRG-VDVVLNSLSGELLRASWRCL-----APFGR 204
Query: 283 FVTLRSPFLKNTDSLGLVPGLVKN----AFDLLKSNFESGELCKTNTIRWGFFMPIPYAV 338
FV + + + LG+ P L +N + DL + E EL + +
Sbjct: 205 FVEIGKRDILSNSKLGMRPFL-RNVSFSSVDLDQLARERPELLRE-------------LL 250
Query: 339 KEINKFIERGQIKPVIDSKYNFCELPTAFEKVQQGHLRGKIIL 381
+E+ + +E G +KP+ + AF +Q G GK++L
Sbjct: 251 REVLELLEAGVLKPLPPTVVPSASEIDAFRLMQSGKHIGKVVL 293
>gnl|CDD|176180 cd05276, p53_inducible_oxidoreductase, PIG3 p53-inducible quinone
oxidoreductase. PIG3 p53-inducible quinone
oxidoreductase, a medium chain dehydrogenase/reductase
family member, acts in the apoptotic pathway. PIG3
reduces ortho-quinones, but its apoptotic activity has
been attributed to oxidative stress generation, since
overexpression of PIG3 accumulates reactive oxygen
species. PIG3 resembles the MDR family member quinone
reductases, which catalyze the reduction of quinone to
hydroxyquinone. NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES.
These proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
have 2 tightly bound zinc atoms per subunit, a catalytic
zinc at the active site, and a structural zinc in a lobe
of the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding domains
at the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 323
Score = 126 bits (318), Expect = 3e-33
Identities = 64/239 (26%), Positives = 97/239 (40%), Gaps = 29/239 (12%)
Query: 29 AWQISSYGGADELQFNDNVKTPILKSKDVLVEMKAVSVNPIDVAM-LGGYGNVVLNSLRQ 87
A I GG + L+ + V P +VL+ + A VN D+ G Y
Sbjct: 3 AIVIKEPGGPEVLELGE-VPKPAPGPGEVLIRVAAAGVNRADLLQRQGLYP--------- 52
Query: 88 LETCSVEPVLEFPLTLGRDFCGKIVAKGPRVTDLNIDDVVYGVIQPHKQGSFSKLILADS 147
P LG + G +VA GP VT + D V ++ G +++ ++ +
Sbjct: 53 -------PPPGASDILGLEVAGVVVAVGPGVTGWKVGDRVCALLA---GGGYAEYVVVPA 102
Query: 148 ALVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRVLVLGASGGVGTMAVQ 207
+ P +S EAA + TAW L L + VL+ G + GVGT A+Q
Sbjct: 103 GQLLPVPEGLSLVEAAALPEVFFTAWQNLFQLGGLK----AGETVLIHGGASGVGTAAIQ 158
Query: 208 LLKAWDIEVVTTCSGDAK-DLVTSLNPNLVIDYNEP---EAMHSIAGAGPYDVILDAAG 262
L KA V+ T + K + +L ++ I+Y E + G DVILD G
Sbjct: 159 LAKALGARVIATAGSEEKLEACRALGADVAINYRTEDFAEEVKEATGGRGVDVILDMVG 217
Score = 37.0 bits (87), Expect = 0.013
Identities = 12/37 (32%), Positives = 19/37 (51%)
Query: 345 IERGQIKPVIDSKYNFCELPTAFEKVQQGHLRGKIIL 381
G+I+PVID + E A +++ GKI+L
Sbjct: 287 FASGRIRPVIDKVFPLEEAAEAHRRMESNEHIGKIVL 323
>gnl|CDD|176236 cd08275, MDR3, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 337
Score = 125 bits (315), Expect = 9e-33
Identities = 99/382 (25%), Positives = 154/382 (40%), Gaps = 77/382 (20%)
Query: 29 AWQISSYGGADELQFNDNVKTPILKSKDVLVEMKAVSVNPIDV-AMLGGYGNVVLNSLRQ 87
A ++ +GG D+L+ P S +V V ++A +N D+ A G Y +
Sbjct: 2 AVVLTGFGGLDKLKVEKEAL-PEPSSGEVRVRVEACGLNFADLMARQGLYDSAP------ 54
Query: 88 LETCSVEPVLEFPLTLGRDFCGKIVAKGPRVTDLNIDDVVYGVIQPHKQGSFSKLILADS 147
+ P G + G + A G V D + D V G+ + G +++++ +
Sbjct: 55 ----------KPPFVPGFECAGTVEAVGEGVKDFKVGDRVMGLT---RFGGYAEVVNVPA 101
Query: 148 ALVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRVLVLGASGGVGTMAVQ 207
V P +S EEAA LTA+ AL LG + P + VLV A+GGVG A Q
Sbjct: 102 DQVFPLPDGMSFEEAAAFPVNYLTAYYAL---FELGNLRP-GQSVLVHSAAGGVGLAAGQ 157
Query: 208 LLKA-WDIEVVTTCSGDAKDLVTSLNPNLVIDYNEP---EAMHSIAGAGPYDVILDAAGI 263
L K ++ VV T S + + VIDY E + I+ G D++LDA G
Sbjct: 158 LCKTVPNVTVVGTASASKHEALKENGVTHVIDYRTQDYVEEVKKISPEG-VDIVLDALGG 216
Query: 264 PLDQINSYLPFLK-TGK-----FSKFVTLRSP-FLK------NTDSLGLVPGLVKNAFDL 310
+ + L LK G+ + VT + K N + + L
Sbjct: 217 EDTRKSYDL--LKPMGRLVVYGAANLVTGEKRSWFKLAKKWWNRPKV--------DPMKL 266
Query: 311 LKSN-----------FESGELCKTNTIRWGFFMPIPYAVKEINKFIERGQIKPVIDSKYN 359
+ N FE EL + + ++ K E G+IKP IDS +
Sbjct: 267 ISENKSVLGFNLGWLFEEREL-----LTE--------VMDKLLKLYEEGKIKPKIDSVFP 313
Query: 360 FCELPTAFEKVQQGHLRGKIIL 381
F E+ A ++Q GK++L
Sbjct: 314 FEEVGEAMRRLQSRKNIGKVVL 335
>gnl|CDD|176227 cd08266, Zn_ADH_like1, Alcohol dehydrogenases of the MDR family.
This group contains proteins related to the
zinc-dependent alcohol dehydrogenases. However, while
the group has structural zinc site characteristic of
these enzymes, it lacks the consensus site for a
catalytic zinc. NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site, and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the cleft
between the catalytic and coenzyme-binding domains at
the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 342
Score = 122 bits (309), Expect = 7e-32
Identities = 97/395 (24%), Positives = 149/395 (37%), Gaps = 97/395 (24%)
Query: 29 AWQISSYGGADELQFNDNVKTPILKSKDVLVEMKAVSVNPIDV-AMLGGYGNVVLNSLRQ 87
A I +GG + L++ D + P +VLV +KA ++N +D+ G G
Sbjct: 3 AVVIRGHGGPEVLEYGD-LPEPEPGPDEVLVRVKAAALNHLDLWVRRGMPG--------- 52
Query: 88 LETCSVEPVLEFPLTLGRDFCGKIVAKGPRVTDLNIDDVV-------------------- 127
L P LG D G + A GP VT++ V
Sbjct: 53 -------IKLPLPHILGSDGAGVVEAVGPGVTNVKPGQRVVIYPGISCGRCEYCLAGREN 105
Query: 128 ----YGVIQPHKQGSFSKLILADSALVHKKPSNISDEEAAGVLYTGLTAWSALQITAALG 183
YG++ H G +++ + + + P N+S EEAA T LTAW L +T A
Sbjct: 106 LCAQYGILGEHVDGGYAEYVAVPARNLLPIPDNLSFEEAAAAPLTFLTAWHML-VTRAR- 163
Query: 184 LVYPRDKRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAK-DLVTSLNPNLVIDYNE- 241
+ P + VLV GA GVG+ A+Q+ K + V+ T + K + L + VIDY +
Sbjct: 164 -LRPGE-TVLVHGAGSGVGSAAIQIAKLFGATVIATAGSEDKLERAKELGADYVIDYRKE 221
Query: 242 --PEAMHSIAGAGPYDVILDAAGIPLDQINSYLPFLKTGKFSKFVT------------LR 287
+ + G DV+++ G L L G + VT LR
Sbjct: 222 DFVREVRELTGKRGVDVVVEHVG--AATWEKSLKSLARG--GRLVTCGATTGYEAPIDLR 277
Query: 288 SPFLKNTDSLGLVPGLVKNAFDLLKSNFESGELCKTNTIRWGFFMPIPYAVKEINKFIER 347
F + LG G + L + + R
Sbjct: 278 HVFWRQLSILGSTMGTKAELDEAL-------------------------------RLVFR 306
Query: 348 GQIKPVIDSKYNFCELPTAFEKVQQGHLRGKIILN 382
G++KPVIDS + E A +++ GKI+L
Sbjct: 307 GKLKPVIDSVFPLEEAAEAHRRLESREQFGKIVLT 341
>gnl|CDD|176237 cd08276, MDR7, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 336
Score = 122 bits (309), Expect = 7e-32
Identities = 107/386 (27%), Positives = 157/386 (40%), Gaps = 91/386 (23%)
Query: 29 AWQISSYGGADELQFNDNVKTPILKSKDVLVEMKAVSVNPIDVAML-GGYGNVVLNSLRQ 87
AW++S GG D L+ + P +VLV + AVS+N D+ +L G Y
Sbjct: 3 AWRLSGGGGLDNLKLVE-EPVPEPGPGEVLVRVHAVSLNYRDLLILNGRYP--------- 52
Query: 88 LETCSVEPVLEFPLTLGRDFCGKIVAKGPRVTDLNIDDVVYGVIQP-HKQGSFSK----- 141
P ++ PL D G++VA G VT + D V P G +
Sbjct: 53 -------PPVKDPLIPLSDGAGEVVAVGEGVTRFKVGDRVVPTFFPNWLDGPPTAEDEAS 105
Query: 142 -------------LILADSALVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYPR 188
++L + LV P ++S EEAA + GLTAW+AL LG + P
Sbjct: 106 ALGGPIDGVLAEYVVLPEEGLVR-APDHLSFEEAATLPCAGLTAWNAL---FGLGPLKPG 161
Query: 189 DKRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAK-DLVTSLNPNLVIDYNE-P---- 242
D VLV G +GGV A+Q KA V+ T S D K + +L + VI+Y P
Sbjct: 162 DT-VLVQG-TGGVSLFALQFAKAAGARVIATSSSDEKLERAKALGADHVINYRTTPDWGE 219
Query: 243 EAMHSIAGAGPYDVILDAAGIP-LDQ-INSYLPFLKTGKFSKFVTLRSPFLKNTDSLGLV 300
E + G G D +++ G L Q I + + G + S F + L+
Sbjct: 220 EVLKLTGGRG-VDHVVEVGGPGTLAQSIKA----VAPGGVISLIGFLSGF---EAPVLLL 271
Query: 301 PGLVKNAFDLLKSNFESGELCKTNTI-------RWGFFMPIPYAVKEINKFIERGQIKPV 353
P L K A T+ R F + +N+ IE +I+PV
Sbjct: 272 PLLTKGA-----------------TLRGIAVGSRAQF--------EAMNRAIEAHRIRPV 306
Query: 354 IDSKYNFCELPTAFEKVQQGHLRGKI 379
ID + F E A+ ++ G GK+
Sbjct: 307 IDRVFPFEEAKEAYRYLESGSHFGKV 332
>gnl|CDD|176189 cd05286, QOR2, Quinone oxidoreductase (QOR). Quinone
oxidoreductase (QOR) and 2-haloacrylate reductase. QOR
catalyzes the conversion of a quinone + NAD(P)H to a
hydroquinone + NAD(P)+. Quinones are cyclic diones
derived from aromatic compounds. Membrane bound QOR
actin the respiratory chains of bacteria and
mitochondria, while soluble QOR acts to protect from
toxic quinones (e.g. DT-diaphorase) or as a soluble
eye-lens protein in some vertebrates (e.g.
zeta-crystalin). QOR reduces quinones through a
semi-quinone intermediate via a NAD(P)H-dependent single
electron transfer. QOR is a member of the medium chain
dehydrogenase/reductase family, but lacks the
zinc-binding sites of the prototypical alcohol
dehydrogenases of this group. 2-haloacrylate reductase,
a member of this subgroup, catalyzes the NADPH-dependent
reduction of a carbon-carbon double bond in
organohalogen compounds. Although similar to QOR,
Burkholderia 2-haloacrylate reductase does not act on
the quinones 1,4-benzoquinone and 1,4-naphthoquinone.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES.
These proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
have 2 tightly bound zinc atoms per subunit, a catalytic
zinc at the active site and a structural zinc in a lobe
of the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding domains
at the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 320
Score = 119 bits (301), Expect = 7e-31
Identities = 72/238 (30%), Positives = 103/238 (43%), Gaps = 33/238 (13%)
Query: 31 QISSYGGADELQFNDNVKTPILKSKDVLVEMKAVSVNPIDVAMLGG-YGNVVLNSLRQLE 89
+I GG + L++ D V P +VLV A+ VN ID G Y
Sbjct: 4 RIHKTGGPEVLEYED-VPVPEPGPGEVLVRNTAIGVNFIDTYFRSGLY------------ 50
Query: 90 TCSVEPVLEFPLTLGRDFCGKIVAKGPRVTDLNIDD-VVYGVIQPHKQGSFSKLILADSA 148
L P LG + G + A GP VT + D V Y G++++ + ++
Sbjct: 51 ------PLPLPFVLGVEGAGVVEAVGPGVTGFKVGDRVAYAGPP----GAYAEYRVVPAS 100
Query: 149 LVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRVLVLGASGGVGTMAVQL 208
+ K P ISDE AA +L GLTA L+ T + VLV A+GGVG + Q
Sbjct: 101 RLVKLPDGISDETAAALLLQGLTAHYLLRETYPVK----PGDTVLVHAAAGGVGLLLTQW 156
Query: 209 LKAWDIEVVTTCSGDAK-DLVTSLNPNLVIDYNE---PEAMHSIAGAGPYDVILDAAG 262
KA V+ T S + K +L + + VI+Y + E + I G DV+ D G
Sbjct: 157 AKALGATVIGTVSSEEKAELARAAGADHVINYRDEDFVERVREITGGRGVDVVYDGVG 214
>gnl|CDD|214840 smart00829, PKS_ER, Enoylreductase. Enoylreductase in Polyketide
synthases.
Length = 287
Score = 118 bits (298), Expect = 9e-31
Identities = 83/344 (24%), Positives = 133/344 (38%), Gaps = 78/344 (22%)
Query: 59 VEMKAVSVNPIDVAMLGGYGNVVLNSLRQLETCSVEPVLEFPLTLGRDFCGKIVAKGPRV 118
+E++A +N DV L +L LG + G + GP V
Sbjct: 1 IEVRAAGLNFRDV----------LIALGLYP---------GEAVLGGECAGVVTRVGPGV 41
Query: 119 TDLNIDDVVYGVIQPHKQGSFSKLILADSALVHKKPSNISDEEAAGVLYTGLTAWSALQI 178
T L + D V G+ G+F+ ++ D+ LV P S EEAA V LTA+ AL
Sbjct: 42 TGLAVGDRVMGLAP----GAFATRVVTDARLVVPIPDGWSFEEAATVPVVFLTAYYALVD 97
Query: 179 TAALGLVYPRDKRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAK-DLVTSLNPNLVI 237
A L + VL+ A+GGVG A+QL + EV T K D + +L I
Sbjct: 98 LARLR----PGESVLIHAAAGGVGQAAIQLARHLGAEVFATAGSPEKRDFLRALG----I 149
Query: 238 D----YN------EPEAMHSIAGAGPYDVILDA-AGIPLDQINSYLPFLKTG-----KFS 281
++ E + + G G DV+L++ +G FL
Sbjct: 150 PDDHIFSSRDLSFADEILRATGGRG-VDVVLNSLSG----------EFLDASLRCLAPGG 198
Query: 282 KFVTLRSPFLKNTDSLGLVPGLVKN----AFDLLKSNFESGELCKTNTIRWGFFMPIPYA 337
+FV + +++ L + P N A DL E + +
Sbjct: 199 RFVEIGKRDIRDNSQLAMAP-FRPNVSYHAVDLDAL-EEGPDRIRE-------------L 243
Query: 338 VKEINKFIERGQIKPVIDSKYNFCELPTAFEKVQQGHLRGKIIL 381
+ E+ + G ++P+ + + + AF +QQG GK++L
Sbjct: 244 LAEVLELFAEGVLRPLPVTVFPISDAEDAFRYMQQGKHIGKVVL 287
>gnl|CDD|223992 COG1064, AdhP, Zn-dependent alcohol dehydrogenases [General
function prediction only].
Length = 339
Score = 111 bits (280), Expect = 7e-28
Identities = 91/382 (23%), Positives = 153/382 (40%), Gaps = 79/382 (20%)
Query: 29 AWQISSYGGADELQFNDNVKTPILKSKDVLVEMKAVSVNPIDVAML-GGYGNVVLNSLRQ 87
A + +G E++ V P +VL++++A V D+ + G + L
Sbjct: 6 AAVLKKFGQPLEIE---EVPVPEPGPGEVLIKVEACGVCHTDLHVAKGDWPVPKL----- 57
Query: 88 LETCSVEPVLEFPLTLGRDFCGKIVAKGPRVTDLNIDDVVYGV----------------- 130
PL G + G +V G VT L + D V GV
Sbjct: 58 ------------PLIPGHEIVGTVVEVGEGVTGLKVGDRV-GVGWLVISCGECEYCRSGN 104
Query: 131 --IQPHK-------QGSFSKLILADSALVHKKPSNISDEEAAGVLYTGLTAWSALQITAA 181
+ P++ G +++ ++ + V K P + EAA +L G+T + AL+
Sbjct: 105 ENLCPNQKITGYTTDGGYAEYVVVPARYVVKIPEGLDLAEAAPLLCAGITTYRALKKAN- 163
Query: 182 LGLVYPRDKRVLVLGASGGVGTMAVQLLKAWDIEVVT-TCSGDAKDLVTSLNPNLVIDYN 240
V P K V V+GA GG+G MAVQ KA EV+ T S + +L L + VI+ +
Sbjct: 164 ---VKP-GKWVAVVGA-GGLGHMAVQYAKAMGAEVIAITRSEEKLELAKKLGADHVINSS 218
Query: 241 EPEAMHSIAGAGPYDVILDAAGIPLDQINSYLPFLKTGKFSKFVTLRSPFLKNTDSLGLV 300
+ +A+ ++ D I+D G + L L+ G V + P L
Sbjct: 219 DSDALEAVKEI--ADAIIDTVGPAT--LEPSLKALRRG--GTLVLVGLPGGGPIPLL--- 269
Query: 301 PGLVKNAFDLLKSNFESGELCKTNTIRWGFFMPIPYAVKEINKFIERGQIKPVIDSKYNF 360
AF L+ E+ +I +E F G+IKP I
Sbjct: 270 -----PAFLLI-----LKEI----SIVGSLVGTRADL-EEALDFAAEGKIKPEILETIPL 314
Query: 361 CELPTAFEKVQQGHLRGKIILN 382
E+ A+E++++G +RG+ +++
Sbjct: 315 DEINEAYERMEKGKVRGRAVID 336
>gnl|CDD|176229 cd08268, MDR2, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 328
Score = 110 bits (278), Expect = 1e-27
Identities = 86/368 (23%), Positives = 142/368 (38%), Gaps = 59/368 (16%)
Query: 29 AWQISSYGGADELQFNDNVKTPILKSKDVLVEMKAVSVNPIDVAM-LGGYGNVVLNSLRQ 87
A + +GG + L+ + + P + +VL+ ++A+ +N D G Y
Sbjct: 3 AVRFHQFGGPEVLRIEE-LPVPAPGAGEVLIRVEAIGLNRADAMFRRGAYI--------- 52
Query: 88 LETCSVEPVLEFPLTLGRDFCGKIVAKGPRVTDLNIDDVVYGVIQP--HKQGSFSKLILA 145
P LG + G + A G VT + D V + + G++++ L
Sbjct: 53 -------EPPPLPARLGYEAAGVVEAVGAGVTGFAVGDRVSVIPAADLGQYGTYAEYALV 105
Query: 146 DSALVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRVLVLGASGGVGTMA 205
+A V K P +S EAA + LTA+ AL L + P D VL+ AS VG A
Sbjct: 106 PAAAVVKLPDGLSFVEAAALWMQYLTAYGAL---VELAGLRPGD-SVLITAASSSVGLAA 161
Query: 206 VQLLKAWD-IEVVTTCSGDAKDLVTSLNPNLVIDYNE---PEAMHSIAGAGPYDVILDAA 261
+Q+ A + TT + + +D + +L VI +E + I G DV+ D
Sbjct: 162 IQIANAAGATVIATTRTSEKRDALLALGAAHVIVTDEEDLVAEVLRITGGKGVDVVFDPV 221
Query: 262 GIPLDQINSYLPFLKTGKFSKFVTLRSPFLKNTDSLGLVPGLVKNAFDLLKSNF-ESGEL 320
G P F+K +P +V A + F L
Sbjct: 222 GGPQ--------------FAKLADALAPGGT---------LVVYGALSGEPTPFPLKAAL 258
Query: 321 CKTNTIR----WGFFMP---IPYAVKEINKFIERGQIKPVIDSKYNFCELPTAFEKVQQG 373
K+ T R + A+ I + G +KPV+D + F ++ A ++ G
Sbjct: 259 KKSLTFRGYSLDEITLDPEARRRAIAFILDGLASGALKPVVDRVFPFDDIVEAHRYLESG 318
Query: 374 HLRGKIIL 381
GKI++
Sbjct: 319 QQIGKIVV 326
>gnl|CDD|176235 cd08274, MDR9, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 350
Score = 106 bits (268), Expect = 4e-26
Identities = 97/391 (24%), Positives = 153/391 (39%), Gaps = 79/391 (20%)
Query: 28 AAWQISSYGGADELQFNDNVKTPILKSKDVLVEMKAVSVNPIDVAM-LGGYGNVV---LN 83
A ++ +GG D+L + D+V P +VL+ + A VN D+ G Y V +
Sbjct: 2 RAVLLTGHGGLDKLVYRDDVPVPTPAPGEVLIRVGACGVNNTDINTREGWYSTEVDGATD 61
Query: 84 SLRQLETCSVEPVLEFPLTLGRDFCGKIVAKGPRVTDLNIDDVVYGVIQP---------- 133
S E L FP G D G++VA G V I + V ++ P
Sbjct: 62 STGAGEAGWWGGTLSFPRIQGADIVGRVVAVGEGVDTARIGERV--LVDPSIRDPPEDDP 119
Query: 134 --------HKQGSFSKLILADSALVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLV 185
+ G F++ + + + S +SD E A + TA + L+ A +G
Sbjct: 120 ADIDYIGSERDGGFAEYTVVPAENAYPVNSPLSDVELATFPCSYSTAENMLE-RAGVG-- 176
Query: 186 YPRDKRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAKDLVTSLNPNLVIDYNEP-EA 244
+ VLV GASGGVG+ VQL K V+ ++ V +L + VI + P A
Sbjct: 177 --AGETVLVTGASGGVGSALVQLAKRRGAIVIAVAGAAKEEAVRALGADTVILRDAPLLA 234
Query: 245 MHSIAGAGPYDVILDAAGIPLDQINSYLPFLKTGKFSKFVT------------LRSPFLK 292
G P DV+ D G PL L L+ G ++VT LR+ +LK
Sbjct: 235 DAKALGGEPVDVVADVVGGPL--FPDLLRLLRPG--GRYVTAGAIAGPVVELDLRTLYLK 290
Query: 293 NTDSLGLVPGLVKNAFDLLKSNFESGELCKTNTIRWGFFMPIPYAVKEINKFIERGQIKP 352
+ G G +R+ IE G+I+P
Sbjct: 291 DLTLFGSTLG-------------TREVF--RRLVRY----------------IEEGEIRP 319
Query: 353 VIDSKYNFCELPTAFEK-VQQGHLRGKIILN 382
V+ + E+ A + +++ H+ GK++L
Sbjct: 320 VVAKTFPLSEIREAQAEFLEKRHV-GKLVLV 349
>gnl|CDD|234024 TIGR02817, adh_fam_1, zinc-binding alcohol dehydrogenase family
protein. Members of this model form a distinct subset
of the larger family of oxidoreductases that includes
zinc-binding alcohol dehydrogenases and NADPH:quinone
reductases (pfam00107). While some current members of
this family carry designations as putative alginate
lyase, it seems no sequence with a direct
characterization as such is detected by this model
[Energy metabolism, Fermentation].
Length = 336
Score = 101 bits (254), Expect = 3e-24
Identities = 63/201 (31%), Positives = 99/201 (49%), Gaps = 29/201 (14%)
Query: 50 PILKSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQLETCSVEPVLEFPLTLGRDFCG 109
P +D+LVE+KA+SVNP+D +R + P P LG D G
Sbjct: 25 PKPGGRDLLVEVKAISVNPVDT------------KVRA----RMAPEAGQPKILGWDAAG 68
Query: 110 KIVAKGPRVTDLNIDDVVY--GVIQPHKQGSFSKLILADSALVHKKPSNISDEEAAGVLY 167
+VA G VT D V+ G I + GS ++ L D +V KP ++S EAA +
Sbjct: 69 VVVAVGDEVTLFKPGDEVWYAGDID--RPGSNAEFHLVDERIVGHKPKSLSFAEAAALPL 126
Query: 168 TGLTAWSA----LQITAALGLVYPRDKRVLVLGASGGVGTMAVQLLKAW-DIEVVTTCS- 221
T +TAW L I V + +L++G +GGVG++ +QL + + V+ T S
Sbjct: 127 TSITAWELLFDRLGINDP---VAGDKRALLIIGGAGGVGSILIQLARQLTGLTVIATASR 183
Query: 222 GDAKDLVTSLNPNLVIDYNEP 242
++++ V L + VID+++P
Sbjct: 184 PESQEWVLELGAHHVIDHSKP 204
>gnl|CDD|176206 cd08244, MDR_enoyl_red, Possible enoyl reductase. Member
identified as possible enoyl reductase of the MDR
family. 2-enoyl thioester reductase (ETR) catalyzes the
NADPH-dependent dependent conversion of trans-2-enoyl
acyl carrier protein/coenzyme A (ACP/CoA) to
acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl
thioester reductase activity has been linked in Candida
tropicalis as essential in maintaining mitiochondrial
respiratory function. This ETR family is a part of the
medium chain dehydrogenase/reductase family, but lack
the zinc coordination sites characteristic of the
alcohol dehydrogenases in this family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. The N-terminal catalytic domain has a
distant homology to GroES. These proteins typically
form dimers (typically higher plants, mammals) or
tetramers (yeast, bacteria), and have 2 tightly bound
zinc atoms per subunit, a catalytic zinc at the active
site, and a structural zinc in a lobe of the catalytic
domain. NAD(H) binding occurs in the cleft between the
catalytic and coenzyme-binding domains at the active
site, and coenzyme binding induces a conformational
closing of this cleft. Coenzyme binding typically
precedes and contributes to substrate binding. Candida
tropicalis enoyl thioester reductase (Etr1p) catalyzes
the NADPH-dependent reduction of trans-2-enoyl
thioesters in mitochondrial fatty acid synthesis. Etr1p
forms homodimers, with each subunit containing a
nucleotide-binding Rossmann fold domain and a catalytic
domain.
Length = 324
Score = 98.6 bits (246), Expect = 3e-23
Identities = 66/239 (27%), Positives = 101/239 (42%), Gaps = 26/239 (10%)
Query: 29 AWQISSYGGADELQFNDNVKTPILKSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQL 88
A ++ +G + L D V P+ V + + A V+ +D + G+G
Sbjct: 3 AIRLHEFGPPEVLVPED-VPDPVPGPGQVRIAVAAAGVHFVDTQLRSGWG---------- 51
Query: 89 ETCSVEPVL-EFPLTLGRDFCGKIVAKGPRVTDLNIDDVVYGVIQPHKQGSFSKLILADS 147
P E P G + G + A GP V + V G +++L +AD
Sbjct: 52 ----PGPFPPELPYVPGGEVAGVVDAVGPGVDPAWLGRRVVAHT-GRAGGGYAELAVADV 106
Query: 148 ALVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRVLVLGASGGVGTMAVQ 207
+H P + E A V++ G TA L + + P D VLV A+GG+G++ VQ
Sbjct: 107 DSLHPVPDGLDLEAAVAVVHDGRTALGLLDLAT----LTPGD-VVLVTAAAGGLGSLLVQ 161
Query: 208 LLKAWDIEVVTTCSGDAK-DLVTSLNPNLVIDYNEP---EAMHSIAGAGPYDVILDAAG 262
L KA VV G AK LV +L ++ +DY P + + G G V+LD G
Sbjct: 162 LAKAAGATVVGAAGGPAKTALVRALGADVAVDYTRPDWPDQVREALGGGGVTVVLDGVG 220
>gnl|CDD|234027 TIGR02824, quinone_pig3, putative NAD(P)H quinone oxidoreductase,
PIG3 family. Members of this family are putative
quinone oxidoreductases that belong to the broader
superfamily (modeled by Pfam pfam00107) of
zinc-dependent alcohol (of medium chain length)
dehydrogenases and quinone oxiooreductases. The
alignment shows no motif of conserved Cys residues as
are found in zinc-binding members of the superfamily,
and members are likely to be quinone oxidoreductases
instead. A member of this family in Homo sapiens, PIG3,
is induced by p53 but is otherwise uncharacterized
[Unknown function, Enzymes of unknown specificity].
Length = 325
Score = 96.6 bits (241), Expect = 2e-22
Identities = 66/238 (27%), Positives = 102/238 (42%), Gaps = 27/238 (11%)
Query: 29 AWQISSYGGADELQFNDNVKTPILKSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQL 88
A +I+ GG + L + V P+ K+ +VL+ + A VN D+ G
Sbjct: 3 AIEITEPGGPEVLVLVE-VPLPVPKAGEVLIRVAAAGVNRPDLLQRAG------------ 49
Query: 89 ETCSVEPVLEFPLTLGRDFCGKIVAKGPRVTDLNIDDVVYGVIQPHKQGSFSKLILADSA 148
P LG + G++VA G V+ + D V ++ G +++ + +
Sbjct: 50 ---KYPPPPGASDILGLEVAGEVVAVGEGVSRWKVGDRVCALVA---GGGYAEYVAVPAG 103
Query: 149 LVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRVLVLGASGGVGTMAVQL 208
V P +S EAA + T T WS L L + VL+ G + G+GT A+QL
Sbjct: 104 QVLPVPEGLSLVEAAALPETFFTVWSNLFQRGGLK----AGETVLIHGGASGIGTTAIQL 159
Query: 209 LKAWDIEVVTTCSGDAK-DLVTSLNPNLVIDYNE---PEAMHSIAGAGPYDVILDAAG 262
KA+ V TT D K +L ++ I+Y E E + + G DVILD G
Sbjct: 160 AKAFGARVFTTAGSDEKCAACEALGADIAINYREEDFVEVVKAETGGKGVDVILDIVG 217
Score = 33.0 bits (76), Expect = 0.21
Identities = 11/37 (29%), Positives = 20/37 (54%)
Query: 345 IERGQIKPVIDSKYNFCELPTAFEKVQQGHLRGKIIL 381
+ G+++PVID + + A ++ G GKI+L
Sbjct: 287 LASGRVRPVIDKVFPLEDAAQAHALMESGDHIGKIVL 323
>gnl|CDD|176234 cd08273, MDR8, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 331
Score = 95.4 bits (238), Expect = 5e-22
Identities = 81/358 (22%), Positives = 131/358 (36%), Gaps = 41/358 (11%)
Query: 32 ISSYGGADELQFNDNVKTPILKSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQLETC 91
++ GG + L+ P + +V+V+++A V+ DV M G
Sbjct: 6 VTRRGGPEVLKV-VEADLPEPAAGEVVVKVEASGVSFADVQMRRG-------------LY 51
Query: 92 SVEPVLEFPLTLGRDFCGKIVAKGPRVTDLNIDDVVYGVIQPHKQGSFSKLILADSALVH 151
+P P T G D G++ A G VT + D V + + G ++ I D+ +
Sbjct: 52 PDQP--PLPFTPGYDLVGRVDALGSGVTGFEVGDRVAALT---RVGGNAEYINLDAKYLV 106
Query: 152 KKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRVLVLGASGGVGTMAVQLLKA 211
P + EA ++ +TA+ L A V +RVL+ GASGGVG ++L
Sbjct: 107 PVPEGVDAAEAVCLVLNYVTAYQMLHRAA---KV-LTGQRVLIHGASGGVGQALLELALL 162
Query: 212 WDIEVVTTCSGDAKDLVTSLN--PNLVIDYNE---PEAMHSIAGAGPYDVILDAAGIPLD 266
EV T S + L P IDY AM + G DV+ D G+ +
Sbjct: 163 AGAEVYGTASERNHAALRELGATP---IDYRTKDWLPAMLTPGGV---DVVFD--GVGGE 214
Query: 267 QINSYLPFLKTGKFSKFVTLRSPFLKNTDSLGLVPGLVKNAFDLLKSNFESGELCKTNTI 326
L G V L A +G +
Sbjct: 215 SYEESYAALAPG--GTLVCYGGNSSLLQGRRSLAALGSLLARLAKLKLLPTGRRATFYYV 272
Query: 327 RWGFFM-PIPYA--VKEINKFIERGQIKPVIDSKYNFCELPTAFEKVQQGHLRGKIIL 381
P + + E+ + +G+I+P I + E+ A ++ G + GKI+L
Sbjct: 273 WRDRAEDPKLFRQDLTELLDLLAKGKIRPKIAKRLPLSEVAEAHRLLESGKVVGKIVL 330
>gnl|CDD|176220 cd08259, Zn_ADH5, Alcohol dehydrogenases of the MDR family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. This group contains proteins that
share the characteristic catalytic and structural
zinc-binding sites of the zinc-dependent alcohol
dehydrogenase family. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the cleft
between the catalytic and coenzyme-binding domains at
the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine
(His-51), the ribose of NAD, a serine (Ser-48), then the
alcohol, which allows the transfer of a hydride to NAD+,
creating NADH and a zinc-bound aldehyde or ketone. In
yeast and some bacteria, the active site zinc binds an
aldehyde, polarizing it, and leading to the reverse
reaction.
Length = 332
Score = 86.6 bits (215), Expect = 5e-19
Identities = 93/370 (25%), Positives = 139/370 (37%), Gaps = 85/370 (22%)
Query: 45 DNVKTPILKSKDVLVEMKAVSVNPID-VAMLGGYGNVVLNSLRQLETCSVEPVLEFPLTL 103
+ V P +VL+++KA V D + G + PL L
Sbjct: 16 EEVPDPEPGPGEVLIKVKAAGVCYRDLLFWKGFFPRGKY-----------------PLIL 58
Query: 104 GRDFCGKIVAKGPRVTDLNIDDVV---------------------------YGVIQPHKQ 136
G + G + G V D V YG
Sbjct: 59 GHEIVGTVEEVGEGVERFKPGDRVILYYYIPCGKCEYCLSGEENLCRNRAEYGEEVD--- 115
Query: 137 GSFSKLILADSALVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRVLVLG 196
G F++ + + K P N+SDE AA TA AL+ A + VLV G
Sbjct: 116 GGFAEYVKVPERSLVKLPDNVSDESAALAACVVGTAVHALKR-AGVKK----GDTVLVTG 170
Query: 197 ASGGVGTMAVQLLKAWDIEVVT-TCSGDAKDLVTSLNPNLVIDYNEP-EAMHSIAGAGPY 254
A GGVG A+QL KA V+ T S + ++ L + VID ++ E + + GA
Sbjct: 171 AGGGVGIHAIQLAKALGARVIAVTRSPEKLKILKELGADYVIDGSKFSEDVKKLGGA--- 227
Query: 255 DVILDAAGIPLDQINSYLPFLKTGKFSKFVTLRSPFLKNTD--SLGLVPGLVKNAFDLLK 312
DV+++ G P I L L G + V + N L PGL+ +LK
Sbjct: 228 DVVIELVGSP--TIEESLRSLNKG--GRLV-----LIGNVTPDPAPLRPGLL-----ILK 273
Query: 313 SNFESGELCKTNTIRWGFFMPIPYAVKEINKFIERGQIKPVIDSKYNFCELPTAFEKVQQ 372
G + T V+E K ++ G+IKPVID + ++ A E ++
Sbjct: 274 EIRIIGSISAT-----------KADVEEALKLVKEGKIKPVIDRVVSLEDINEALEDLKS 322
Query: 373 GHLRGKIILN 382
G + G+I+L
Sbjct: 323 GKVVGRIVLK 332
>gnl|CDD|176213 cd08251, polyketide_synthase, polyketide synthase. Polyketide
synthases produce polyketides in step by step mechanism
that is similar to fatty acid synthesis. Enoyl reductase
reduces a double to single bond. Erythromycin is one
example of a polyketide generated by 3 complex enzymes
(megasynthases). 2-enoyl thioester reductase (ETR)
catalyzes the NADPH-dependent dependent conversion of
trans-2-enoyl acyl carrier protein/coenzyme A (ACP/CoA)
to acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl
thioester reductase activity has been linked in Candida
tropicalis as essential in maintaining mitiochondrial
respiratory function. This ETR family is a part of the
medium chain dehydrogenase/reductase family, but lack
the zinc coordination sites characteristic of the
alcohol dehydrogenases in this family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. The N-terminal catalytic domain has a
distant homology to GroES. These proteins typically form
dimers (typically higher plants, mammals) or tetramers
(yeast, bacteria), and have 2 tightly bound zinc atoms
per subunit, a catalytic zinc at the active site, and a
structural zinc in a lobe of the catalytic domain.
NAD(H)-binding occurs in the cleft between the catalytic
and coenzyme-binding domains at the active site, and
coenzyme binding induces a conformational closing of
this cleft. Coenzyme binding typically precedes and
contributes to substrate binding.
Length = 303
Score = 84.4 bits (209), Expect = 2e-18
Identities = 77/290 (26%), Positives = 124/290 (42%), Gaps = 28/290 (9%)
Query: 98 EFPLTLGRDFCGKIVAKGPRVTDLNIDDVVYGVIQPHKQGSFSKLILADSALVHKKPSNI 157
+P T G + G + A GP VT L + D V G + L+ V +KP+++
Sbjct: 36 PYPFTPGFEASGVVRAVGPHVTRLAVGDEVIAGTGE-SMGGHATLVTVPEDQVVRKPASL 94
Query: 158 SDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRVLVLGASGGVGTMAVQLLKAWDIEVV 217
S EEA + LT A A GL + + +L+ A+GG G MAVQL + E+
Sbjct: 95 SFEEACALPVVFLTVIDAF---ARAGL--AKGEHILIQTATGGTGLMAVQLARLKGAEIY 149
Query: 218 TTCSGDAK-DLVTSLNPNLVIDYNE----PEAMHSIAGAGPYDVILDAAGIPLDQ-INSY 271
T S D K + + L VI+Y E E M G G VI +G + + +N
Sbjct: 150 ATASSDDKLEYLKQLGVPHVINYVEEDFEEEIMRLTGGRGVDVVINTLSGEAIQKGLNCL 209
Query: 272 LPFLKTGKFSKFVTLRSPFLKNTDSLGLVPGLVKNAFDLLKSNFESGELCKTNTIRWGFF 331
P ++V + LK+ S+ L L N +F S +L K + F
Sbjct: 210 AP------GGRYVEIAMTALKSAPSVDL-SVLSNN------QSFHSVDLRKLLLLDPEF- 255
Query: 332 MPIPYAVKEINKFIERGQIKPVIDSKYNFCELPTAFEKVQQGHLRGKIIL 381
I E+ +E G+++P + + F ++ A+ + GK+++
Sbjct: 256 --IADYQAEMVSLVEEGELRPTVSRIFPFDDIGEAYRYLSDRENIGKVVV 303
>gnl|CDD|176257 cd08297, CAD3, Cinnamyl alcohol dehydrogenases (CAD). These
alcohol dehydrogenases are related to the cinnamyl
alcohol dehydrogenases (CAD), members of the medium
chain dehydrogenase/reductase family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Cinnamyl alcohol dehydrogenases
(CAD) reduce cinnamaldehydes to cinnamyl alcohols in the
last step of monolignal metabolism in plant cells walls.
CAD binds 2 zinc ions and is NADPH- dependent. CAD
family members are also found in non-plant species, e.g.
in yeast where they have an aldehyde reductase activity.
The medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 341
Score = 84.9 bits (211), Expect = 2e-18
Identities = 93/393 (23%), Positives = 152/393 (38%), Gaps = 96/393 (24%)
Query: 29 AWQISSYGGADELQFNDNVKTPILKSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQL 88
A + +G +V P +VLV+++A V D+ G V
Sbjct: 3 AAVVEEFGEK--PYEVKDVPVPEPGPGEVLVKLEASGVCHTDLHAALGDWPVKPK----- 55
Query: 89 ETCSVEPVLEFPLTLGRDFCGKIVAKGPRVTDLNIDDVVYGVIQ---------------- 132
PL G + G +VA GP V+ L + D V GV
Sbjct: 56 ----------LPLIGGHEGAGVVVAVGPGVSGLKVGDRV-GVKWLYDACGKCEYCRTGDE 104
Query: 133 ---PHKQ-------GSFSKLILADSALVHKKPSNISDEEAAGVLYTGLTAWSALQITAAL 182
P+++ G+F++ +AD+ V P +S E+AA +L G+T + AL+
Sbjct: 105 TLCPNQKNSGYTVDGTFAEYAIADARYVTPIPDGLSFEQAAPLLCAGVTVYKALKKAG-- 162
Query: 183 GLVYPRDKRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAK-DLVTSLNPNLVIDYNE 241
+ P D V++ GA GG+G + VQ KA + V+ GD K +L L + +D+ +
Sbjct: 163 --LKPGD-WVVISGAGGGLGHLGVQYAKAMGLRVIAIDVGDEKLELAKELGADAFVDFKK 219
Query: 242 ---PEAMHSIA-GAGPYDVILDAAGI-PLDQINSYLPFLKT--------GKFSKFVTLRS 288
EA+ + G G + V++ A +Q YL T G F
Sbjct: 220 SDDVEAVKELTGGGGAHAVVVTAVSAAAYEQALDYLRPGGTLVCVGLPPGGFIPL----D 275
Query: 289 PFLKNTDSLGLVPGLVKNAFDLLKSNFESGELCKTNTIRWGFFMPIPYAVKEINKFIERG 348
PF + +V LV DL +E +F RG
Sbjct: 276 PFDLVLRGITIVGSLVGTRQDL----------------------------QEALEFAARG 307
Query: 349 QIKPVIDSKYNFCELPTAFEKVQQGHLRGKIIL 381
++KP I +L FEK+++G + G++++
Sbjct: 308 KVKPHI-QVVPLEDLNEVFEKMEEGKIAGRVVV 339
>gnl|CDD|176645 cd05282, ETR_like, 2-enoyl thioester reductase-like. 2-enoyl
thioester reductase (ETR) catalyzes the NADPH-dependent
conversion of trans-2-enoyl acyl carrier
protein/coenzyme A (ACP/CoA) to acyl-(ACP/CoA) in fatty
acid synthesis. 2-enoyl thioester reductase activity has
been linked in Candida tropicalis as essential in
maintaining mitiochondrial respiratory function. This
ETR family is a part of the medium chain
dehydrogenase/reductase family, but lack the zinc
coordination sites characteristic of the alcohol
dehydrogenases in this family. NAD(P)(H)-dependent
oxidoreductases are the major enzymes in the
interconversion of alcohols and aldehydes, or ketones.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation. ADH
is a member of the medium chain alcohol dehydrogenase
family (MDR), which has a NAD(P)(H)-binding domain in a
Rossmann fold of a beta-alpha form. The NAD(H)-binding
region is comprised of 2 structurally similar halves,
each of which contacts a mononucleotide. The N-terminal
catalytic domain has a distant homology to GroES.
These proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
have 2 tightly bound zinc atoms per subunit, a catalytic
zinc at the active site and a structural zinc in a lobe
of the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding domains
at the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
Candida tropicalis enoyl thioester reductase (Etr1p)
catalyzes the NADPH-dependent reduction of trans-2-enoyl
thioesters in mitochondrial fatty acid synthesis. Etr1p
forms homodimers with each subunit containing a
nucleotide-binding Rossmann fold domain and a catalytic
domain.
Length = 323
Score = 81.9 bits (203), Expect = 2e-17
Identities = 79/369 (21%), Positives = 134/369 (36%), Gaps = 66/369 (17%)
Query: 31 QISSYGGADELQF-NDNVKTPILKSKDVLVEMKAVSVNPIDV-AMLGGYGNVVLNSLRQL 88
+ +G L ++ P +VLV M A +NP D+ + G YG
Sbjct: 2 VYTQFGEPLPLVLELVSLPIPPPGPGEVLVRMLAAPINPSDLITISGAYG---------- 51
Query: 89 ETCSVEPVLEFPLTLGRDFCGKIVAKGPRVTDLNIDDVVYGVIQPHKQGSFSKLILADSA 148
P L P G + G +V G V+ L + V + +G++ + ++A +
Sbjct: 52 ----SRPPL--PAVPGNEGVGVVVEVGSGVSGLLVGQRV---LPLGGEGTWQEYVVAPAD 102
Query: 149 LVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRVLVLGASGGVGTMAVQL 208
+ P +ISDE+AA + LTAW L L P V+ A+ VG M +QL
Sbjct: 103 DLIPVPDSISDEQAAMLYINPLTAWLMLTEYLKL----PPGDWVIQNAANSAVGRMLIQL 158
Query: 209 LKAWDIEVV-TTCSGDAKDLVTSLNPNLVIDYNEPEAMHSIA---GAGPYDVILDAAG-- 262
K + + + + + +L + VID + + + G + LDA G
Sbjct: 159 AKLLGFKTINVVRRDEQVEELKALGADEVIDSSPEDLAQRVKEATGGAGARLALDAVGGE 218
Query: 263 IPLDQINSYLPFLKTGKFSKFVTLRSPFLKNTDSLGLVPGLVKNAFDLLKSNFESGELCK 322
S L+ G V + GL+ G + K
Sbjct: 219 SATRLARS----LRPG--GTLV-----------NYGLLSGEPVPFPRSVFIF-------K 254
Query: 323 TNTIRWGFFM----------PIPYAVKEINKFIERGQIKPVIDSKYNFCELPTAFEKVQQ 372
T+R GF++ E+ K +E G + + +K+ + A +Q
Sbjct: 255 DITVR-GFWLRQWLHSATKEAKQETFAEVIKLVEAGVLTTPVGAKFPLEDFEEAVAAAEQ 313
Query: 373 GHLRGKIIL 381
GK++L
Sbjct: 314 PGRGGKVLL 322
>gnl|CDD|176207 cd08245, CAD, Cinnamyl alcohol dehydrogenases (CAD) and related
proteins. Cinnamyl alcohol dehydrogenases (CAD),
members of the medium chain dehydrogenase/reductase
family, reduce cinnamaldehydes to cinnamyl alcohols in
the last step of monolignal metabolism in plant cells
walls. CAD binds 2 zinc ions and is NADPH- dependent.
CAD family members are also found in non-plant species,
e.g. in yeast where they have an aldehyde reductase
activity. The medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes, or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 330
Score = 79.7 bits (197), Expect = 1e-16
Identities = 68/262 (25%), Positives = 103/262 (39%), Gaps = 59/262 (22%)
Query: 29 AWQISSYGGADELQFNDNVKTPILKSKDVLVEMKAVSVNPIDV-AMLGGYGNVVLNSLRQ 87
A + + GG E + V P +VL++++A V D+ A G +G
Sbjct: 2 AAVVHAAGGPLEPE---EVPVPEPGPGEVLIKIEACGVCHTDLHAAEGDWGGSKY----- 53
Query: 88 LETCSVEPVLEFPLTLGRDFCGKIVAKGPRVTDLNIDDVVYGV--IQP------------ 133
PL G + G++V G V + D V GV +
Sbjct: 54 ------------PLVPGHEIVGEVVEVGAGVEGRKVGDRV-GVGWLVGSCGRCEYCRRGL 100
Query: 134 ------------HKQGSFSKLILADSALVHKKPSNISDEEAAGVLYTGLTAWSALQITAA 181
QG +++ ++AD+ P + +AA +L G+T +SAL+
Sbjct: 101 ENLCQKAVNTGYTTQGGYAEYMVADAEYTVLLPDGLPLAQAAPLLCAGITVYSALRDAG- 159
Query: 182 LGLVYPRD-KRVLVLGASGGVGTMAVQLLKAWDIEVVT-TCSGDAKDLVTSLNPNLVIDY 239
PR +RV VLG GG+G +AVQ +A E V T S D ++L L + V+D
Sbjct: 160 -----PRPGERVAVLGI-GGLGHLAVQYARAMGFETVAITRSPDKRELARKLGADEVVDS 213
Query: 240 NEPEAMHSIAGAGPYDVILDAA 261
A AG DVIL
Sbjct: 214 GAELDEQ--AAAGGADVILVTV 233
>gnl|CDD|176186 cd05283, CAD1, Cinnamyl alcohol dehydrogenases (CAD). Cinnamyl
alcohol dehydrogenases (CAD), members of the medium
chain dehydrogenase/reductase family, reduce
cinnamaldehydes to cinnamyl alcohols in the last step of
monolignal metabolism in plant cells walls. CAD binds 2
zinc ions and is NADPH- dependent. CAD family members
are also found in non-plant species, e.g. in yeast where
they have an aldehyde reductase activity. The medium
chain dehydrogenases/reductase (MDR)/zinc-dependent
alcohol dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases
(ADHs) catalyze the NAD(P)(H)-dependent interconversion
of alcohols to aldehydes or ketones. Active site zinc
has a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 337
Score = 79.1 bits (196), Expect = 2e-16
Identities = 73/315 (23%), Positives = 114/315 (36%), Gaps = 73/315 (23%)
Query: 99 FPLTLGRDFCGKIVAKGPRVTDLNIDDVV------------------------------Y 128
+PL G + G +VA G +VT + D V
Sbjct: 53 YPLVPGHEIVGIVVAVGSKVTKFKVGDRVGVGCQVDSCGTCEQCKSGEEQYCPKGVVTYN 112
Query: 129 GVIQPHK--QGSFSKLILADSALVHKKPSNISDEEAAGVLYTGLTAWSALQ---ITAALG 183
G QG ++ I+ D V K P + AA +L G+T +S L+ +
Sbjct: 113 GKYPDGTITQGGYADHIVVDERFVFKIPEGLDSAAAAPLLCAGITVYSPLKRNGVGPG-- 170
Query: 184 LVYPRDKRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAK-DLVTSLNPNLVIDYNEP 242
KRV V+G GG+G +AV+ KA EV +K + L + I +P
Sbjct: 171 ------KRVGVVGI-GGLGHLAVKFAKALGAEVTAFSRSPSKKEDALKLGADEFIATKDP 223
Query: 243 EAMHSIAGAGPYDVILDAAGIPLDQINSYLPFLKTGKFSKFVTLRSPFLKNTDSLGLVPG 302
EAM AG D+I+D D ++ YL LK G V +G
Sbjct: 224 EAM--KKAAGSLDLIIDTVSASHD-LDPYLSLLKPG--GTLV-----------LVGAPEE 267
Query: 303 -LVKNAFDLLKSNFESGELCKTNTIRWGFFMPIPYAVKEINKFIERGQIKPVIDSKYNFC 361
L F L+ ++ G + +E+ F IKP ++
Sbjct: 268 PLPVPPFPLIFGRK---------SV-AGSLIGGRKETQEMLDFAAEHGIKPWVE-VIPMD 316
Query: 362 ELPTAFEKVQQGHLR 376
+ A E++++G +R
Sbjct: 317 GINEALERLEKGDVR 331
>gnl|CDD|176202 cd08240, 6_hydroxyhexanoate_dh_like, 6-hydroxyhexanoate
dehydrogenase. 6-hydroxyhexanoate dehydrogenase, an
enzyme of the zinc-dependent alcohol dehydrogenase-like
family of medium chain dehydrogenases/reductases
catalyzes the conversion of 6-hydroxyhexanoate and
NAD(+) to 6-oxohexanoate + NADH and H+.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the
cleft between the catalytic and coenzyme-binding
domains, at the active site, and coenzyme binding
induces a conformational closing of this cleft. Coenzyme
binding typically precedes and contributes to substrate
binding. In human ADH catalysis, the zinc ion helps
coordinate the alcohol, followed by deprotonation of a
histidine, the ribose of NAD, a serine, then the
alcohol, which allows the transfer of a hydride to NAD+,
creating NADH and a zinc-bound aldehyde or ketone. In
yeast and some bacteria, the active site zinc binds an
aldehyde, polarizing it, and leading to the reverse
reaction.
Length = 350
Score = 76.5 bits (189), Expect = 1e-15
Identities = 84/393 (21%), Positives = 157/393 (39%), Gaps = 83/393 (21%)
Query: 29 AWQISSYGGADELQFNDNVKTPILKSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQL 88
A + G E + TP +VLV++ A V D+ + G + L + +
Sbjct: 3 AAAVVEPGKPLEEV---EIDTPKPPGTEVLVKVTACGVCHSDLHIWDGGYD--LGGGKTM 57
Query: 89 ETCSVEPVLEFPLTLGRDFCGKIVAKGPRVTDLNIDD--VVY------------------ 128
+ ++ PL LG + G++VA GP D+ + D +VY
Sbjct: 58 SL--DDRGVKLPLVLGHEIVGEVVAVGPDAADVKVGDKVLVYPWIGCGECPVCLAGDENL 115
Query: 129 -------GVIQPHKQGSFSKLILADSALVHKKPSNISDEEAAGVLYTGLTAWSALQITAA 181
G+ Q G +++ ++ + P + AA + +GLTA+SA++
Sbjct: 116 CAKGRALGIFQD---GGYAEYVIVPHSRYLVDPGGLDPALAATLACSGLTAYSAVKKLMP 172
Query: 182 LGLVYPRDKRVLVLGASGGVGTMAVQLLKAW--------DIEVVTTCSGDAK-DLVTSLN 232
L D+ V+++GA GG+G MA+ LLKA DI+ +AK + +
Sbjct: 173 L----VADEPVVIIGA-GGLGLMALALLKALGPANIIVVDID-------EAKLEAAKAAG 220
Query: 233 PNLVIDYNEPEAMHSI--AGAGPYDVILDAAGIPLDQINSYLPFLKTGKFSKFVTLRSPF 290
++V++ ++P+A I A G D ++D T + +
Sbjct: 221 ADVVVNGSDPDAAKRIIKAAGGGVDAVIDFVNNS-----------ATASLAFDI------ 263
Query: 291 LKNTDSLGLVPGLVKNAFDLLKSNFESGELCKTNTIRWGFFMPIPYAVKEINKFIERGQI 350
L L LV GL L L TI+ G ++ ++E+ + G++
Sbjct: 264 LAKGGKLVLV-GLFGGEATLPLPLLPLRAL----TIQ-GSYVGSLEELRELVALAKAGKL 317
Query: 351 KPVIDSKYNFCELPTAFEKVQQGHLRGKIILNA 383
KP+ ++ ++ A + ++ G + G+ +L
Sbjct: 318 KPIPLTERPLSDVNDALDDLKAGKVVGRAVLKP 350
>gnl|CDD|173547 PTZ00354, PTZ00354, alcohol dehydrogenase; Provisional.
Length = 334
Score = 75.5 bits (186), Expect = 3e-15
Identities = 85/358 (23%), Positives = 139/358 (38%), Gaps = 50/358 (13%)
Query: 35 YGGADELQFNDNVKTPILKSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQLETCSVE 94
+GG D L+ ++ K P K DVL+++ A VN D G +
Sbjct: 10 FGGVDVLKIGESPK-PAPKRNDVLIKVSAAGVNRADTLQRQG---------KYPPPPGSS 59
Query: 95 PVLEFPLTLGRDFCGKIVAKGPRVTDLNIDDVVYGVIQPHKQGSFSKLILADSALVHKKP 154
+L G + G + G V D V ++ G +++ +A V P
Sbjct: 60 EIL------GLEVAGYVEDVGSDVKRFKEGDRVMALL---PGGGYAEYAVAHKGHVMHIP 110
Query: 155 SNISDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRVLVLGASGGVGTMAVQLLKAW-D 213
+ EEAA + LTAW L+ G V VL+ + GVGT A QL + +
Sbjct: 111 QGYTFEEAAAIPEAFLTAWQLLK---KHGDVKKGQ-SVLIHAGASGVGTAAAQLAEKYGA 166
Query: 214 IEVVTTCSGDAKDLVTSLNPNLVIDY----NEPEAMHSIAGAGPYDVILDAAGIPLDQIN 269
++TT S + D L ++I Y + + G +++LD G
Sbjct: 167 ATIITTSSEEKVDFCKKLAAIILIRYPDEEGFAPKVKKLTGEKGVNLVLDCVG------G 220
Query: 270 SYLP-----FLKTGKFSKFVTLRSPFLKNTDSLGLVPGLVKNAFDLLKSNFESGELCKTN 324
SYL GK+ + + ++ + L L+ F L+S S E K +
Sbjct: 221 SYLSETAEVLAVDGKWIVYGFMGGAKVEKFNLLPLLRKRASIIFSTLRS--RSDEY-KAD 277
Query: 325 TIRWGFFMPIPYAVKEINKFIERGQIKPVIDSKYNFCELPTAFEKVQQGHLRGKIILN 382
+ +PY +E G+IKP++D Y E+ A ++Q GK++L
Sbjct: 278 LVASFEREVLPY--------MEEGEIKPIVDRTYPLEEVAEAHTFLEQNKNIGKVVLT 327
>gnl|CDD|176225 cd08264, Zn_ADH_like2, Alcohol dehydrogenases of the MDR family.
This group resembles the zinc-dependent alcohol
dehydrogenases of the medium chain dehydrogenase family.
However, this subgroup does not contain the
characteristic catalytic zinc site. Also, it contains an
atypical structural zinc-binding pattern:
DxxCxxCxxxxxxxC. NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the cleft
between the catalytic and coenzyme-binding domains at
the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 325
Score = 75.5 bits (186), Expect = 4e-15
Identities = 71/251 (28%), Positives = 106/251 (42%), Gaps = 53/251 (21%)
Query: 37 GADELQFNDNVKTPILKSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQLETCSVEPV 96
G + L+ D VK P +VL+ +K VNP+D ++ V+P+
Sbjct: 10 GIENLKVED-VKDPKPGPGEVLIRVKMAGVNPVDYNVINAVK--------------VKPM 54
Query: 97 LEFPLTLGRDFCGKIVAKGPRVTDLNIDD--VVY----------------------GVIQ 132
P G +F G + G V + D VVY G+I
Sbjct: 55 PHIP---GAEFAGVVEEVGDHVKGVKKGDRVVVYNRVFDGTCDMCLSGNEMLCRNGGIIG 111
Query: 133 PHKQGSFSKLILADSALVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRV 192
G +++ I+ + K P +ISDE AA + LTA+ AL+ TA LG + V
Sbjct: 112 VVSNGGYAEYIVVPEKNLFKIPDSISDELAASLPVAALTAYHALK-TAGLG----PGETV 166
Query: 193 LVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAKDLVTSLNPNLVIDYNE-PEAMHSIAGA 251
+V GASG G AVQL K EV+ KD + + V+DY+E E + I
Sbjct: 167 VVFGASGNTGIFAVQLAKMMGAEVIAVSR---KDWLKEFGADEVVDYDEVEEKVKEITKM 223
Query: 252 GPYDVILDAAG 262
DV++++ G
Sbjct: 224 --ADVVINSLG 232
>gnl|CDD|176198 cd08236, sugar_DH, NAD(P)-dependent sugar dehydrogenases. This
group contains proteins identified as sorbitol
dehydrogenases and other sugar dehydrogenases of the
medium-chain dehydrogenase/reductase family (MDR), which
includes zinc-dependent alcohol dehydrogenase and
related proteins. Sorbitol and aldose reductase are
NAD(+) binding proteins of the polyol pathway, which
interconverts glucose and fructose. Sorbitol
dehydrogenase is tetrameric and has a single catalytic
zinc per subunit. NAD(P)(H)-dependent oxidoreductases
are the major enzymes in the interconversion of alcohols
and aldehydes, or ketones. Related proteins include
threonine dehydrogenase, formaldehyde dehydrogenase, and
butanediol dehydrogenase. The medium chain alcohol
dehydrogenase family (MDR) has a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit. Horse
liver alcohol dehydrogenase is a dimeric enzyme and each
subunit has two domains. The NAD binding domain is in a
Rossmann fold and the catalytic domain contains a zinc
ion to which substrates bind. There is a cleft between
the domains that closes upon formation of the ternary
complex.
Length = 343
Score = 71.1 bits (175), Expect = 9e-14
Identities = 81/384 (21%), Positives = 140/384 (36%), Gaps = 87/384 (22%)
Query: 37 GADELQFNDNVKTPILKSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQLETCSVEPV 96
G +L++ D + P +VLV++KA + D+ G G
Sbjct: 8 GPGDLRYED-IPKPEPGPGEVLVKVKACGICGSDIPRYLGTG-----------------A 49
Query: 97 LEFPLTLGRDFCGKIVAKGPRVTDLNIDDVV------------------------YGVIQ 132
PL LG +F G + G V DL + D V Y I
Sbjct: 50 YHPPLVLGHEFSGTVEEVGSGVDDLAVGDRVAVNPLLPCGKCEYCKKGEYSLCSNYDYIG 109
Query: 133 PHKQGSFSKLILADSALVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRV 192
+ G+F++ + + + K P ++ EEAA + +A+ + A V
Sbjct: 110 SRRDGAFAEYVSVPARNLIKIPDHVDYEEAA------MIEPAAVALHAVRLAGITLGDTV 163
Query: 193 LVLGASGGVGTMAVQLLKAWDIE-VVTTCSGDAK-DLVTSLNPNLVID--YNEPEAMHSI 248
+V+GA G +G +A+Q LK + V+ D K + L + I+ + E + +
Sbjct: 164 VVIGA-GTIGLLAIQWLKILGAKRVIAVDIDDEKLAVARELGADDTINPKEEDVEKVREL 222
Query: 249 AGAGPYDVILDAAGIPLDQINSYLPFLKTGKFSKFVTLRSPFLKNTDSLGLVPGLVKNAF 308
D++++AAG P + K V + G+
Sbjct: 223 TEGRGADLVIEAAGSPATIEQA---LALARPGGKVVLV---------------GIPYGDV 264
Query: 309 DLLKSNFES---GELCKTNTIRWGFFMPI--PYAVKEINK---FIERGQI--KPVIDSKY 358
L + FE EL TI+ G + P+ E + G+I +P+I +
Sbjct: 265 TLSEEAFEKILRKEL----TIQ-GSWNSYSAPFPGDEWRTALDLLASGKIKVEPLITHRL 319
Query: 359 NFCELPTAFEKVQQG-HLRGKIIL 381
+ P AFE++ GK++L
Sbjct: 320 PLEDGPAAFERLADREEFSGKVLL 343
>gnl|CDD|184316 PRK13771, PRK13771, putative alcohol dehydrogenase; Provisional.
Length = 334
Score = 70.5 bits (173), Expect = 2e-13
Identities = 79/319 (24%), Positives = 132/319 (41%), Gaps = 69/319 (21%)
Query: 95 PVLEFPLTLGRDFCGKIVAKGPRVTDLNIDDVVYGVIQ-----------------PHK-- 135
P +++P+ LG + G + G V D V ++ ++
Sbjct: 50 PRMKYPVILGHEVVGTVEEVGENVKGFKPGDRVASLLYAPDGTCEYCRSGEEAYCKNRLG 109
Query: 136 -----QGSFSKLILAD-SALVHKKPSNISDEEA------AGVLYTGLTAWSALQITAALG 183
G F++ ++LV K P N+SDE A G++Y GL + G
Sbjct: 110 YGEELDGFFAEYAKVKVTSLV-KVPPNVSDEGAVIVPCVTGMVYRGLR-----RAGVKKG 163
Query: 184 LVYPRDKRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAKDLVTSLNPNLVIDYNE-P 242
+ VLV GA GGVG A+Q+ KA +V+ S ++K + S + VI ++
Sbjct: 164 ------ETVLVTGAGGGVGIHAIQVAKALGAKVIAVTSSESKAKIVSKYADYVIVGSKFS 217
Query: 243 EAMHSIAGAGPYDVILDAAGIPLDQINSYLPFLKTGKFSKFVTLRSPFLKNTDSLGLVPG 302
E + I GA D++++ G P + L L G K + + + T SL L G
Sbjct: 218 EEVKKIGGA---DIVIETVGTP--TLEESLRSLNMG--GKIIQIGNVDPSPTYSLRL--G 268
Query: 303 LVKNAFDLLKSNFESGELCKTNTIRWGFFMPIPYAVKEINKFIERGQIKPVIDSKYNFCE 362
+ +LK G + T V+E K + G+IKPVI ++ + E
Sbjct: 269 YI-----ILKDIEIIGHISATK-----------RDVEEALKLVAEGKIKPVIGAEVSLSE 312
Query: 363 LPTAFEKVQQGHLRGKIIL 381
+ A E+++ GKI++
Sbjct: 313 IDKALEELKDKSRIGKILV 331
>gnl|CDD|176212 cd08250, Mgc45594_like, Mgc45594 gene product and other MDR family
members. Includes Human Mgc45594 gene product of
undetermined function. The medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES.
Length = 329
Score = 69.2 bits (170), Expect = 4e-13
Identities = 56/195 (28%), Positives = 84/195 (43%), Gaps = 28/195 (14%)
Query: 47 VKTPILKSKDVLVEMKAVSVNPIDV-AMLGGYGNVVLNSLRQLETCSVEPVLEFPLTLGR 105
V P+ +VLV+ + V +N D+ G Y V+P P G
Sbjct: 23 VPVPLPGPGEVLVKNRFVGINASDINFTAGRYDP------------GVKP----PFDCGF 66
Query: 106 DFCGKIVAKGPRVTDLNIDDVVYGVIQPHKQGSFSKLILADSALVHKKPSNISDEEAAGV 165
+ G++VA G VTD + D V + G+F++ + + P E +
Sbjct: 67 EGVGEVVAVGEGVTDFKVGDAV-ATMSF---GAFAEYQVVPARHAVPVPE--LKPEVLPL 120
Query: 166 LYTGLTAWSALQITAALGLVYPRDKRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAK 225
L +GLTA AL+ + + VLV A+GG G AVQL K V+ TCS D K
Sbjct: 121 LVSGLTASIALEEVGEMK----SGETVLVTAAAGGTGQFAVQLAKLAGCHVIGTCSSDEK 176
Query: 226 -DLVTSLNPNLVIDY 239
+ + SL + I+Y
Sbjct: 177 AEFLKSLGCDRPINY 191
>gnl|CDD|176250 cd08290, ETR, 2-enoyl thioester reductase (ETR). 2-enoyl thioester
reductase (ETR) catalyzes the NADPH-dependent conversion
of trans-2-enoyl acyl carrier protein/coenzyme A
(ACP/CoA) to acyl-(ACP/CoA) in fatty acid synthesis.
2-enoyl thioester reductase activity has been linked in
Candida tropicalis as essential in maintaining
mitiochondrial respiratory function. This ETR family is
a part of the medium chain dehydrogenase/reductase
family, but lack the zinc coordination sites
characteristic of the alcohol dehydrogenases in this
family. NAD(P)(H)-dependent oxidoreductases are the
major enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. The N-terminal catalytic domain has a
distant homology to GroES. These proteins typically form
dimers (typically higher plants, mammals) or tetramers
(yeast, bacteria), and have 2 tightly bound zinc atoms
per subunit, a catalytic zinc at the active site, and a
structural zinc in a lobe of the catalytic domain.
NAD(H) binding occurs in the cleft between the catalytic
and coenzyme-binding domains, at the active site, and
coenzyme binding induces a conformational closing of
this cleft. Coenzyme binding typically precedes and
contributes to substrate binding. Candida tropicalis
enoyl thioester reductase (Etr1p) catalyzes the
NADPH-dependent reduction of trans-2-enoyl thioesters in
mitochondrial fatty acid synthesis. Etr1p forms
homodimers, with each subunit containing a
nucleotide-binding Rossmann fold domain and a catalytic
domain.
Length = 341
Score = 69.2 bits (170), Expect = 5e-13
Identities = 48/223 (21%), Positives = 85/223 (38%), Gaps = 27/223 (12%)
Query: 27 TAAWQISSYGGADE-LQFNDNVKTPILKSKDVLVEMKAVSVNPIDVAML-GGYGNVVLNS 84
A + +G E LQ P +VLV+M A +NP D+ + G Y
Sbjct: 1 AKALVYTEHGEPKEVLQLESYEIPPPGPPNEVLVKMLAAPINPADINQIQGVYP-----I 55
Query: 85 LRQLETCSVEPVLEFPLTLGRDFCGKIVAKGPRVTDLNIDDVVYGVIQPHKQGSFSKLIL 144
E P G + G++V G V L D V + G++ +
Sbjct: 56 KPPTTP-------EPPAVGGNEGVGEVVKVGSGVKSLKPGDWV--IPLRPGLGTWRTHAV 106
Query: 145 ADSALVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRVLVL-GASGGVGT 203
+ + K P+++ E+AA + TA+ ++ + P D ++ GA+ VG
Sbjct: 107 VPADDLIKVPNDVDPEQAATLSVNPCTAY---RLLEDFVKLQPGD--WVIQNGANSAVGQ 161
Query: 204 MAVQLLKAWDIEVVTTC-----SGDAKDLVTSLNPNLVIDYNE 241
+QL K I+ + + K+ + +L + V+ E
Sbjct: 162 AVIQLAKLLGIKTINVVRDRPDLEELKERLKALGADHVLTEEE 204
>gnl|CDD|222256 pfam13602, ADH_zinc_N_2, Zinc-binding dehydrogenase.
Length = 129
Score = 64.3 bits (157), Expect = 9e-13
Identities = 35/151 (23%), Positives = 55/151 (36%), Gaps = 32/151 (21%)
Query: 236 VIDYNEPEAMHSIAGAGPYDVILDAAGIPLDQINSYLPFLKTGKFSKFVTLRSPFLKNTD 295
VIDY + + AG G DV+LD G + + L G+
Sbjct: 6 VIDYTTEDFEEATAGEG-VDVVLDTVGGE-TLLRALLALKPGGRLV-------------- 49
Query: 296 SLGLVPGLVKNAFDLLKSNFESGELCKTNTIRWGFFMPIPYAV-----KEINKFIERGQI 350
S+G L+ A R F P+ E+ + +E G++
Sbjct: 50 SIGGPDLLLSVAAKAGGRGV-----------RGVFLFPVSPGEAGADLAELAELVEAGKL 98
Query: 351 KPVIDSKYNFCELPTAFEKVQQGHLRGKIIL 381
+PVID + E A ++ G RGK++L
Sbjct: 99 RPVIDRVFPLEEAAEAHRYLESGRARGKVVL 129
>gnl|CDD|176196 cd08234, threonine_DH_like, L-threonine dehydrogenase. L-threonine
dehydrogenase (TDH) catalyzes the zinc-dependent
formation of 2-amino-3-ketobutyrate from L-threonine,
via NAD(H)-dependent oxidation. THD is a member of the
zinc-requiring, medium chain NAD(H)-dependent alcohol
dehydrogenase family (MDR). MDRs have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes, or ketones. The N-terminal region typically
has an all-beta catalytic domain. These proteins
typically form dimers (typically higher plants, mammals)
or tetramers (yeast, bacteria), and have 2 tightly
bound zinc atoms per subunit. Sorbitol and aldose
reductase are NAD(+) binding proteins of the polyol
pathway, which interconverts glucose and fructose.
Length = 334
Score = 67.9 bits (167), Expect = 1e-12
Identities = 61/252 (24%), Positives = 93/252 (36%), Gaps = 63/252 (25%)
Query: 46 NVKTPILKSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQLETCSVEPVLEFPLTLGR 105
V P +VL+++ A + D+ + G E PL G
Sbjct: 16 EVPVPEPGPDEVLIKVAACGICGTDLHIYEG-----------------EFGAAPPLVPGH 58
Query: 106 DFCGKIVAKGPRVTDLNIDDVV---------------------------YGVIQPHKQGS 138
+F G +VA G +VT + D V GV + G
Sbjct: 59 EFAGVVVAVGSKVTGFKVGDRVAVDPNIYCGECFYCRRGRPNLCENLTAVGVTRN---GG 115
Query: 139 FSKLILADSALVHKKPSNISDEEAAGV--LYTGLTAWSALQITAALGLVYPRDKRVLVLG 196
F++ ++ + V+K P N+S EEAA L + L I VLV G
Sbjct: 116 FAEYVVVPAKQVYKIPDNLSFEEAALAEPLSCAVHGLDLLGIKPG--------DSVLVFG 167
Query: 197 ASGGVGTMAVQLLKAWDIEVVTTC--SGDAKDLVTSLNPNLVID--YNEPEAMHSIAGAG 252
A G +G + QLLK VT + + +L L +D +PEA G
Sbjct: 168 A-GPIGLLLAQLLKLNGASRVTVAEPNEEKLELAKKLGATETVDPSREDPEAQKEDNPYG 226
Query: 253 PYDVILDAAGIP 264
+DV+++A G+P
Sbjct: 227 -FDVVIEATGVP 237
>gnl|CDD|176183 cd05280, MDR_yhdh_yhfp, Yhdh and yhfp-like putative quinone
oxidoreductases. Yhdh and yhfp-like putative quinone
oxidoreductases (QOR). QOR catalyzes the conversion of a
quinone + NAD(P)H to a hydroquinone + NAD(P)+. Quinones
are cyclic diones derived from aromatic compounds.
Membrane bound QOR actin the respiratory chains of
bacteria and mitochondria, while soluble QOR acts to
protect from toxic quinones (e.g. DT-diaphorase) or as a
soluble eye-lens protein in some vertebrates (e.g.
zeta-crystalin). QOR reduces quinones through a
semi-quinone intermediate via a NAD(P)H-dependent single
electron transfer. QOR is a member of the medium chain
dehydrogenase/reductase family, but lacks the
zinc-binding sites of the prototypical alcohol
dehydrogenases of this group. NAD(P)(H)-dependent
oxidoreductases are the major enzymes in the
interconversion of alcohols and aldehydes, or ketones.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation. ADH
is a member of the medium chain alcohol dehydrogenase
family (MDR), which has a NAD(P)(H)-binding domain in a
Rossmann fold of a beta-alpha form. The NAD(H)-binding
region is comprised of 2 structurally similar halves,
each of which contacts a mononucleotide. A GxGxxG motif
after the first mononucleotide contact half allows the
close contact of the coenzyme with the ADH backbone.
The N-terminal catalytic domain has a distant homology
to GroES. These proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and have 2 tightly bound zinc atoms per
subunit, a catalytic zinc at the active site and a
structural zinc in a lobe of the catalytic domain.
NAD(H) binding occurs in the cleft between the catalytic
and coenzyme-binding domains at the active site, and
coenzyme binding induces a conformational closing of
this cleft. Coenzyme binding typically precedes and
contributes to substrate binding. In human ADH
catalysis, the zinc ion helps coordinate the alcohol,
followed by deprotonation of a histidine, the ribose of
NAD, a serine, then the alcohol, which allows the
transfer of a hydride to NAD+, creating NADH and a
zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 325
Score = 66.4 bits (163), Expect = 3e-12
Identities = 59/220 (26%), Positives = 84/220 (38%), Gaps = 29/220 (13%)
Query: 29 AWQISSYGGADELQFNDNVKTPILKSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQL 88
A + G L + L DVL+ + S+N D G G V R
Sbjct: 3 ALVVEEQDGGVSLFL-RTLPLDDLPEGDVLIRVHYSSLNYKDALAATGNGGV----TRN- 56
Query: 89 ETCSVEPVLEFPLTLGRDFCGKIVAKGPRVTDLNIDDVV----YGVIQPHKQGSFSKLIL 144
+P T G D G +V+ D V Y + G F++ +
Sbjct: 57 ----------YPHTPGIDAAGTVVSS--DDPRFREGDEVLVTGYDLGMNT-DGGFAEYVR 103
Query: 145 ADSALVHKKPSNISDEEAAGVLYT-GLTAWSALQITAAL-GLVYPRDKRVLVLGASGGVG 202
+ V P +S EA +L T G TA AL + P D VLV GA+GGVG
Sbjct: 104 VPADWVVPLPEGLSLREAM-ILGTAGFTA--ALSVHRLEDNGQTPEDGPVLVTGATGGVG 160
Query: 203 TMAVQLLKAWDIEVV-TTCSGDAKDLVTSLNPNLVIDYNE 241
++AV +L VV T + D + SL + V+D +
Sbjct: 161 SIAVAILAKLGYTVVALTGKEEQADYLKSLGASEVLDRED 200
>gnl|CDD|176195 cd08233, butanediol_DH_like, (2R,3R)-2,3-butanediol dehydrogenase.
(2R,3R)-2,3-butanediol dehydrogenase, a zinc-dependent
medium chain alcohol dehydrogenase, catalyzes the
NAD(+)-dependent oxidation of (2R,3R)-2,3-butanediol and
meso-butanediol to acetoin. BDH functions as a
homodimer. NAD(P)(H)-dependent oxidoreductases are the
major enzymes in the interconversion of alcohols and
aldehydes, or ketones. The medium chain alcohol
dehydrogenase family (MDR) have a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit.
Sorbitol and aldose reductase are NAD(+) binding
proteins of the polyol pathway, which interconverts
glucose and fructose. Sorbitol dehydrogenase is
tetrameric and has a single catalytic zinc per subunit.
Length = 351
Score = 65.6 bits (161), Expect = 7e-12
Identities = 52/207 (25%), Positives = 80/207 (38%), Gaps = 57/207 (27%)
Query: 98 EFPLTLGRDFCGKIVAKGPRVTDLNIDDVVYGVIQPHKQ--------------------- 136
P+TLG +F G +V G VT + D V V++P +
Sbjct: 63 TAPVTLGHEFSGVVVEVGSGVTGFKVGDRV--VVEPTIKCGTCGACKRGLYNLCDSLGFI 120
Query: 137 ------GSFSKLILADSALVHKKPSNISDEEAAGVLYTGLT-----AWSALQITAALGLV 185
G F++ ++ + VHK P N+ EEAA L AW A++ +
Sbjct: 121 GLGGGGGGFAEYVVVPAYHVHKLPDNVPLEEAA------LVEPLAVAWHAVRRSG----- 169
Query: 186 YPRDKRVLVLGASGGVGTMAVQLLKAW---DIEVVTTCSGD---AKDL--VTSLNPNLVI 237
+ LVLGA G +G + + LKA I V A++L L+P
Sbjct: 170 FKPGDTALVLGA-GPIGLLTILALKAAGASKIIVSEPSEARRELAEELGATIVLDP---T 225
Query: 238 DYNEPEAMHSIAGAGPYDVILDAAGIP 264
+ + + + G G DV D AG+
Sbjct: 226 EVDVVAEVRKLTGGGGVDVSFDCAGVQ 252
>gnl|CDD|176216 cd08254, hydroxyacyl_CoA_DH, 6-hydroxycyclohex-1-ene-1-carboxyl-CoA
dehydrogenase, N-benzyl-3-pyrrolidinol dehydrogenase,
and other MDR family members. This group contains
enzymes of the zinc-dependent alcohol dehydrogenase
family, including members (aka MDR) identified as
6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase and
N-benzyl-3-pyrrolidinol dehydrogenase.
6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase
catalyzes the conversion of
6-Hydroxycyclohex-1-enecarbonyl-CoA and NAD+ to
6-Ketoxycyclohex-1-ene-1-carboxyl-CoA,NADH, and H+. This
group displays the characteristic catalytic and
structural zinc sites of the zinc-dependent alcohol
dehydrogenases. NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the cleft
between the catalytic and coenzyme-binding domains at
the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 338
Score = 63.0 bits (154), Expect = 5e-11
Identities = 64/264 (24%), Positives = 101/264 (38%), Gaps = 51/264 (19%)
Query: 29 AWQISSYGGADELQFNDNVKTPILKSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQL 88
AW+ G+ L + V P +VLV++KA V D+ +L G
Sbjct: 3 AWRFH--KGSKGLLVLEEVPVPEPGPGEVLVKVKAAGVCHSDLHILDG------------ 48
Query: 89 ETCSVEPVLEFPLTLGRDFCGKIVAKGPRVTDLNIDDVVY-------------------- 128
V + + PLTLG + G +V G VT+ + D V
Sbjct: 49 ---GVPTLTKLPLTLGHEIAGTVVEVGAGVTNFKVGDRVAVPAVIPCGACALCRRGRGNL 105
Query: 129 ----GVIQPHKQGSFSKLILADSALVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGL 184
G+ G F++ I+ + + P + +AA LT + A+ G
Sbjct: 106 CLNQGMPGLGIDGGFAEYIVVPARALVPVPDGVPFAQAAVATDAVLTPYHAVVRA---GE 162
Query: 185 VYPRDKRVLVLGASGGVGTMAVQLLKAWDIEV-VTTCSGDAKDLVTSLNPNLVIDYNEPE 243
V P + VLV+G GG+G AVQ+ KA V + +L L + V++ + +
Sbjct: 163 VKPGET-VLVIGL-GGLGLNAVQIAKAMGAAVIAVDIKEEKLELAKELGADEVLN-SLDD 219
Query: 244 AMHSIAGAGP---YDVILDAAGIP 264
+ AG +DVI D G
Sbjct: 220 SPKDKKAAGLGGGFDVIFDFVGTQ 243
>gnl|CDD|188164 TIGR01751, crot-CoA-red, crotonyl-CoA reductase. The enzyme
modelled by This model is responsible for the conversion
of crotonyl-CoA reductase to butyryl-CoA. In serine
cycle methylotrophic bacteria this enzyme is involved in
the process of acetyl-CoA to glyoxylate. In other
bacteria the enzyme is used to produce butyrate for
incorporation into polyketides such as tylosin from
Streptomyces fradiae and coronatine from Pseudomonas
syringae.
Length = 398
Score = 61.0 bits (148), Expect = 3e-10
Identities = 61/232 (26%), Positives = 87/232 (37%), Gaps = 51/232 (21%)
Query: 45 DNVKTPILKSKDVLVEMKAVSVNPIDVAMLGGYGNV---------VLNSLRQLETCSVEP 95
+ V P L +VLV + A VN Y NV LR+
Sbjct: 28 EVVPVPELGPGEVLVAVMAAGVN---------YNNVWAALGEPVSTFAFLRKYGKLD--- 75
Query: 96 VLEFPLTLGRDFCGKIVAKGPRVTDLNI-DDVVYGVIQPHKQ------------------ 136
L F + +G D G + GP VT + D+VV +Q
Sbjct: 76 -LPFHI-IGSDASGVVWRVGPGVTRWKVGDEVVASCLQVDLTAPDGRDGDPMLSSEQRIW 133
Query: 137 ------GSFSKLILADSALVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYPRDK 190
GSF++ L + KP +++ EEAA TG TA+ Q+
Sbjct: 134 GYETNFGSFAEFALVKDYQLMPKPKHLTWEEAACPGLTGATAYR--QLVGWNPAAVKPGD 191
Query: 191 RVLVLGASGGVGTMAVQLLKAWD-IEVVTTCSGDAKDLVTSLNPNLVIDYNE 241
VL+ GA+GG+G+ A QL +A V S + + SL VID N+
Sbjct: 192 NVLIWGAAGGLGSYATQLARAGGGNPVAVVSSPEKAEYCRSLGAEAVIDRND 243
Score = 34.8 bits (80), Expect = 0.066
Identities = 11/40 (27%), Positives = 21/40 (52%)
Query: 340 EINKFIERGQIKPVIDSKYNFCELPTAFEKVQQGHLRGKI 379
E N+ + +G+I P + Y E+ A + V + H +G +
Sbjct: 344 EANRLVAKGRIDPTLSKTYPLEEIGQAHQDVHRNHHQGNV 383
>gnl|CDD|176217 cd08255, 2-desacetyl-2-hydroxyethyl_bacteriochlorophyllide_like,
2-desacetyl-2-hydroxyethyl bacteriochlorophyllide and
other MDR family members. This subgroup of the medium
chain dehydrogenases/reductase (MDR)/zinc-dependent
alcohol dehydrogenase-like family has members identified
as 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide A
dehydrogenase and alcohol dehydrogenases. The medium
chain dehydrogenases/reductase (MDR)/zinc-dependent
alcohol dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability.
Length = 277
Score = 60.0 bits (146), Expect = 3e-10
Identities = 42/175 (24%), Positives = 64/175 (36%), Gaps = 29/175 (16%)
Query: 97 LEFPLTLGRDFCGKIVAKGPRVTDLNIDDVVYGVIQPHKQGSFSKLILADSALVHKKPSN 156
L PL G G++V G VT D V+ PH + ++ + L+ P
Sbjct: 18 LPLPLPPGYSSVGRVVEVGSGVTGFKPGDRVF-CFGPHAE-----RVVVPANLLVPLPDG 71
Query: 157 ISDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRVLVLGASGGVGTMAVQLLKAWDIEV 216
+ E AA LTA +A + +RV V+G G VG +A QL KA
Sbjct: 72 LPPERAA------LTALAATALNGVRDAEPRLGERVAVVGL-GLVGLLAAQLAKA----- 119
Query: 217 VTTCSGDAKDLVTSLNPN-------LVIDYNEPEAMHSIAGAGPYDVILDAAGIP 264
+G + + + L G DV+++A+G P
Sbjct: 120 ----AGAREVVGVDPDAARRELAEALGPADPVAADTADEIGGRGADVVIEASGSP 170
>gnl|CDD|176205 cd08243, quinone_oxidoreductase_like_1, Quinone oxidoreductase
(QOR). NAD(P)(H)-dependent oxidoreductases are the
major enzymes in the interconversion of alcohols and
aldehydes, or ketones. The medium chain alcohol
dehydrogenase family (MDR) have a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit.
Length = 320
Score = 60.3 bits (147), Expect = 3e-10
Identities = 79/364 (21%), Positives = 135/364 (37%), Gaps = 60/364 (16%)
Query: 29 AWQISSYGGADELQFNDNVKTPILKSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQL 88
A I GG + L+ + + P K VL+ +KA +N ++ RQ
Sbjct: 3 AIVIEQPGGPEVLKLRE-IPIPEPKPGWVLIRVKAFGLNRSEIFT------------RQG 49
Query: 89 ETCSVEPVLEFPLTLGRDFCGKIVA-------KGPRVTDLNIDDVVYGVIQPHKQGSFSK 141
+ SV+ FP LG + G++ G RV G + GS+++
Sbjct: 50 HSPSVK----FPRVLGIEAVGEVEEAPGGTFTPGQRVATAM------GGMGRTFDGSYAE 99
Query: 142 LILADSALVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRVLVLGASGGV 201
L + V+ S++S E A + T TAW +L +LGL +L+ G + V
Sbjct: 100 YTLVPNEQVYAIDSDLSWAELAALPETYYTAWGSL--FRSLGL--QPGDTLLIRGGTSSV 155
Query: 202 GTMAVQLLKAWDIEVV-TTCSGDAKDLVTSLNPNLVIDYNEPEAMHSIAGAGPYDVILDA 260
G A++L KA V TT S + L+ L + V+ + A A G +D +L+
Sbjct: 156 GLAALKLAKALGATVTATTRSPERAALLKELGADEVVIDDGAIAEQLRAAPGGFDKVLEL 215
Query: 261 AGIP--LDQINSYLPFLKTGKFSKFVTL--RSPFLKNTDSLGLVPGLVKNAFDLLKSNFE 316
G D + L+ G L L++ + + +P V
Sbjct: 216 VGTATLKDSLRH----LRPGGIVCMTGLLGGQWTLEDFNPMDDIPSGV-------NLTLT 264
Query: 317 SGELCKTNTIRWGFFMPIPYAVKEINKFIERGQIKPVIDSKYNFCELPTAFEKVQQGHLR 376
G P ++E+ F+ G + + F E+ A ++
Sbjct: 265 GSSS--------GDVPQTP--LQELFDFVAAGHLDIPPSKVFTFDEIVEAHAYMESNRAF 314
Query: 377 GKII 380
GK++
Sbjct: 315 GKVV 318
>gnl|CDD|176221 cd08260, Zn_ADH6, Alcohol dehydrogenases of the MDR family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. This group has the characteristic
catalytic and structural zinc sites of the
zinc-dependent alcohol dehydrogenases. Alcohol
dehydrogenase in the liver converts ethanol and NAD+ to
acetaldehyde and NADH, while in yeast and some other
microorganisms ADH catalyzes the conversion acetaldehyde
to ethanol in alcoholic fermentation. ADH is a member of
the medium chain alcohol dehydrogenase family (MDR),
which has a NAD(P)(H)-binding domain in a Rossmann fold
of a beta-alpha form. The NAD(H)-binding region is
comprised of 2 structurally similar halves, each of
which contacts a mononucleotide. A GxGxxG motif after
the first mononucleotide contact half allows the close
contact of the coenzyme with the ADH backbone. The
N-terminal catalytic domain has a distant homology to
GroES. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit, a
catalytic zinc at the active site and a structural zinc
in a lobe of the catalytic domain. NAD(H)-binding occurs
in the cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 345
Score = 60.3 bits (147), Expect = 4e-10
Identities = 55/203 (27%), Positives = 79/203 (38%), Gaps = 39/203 (19%)
Query: 100 PLTLGRDFCGKIVAKGPRVTDLNIDDVV-----------------YGVIQPHKQ------ 136
P G +F G +V G V+ + D V + H+
Sbjct: 55 PHVPGHEFAGVVVEVGEDVSRWRVGDRVTVPFVLGCGTCPYCRAGDSNVCEHQVQPGFTH 114
Query: 137 -GSFSKLIL---ADSALVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRV 192
GSF++ + AD LV + P ++ AAG+ TA+ AL V P + V
Sbjct: 115 PGSFAEYVAVPRADVNLV-RLPDDVDFVTAAGLGCRFATAFRAL---VHQARVKPGE-WV 169
Query: 193 LVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAK-DLVTSLNPNLVIDYNEPE----AMHS 247
V G GGVG AV + A V+ D K +L L ++ +E E A+
Sbjct: 170 AVHGC-GGVGLSAVMIASALGARVIAVDIDDDKLELARELGAVATVNASEVEDVAAAVRD 228
Query: 248 IAGAGPYDVILDAAGIPLDQINS 270
+ G G V +DA GIP NS
Sbjct: 229 LTGGGA-HVSVDALGIPETCRNS 250
>gnl|CDD|234026 TIGR02823, oxido_YhdH, putative quinone oxidoreductase, YhdH/YhfP
family. This model represents a subfamily of pfam00107
as defined by Pfam, a superfamily in which some members
are zinc-binding medium-chain alcohol dehydrogenases
while others are quinone oxidoreductases with no bound
zinc. This subfamily includes proteins studied
crystallographically for insight into function: YhdH
from Escherichia coli and YhfP from Bacillus subtilis.
Members bind NADPH or NAD, but not zinc [Unknown
function, Enzymes of unknown specificity].
Length = 323
Score = 59.9 bits (146), Expect = 5e-10
Identities = 60/193 (31%), Positives = 90/193 (46%), Gaps = 28/193 (14%)
Query: 56 DVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQLETCSVEPVLEFPLTLGRDFCGKIVA-K 114
DVL+++ S+N D + G G VV R +P+ G D G +V+ +
Sbjct: 28 DVLIKVAYSSLNYKDALAITGKGGVV----RS-----------YPMIPGIDAAGTVVSSE 72
Query: 115 GPRVTDLNIDDVV---YGVIQPHKQGSFSKLILADSALVHKKPSNISDEEAAGVLYTGLT 171
PR + D+V+ YG+ H G +S+ + + P +S EA + G T
Sbjct: 73 DPRFREG--DEVIVTGYGLGVSH-DGGYSQYARVPADWLVPLPEGLSLREAMALGTAGFT 129
Query: 172 AWSALQITA--ALGLVYPRDKRVLVLGASGGVGTMAVQLLKAWDIEVVT-TCSGDAKDLV 228
A AL + A GL P D VLV GA+GGVG++AV +L EVV T + +D +
Sbjct: 130 A--ALSVMALERNGLT-PEDGPVLVTGATGGVGSLAVAILSKLGYEVVASTGKAEEEDYL 186
Query: 229 TSLNPNLVIDYNE 241
L + VID +
Sbjct: 187 KELGASEVIDRED 199
>gnl|CDD|176208 cd08246, crotonyl_coA_red, crotonyl-CoA reductase. Crotonyl-CoA
reductase, a member of the medium chain
dehydrogenase/reductase family, catalyzes the
NADPH-dependent conversion of crotonyl-CoA to
butyryl-CoA, a step in (2S)-methylmalonyl-CoA
production for straight-chain fatty acid biosynthesis.
Like enoyl reductase, another enzyme in fatty acid
synthesis, crotonyl-CoA reductase is a member of the
zinc-dependent alcohol dehydrogenase-like medium chain
dehydrogenase/reductase family. The medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES.
Length = 393
Score = 59.7 bits (145), Expect = 6e-10
Identities = 58/223 (26%), Positives = 93/223 (41%), Gaps = 34/223 (15%)
Query: 45 DNVKTPILKSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQLETCSVEPVLEFPLTLG 104
++V P L +VLV + A VN +V G + ++ + + G
Sbjct: 33 EDVPVPELGPGEVLVAVMAAGVNYNNVWAALGEPVSTFAARQRRGR-----DEPYHIG-G 86
Query: 105 RDFCGKIVAKGPRVTDLNIDD--VVYGVI---------------QPHKQ--------GSF 139
D G + A G V + + D VV+ + P ++ GSF
Sbjct: 87 SDASGIVWAVGEGVKNWKVGDEVVVHCSVWDGNDPERAGGDPMFDPSQRIWGYETNYGSF 146
Query: 140 SKLILADSALVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRVLVLGASG 199
++ L + + KP ++S EEAA + G TA+ L V P D VL+ GASG
Sbjct: 147 AQFALVQATQLMPKPKHLSWEEAAAYMLVGATAYRML-FGWNPNTVKPGDN-VLIWGASG 204
Query: 200 GVGTMAVQLLKAWDIEVVTTCSGDAK-DLVTSLNPNLVIDYNE 241
G+G+MA+QL +A V S + K + +L VI+ +
Sbjct: 205 GLGSMAIQLARAAGANPVAVVSSEEKAEYCRALGAEGVINRRD 247
Score = 28.9 bits (65), Expect = 4.9
Identities = 10/42 (23%), Positives = 21/42 (50%), Gaps = 1/42 (2%)
Query: 339 KEINKFIERGQIKPVIDSKYNFCELPTAFEKVQQG-HLRGKI 379
E N+ + +G+I P + ++ E P A + + + H G +
Sbjct: 348 AEANRLVMKGRIDPCLSKVFSLDETPDAHQLMHRNQHHVGNM 389
>gnl|CDD|176188 cd05285, sorbitol_DH, Sorbitol dehydrogenase. Sorbitol and aldose
reductase are NAD(+) binding proteins of the polyol
pathway, which interconverts glucose and fructose.
Sorbitol dehydrogenase is tetrameric and has a single
catalytic zinc per subunit. Aldose reductase catalyzes
the NADP(H)-dependent conversion of glucose to sorbital,
and SDH uses NAD(H) in the conversion of sorbitol to
fructose. NAD(P)(H)-dependent oxidoreductases are the
major enzymes in the interconversion of alcohols and
aldehydes, or ketones. The medium chain alcohol
dehydrogenase family (MDR) have a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit.
Length = 343
Score = 59.4 bits (145), Expect = 7e-10
Identities = 61/268 (22%), Positives = 96/268 (35%), Gaps = 68/268 (25%)
Query: 37 GADELQFNDNVKTPILKSKDVLVEMKAVSVNPIDVAML--GGYGNVVLNSLRQLETCSVE 94
G +L+ + P +VLV ++AV + DV G G+ V+
Sbjct: 6 GPGDLRLEE-RPIPEPGPGEVLVRVRAVGICGSDVHYYKHGRIGDFVVKE---------- 54
Query: 95 PVLEFPLTLGRDFCGKIVAKGPRVTDLNIDDVVYGVIQPH-------------------- 134
P+ LG + G +VA G VT L + D V I+P
Sbjct: 55 -----PMVLGHESAGTVVAVGSGVTHLKVGDRV--AIEPGVPCRTCEFCKSGRYNLCPDM 107
Query: 135 -------KQGSFSKLILADSALVHKKPSNISDEEAAGV--LYTGLTAWSALQITAALGLV 185
G+ + + + HK P N+S EE A V L G+ + + G
Sbjct: 108 RFAATPPVDGTLCRYVNHPADFCHKLPDNVSLEEGALVEPLSVGV--HACRRAGVRPG-- 163
Query: 186 YPRDKRVLVLGASGGVGTMAVQLLKAW---DIEVVTTCSGD----AKDL--VTSLNPNLV 236
VLV GA G +G + + KA+ + VVT AK+L ++N
Sbjct: 164 ----DTVLVFGA-GPIGLLTAAVAKAFGATKV-VVTDIDPSRLEFAKELGATHTVNVRTE 217
Query: 237 IDYNEPEAMHSIAGAGPYDVILDAAGIP 264
E + + G DV+++ G
Sbjct: 218 DTPESAEKIAELLGGKGPDVVIECTGAE 245
>gnl|CDD|176187 cd05284, arabinose_DH_like, D-arabinose dehydrogenase. This group
contains arabinose dehydrogenase (AraDH) and related
alcohol dehydrogenases. AraDH is a member of the medium
chain dehydrogenase/reductase family and catalyzes the
NAD(P)-dependent oxidation of D-arabinose and other
pentoses, the initial step in the metabolism of
d-arabinose into 2-oxoglutarate. Like the alcohol
dehydrogenases, AraDH binds a zinc in the catalytic
cleft as well as a distal structural zinc. AraDH forms
homotetramers as a dimer of dimers. AraDH replaces a
conserved catalytic His with replace with Arg, compared
to the canonical ADH site. NAD(P)(H)-dependent
oxidoreductases are the major enzymes in the
interconversion of alcohols and aldehydes, or ketones.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation. ADH
is a member of the medium chain alcohol dehydrogenase
family (MDR), which has a NAD(P)(H)-binding domain in a
Rossmann fold of a beta-alpha form. The NAD(H)-binding
region is comprised of 2 structurally similar halves,
each of which contacts a mononucleotide. A GxGxxG motif
after the first mononucleotide contact half allows the
close contact of the coenzyme with the ADH backbone.
The N-terminal catalytic domain has a distant homology
to GroES. These proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and have 2 tightly bound zinc atoms per
subunit, a catalytic zinc at the active site and a
structural zinc in a lobe of the catalytic domain.
NAD(H) binding occurs in the cleft between the catalytic
and coenzyme-binding domains at the active site, and
coenzyme binding induces a conformational closing of
this cleft. Coenzyme binding typically precedes and
contributes to substrate binding. In human ADH
catalysis, the zinc ion helps coordinate the alcohol,
followed by deprotonation of a histidine, the ribose of
NAD, a serine, then the alcohol, which allows the
transfer of a hydride to NAD+, creating NADH and a
zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 340
Score = 59.5 bits (145), Expect = 7e-10
Identities = 64/281 (22%), Positives = 107/281 (38%), Gaps = 55/281 (19%)
Query: 29 AWQISSYGGADELQFNDNVKTPILKSKDVLVEMKAVSVNPIDVAML-GGYGNVVLNSLRQ 87
A ++ YG L+ +V P VLV + V D+ ++ G +G ++
Sbjct: 3 AARLYEYGKPLRLE---DVPVPEPGPGQVLVRVGGAGVCHSDLHVIDGVWGGIL------ 53
Query: 88 LETCSVEPVLEFPLTLGRDFCGKIVAKGPRVTDLNIDD--VVYGVI---------QPHKQ 136
+ P TLG + G + G V L D VV+ + +
Sbjct: 54 --------PYKLPFTLGHENAGWVEEVGSGVDGLKEGDPVVVHPPWGCGTCRYCRRGEEN 105
Query: 137 -------------GSFSKLILADSALVHKKPSNISDEEAAGVLYTGLTAWSALQITAALG 183
G F++ +L S + K P + EAA + GLTA+ A + AL
Sbjct: 106 YCENARFPGIGTDGGFAEYLLVPSRRLVKLPRGLDPVEAAPLADAGLTAYHA--VKKALP 163
Query: 184 LVYPRDKRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAKDLVTSLNPNLVIDY---- 239
+ P V+V+G GG+G +AVQ+L+A + T + D + L L D+
Sbjct: 164 YLDP-GSTVVVIGV-GGLGHIAVQILRA--LTPATVIAVDRSEEALKLAERLGADHVLNA 219
Query: 240 --NEPEAMHSIAGAGPYDVILDAAGIPLDQINSYLPFLKTG 278
+ E + + G D ++D G + + L G
Sbjct: 220 SDDVVEEVRELTGGRGADAVIDFVGSD-ETLALAAKLLAKG 259
>gnl|CDD|176231 cd08270, MDR4, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 305
Score = 58.9 bits (143), Expect = 9e-10
Identities = 53/187 (28%), Positives = 78/187 (41%), Gaps = 39/187 (20%)
Query: 104 GRDFCGKIV---------AKGPRVTDLNIDDVVYGVIQPHKQGSFSKLILADSALVHKKP 154
G D G + A G RV L G++++L+ + + P
Sbjct: 56 GWDAAGVVERAAADGSGPAVGARVVGLGAM------------GAWAELVAVPTGWLAVLP 103
Query: 155 SNISDEEAAGVLYTGLTAWSAL-QITAALGLVYPRDKRVLVLGASGGVGTMAVQLLKAWD 213
+S +AA + G+TA AL + LG +RVLV GASGGVG AVQL
Sbjct: 104 DGVSFAQAATLPVAGVTALRALRRGGPLLG------RRVLVTGASGGVGRFAVQLAALAG 157
Query: 214 IEVVTTCSGDAK--DLVTSLNPNLVIDYNEPEAMHSIAGAGPYDVILDAAGIPLDQINSY 271
VV A+ L +V+ +E ++GA P D+++D+ G P Q+
Sbjct: 158 AHVVAVVGSPARAEGLRELGAAEVVVGGSE------LSGA-PVDLVVDSVGGP--QLARA 208
Query: 272 LPFLKTG 278
L L G
Sbjct: 209 LELLAPG 215
>gnl|CDD|176258 cd08298, CAD2, Cinnamyl alcohol dehydrogenases (CAD). These
alcohol dehydrogenases are related to the cinnamyl
alcohol dehydrogenases (CAD), members of the medium
chain dehydrogenase/reductase family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Cinnamyl alcohol dehydrogenases
(CAD) reduce cinnamaldehydes to cinnamyl alcohols in the
last step of monolignal metabolism in plant cells walls.
CAD binds 2 zinc ions and is NADPH- dependent. CAD
family members are also found in non-plant species, e.g.
in yeast where they have an aldehyde reductase activity.
The medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 329
Score = 58.7 bits (143), Expect = 1e-09
Identities = 49/218 (22%), Positives = 88/218 (40%), Gaps = 53/218 (24%)
Query: 95 PVLEFPLTLGRDFCGKIVAKGPRVTDLNIDDVVYGV-------------------IQPHK 135
P + PL G + G++ A GP VT ++ D V GV + +
Sbjct: 54 PPPKLPLIPGHEIVGRVEAVGPGVTRFSVGDRV-GVPWLGSTCGECRYCRSGRENLCDNA 112
Query: 136 Q-------GSFSKLILADSALVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYPR 188
+ G +++ ++AD + P + DEEAA +L G+ + AL++
Sbjct: 113 RFTGYTVDGGYAEYMVADERFAYPIPEDYDDEEAAPLLCAGIIGYRALKLAGL-----KP 167
Query: 189 DKRVLVLGASGGVGTMAVQLLKAWDIEV-VTTCSGDAKDLVTSLNPNLVIDYNE--PEAM 245
+R+ + G G +A+Q+ + EV T SG+ ++L L + D ++ PE +
Sbjct: 168 GQRLGLYGF-GASAHLALQIARYQGAEVFAFTRSGEHQELARELGADWAGDSDDLPPEPL 226
Query: 246 HSI---AGAGPYDVILDA------------AGIPLDQI 268
+ A G ++ A AGI + I
Sbjct: 227 DAAIIFAPVG--ALVPAALRAVKKGGRVVLAGIHMSDI 262
>gnl|CDD|225041 COG2130, COG2130, Putative NADP-dependent oxidoreductases [General
function prediction only].
Length = 340
Score = 57.7 bits (140), Expect = 2e-09
Identities = 77/349 (22%), Positives = 127/349 (36%), Gaps = 58/349 (16%)
Query: 47 VKTPILKSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQLETCSVEPVLEFPLTLGRD 106
V P VL+ +S++P M G R + S P P+ LG
Sbjct: 32 VDVPEPGEGQVLLRTLYLSLDP---YMRG----------RMSDAPSYAP----PVELGEV 74
Query: 107 FCGKIVAKG--PRVTDLNIDDVVYGVIQPHKQGSFSKLILADSALVHKKPSNISDEEAA- 163
G VAK D+V GV + + ++D + K + + A
Sbjct: 75 MVGGTVAKVVASNHPGFQPGDIVVGV------SGWQEYAISDGEGLRKLDPSPAPLSAYL 128
Query: 164 GVL-YTGLTAWSALQITAALGLVYPRD-KRVLVLGASGGVGTMAVQLLKAWDIEVVTTCS 221
GVL GLTA+ L P+ + V+V A+G VG++ Q+ K VV
Sbjct: 129 GVLGMPGLTAYFGLLDIGQ-----PKAGETVVVSAAAGAVGSVVGQIAKLKGCRVVGIAG 183
Query: 222 GDAK-DLVTS-LNPNLVIDYNEPEAMHSIAGAGP--YDVILDAAGIP-----LDQINSYL 272
G K D +T L + IDY + ++ A P DV + G L +N +
Sbjct: 184 GAEKCDFLTEELGFDAGIDYKAEDFAQALKEACPKGIDVYFENVGGEVLDAVLPLLNLFA 243
Query: 273 PFLKTGKFSKFVTLRSPFLKNTDSLGLVPGLVKNAFDLLKSNFESGELCKTNTIRWGFFM 332
G S++ P L + L F ++ S+++
Sbjct: 244 RIPVCGAISQYNAPELPPGPRRLPLLMAKRLRVQGF-IVASDYDQR-------------- 288
Query: 333 PIPYAVKEINKFIERGQIKPVIDSKYNFCELPTAFEKVQQGHLRGKIIL 381
P A++E+ +++ G+I+ P AF + G GK+++
Sbjct: 289 -FPEALRELGGWVKEGKIQYRETIVDGLENAPEAFIGLLSGKNFGKLVV 336
>gnl|CDD|176256 cd08296, CAD_like, Cinnamyl alcohol dehydrogenases (CAD). Cinnamyl
alcohol dehydrogenases (CAD), members of the medium
chain dehydrogenase/reductase family, reduce
cinnamaldehydes to cinnamyl alcohols in the last step of
monolignal metabolism in plant cells walls. CAD binds 2
zinc ions and is NADPH- dependent. CAD family members
are also found in non-plant species, e.g. in yeast where
they have an aldehyde reductase activity. The medium
chain dehydrogenases/reductase (MDR)/zinc-dependent
alcohol dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADHs), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 333
Score = 57.6 bits (140), Expect = 3e-09
Identities = 82/385 (21%), Positives = 140/385 (36%), Gaps = 85/385 (22%)
Query: 29 AWQISSYGGADELQFNDNVKTPILKSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQL 88
A Q++ GG EL D P+ +VL++++A V D + G
Sbjct: 3 AVQVTEPGGPLELVERD---VPLPGPGEVLIKVEACGVCHSDAFVKEG------------ 47
Query: 89 ETCSVEPVLEFPLTLGRDFCGKIVAKGPRVTDLNIDDVV--------YGVIQPHKQGSF- 139
P L +P G + G+I A G V+ + D V G ++G F
Sbjct: 48 ----AMPGLSYPRVPGHEVVGRIDAVGEGVSRWKVGDRVGVGWHGGHCGTCDACRRGDFV 103
Query: 140 -----------------SKLILADSALVHKKPSNISDEEAAGVLYTGLTAWSALQITAAL 182
++ AL P ++ EAA +L G+T ++AL+ + A
Sbjct: 104 HCENGKVTGVTRDGGYAEYMLAPAEALARI-PDDLDAAEAAPLLCAGVTTFNALRNSGAK 162
Query: 183 GLVYPRDKRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAK-DLVTSLNPNLVIDYNE 241
P D V V G GG+G +AVQ V G K DL L + ID ++
Sbjct: 163 ----PGD-LVAVQGI-GGLGHLAVQYAAKMGFRTVAISRGSDKADLARKLGAHHYIDTSK 216
Query: 242 ---PEAMHSIAGAGPYDVILDAAGIPLDQINSYLPFLKTGKFSKFVTLRSPFLKNTDSLG 298
EA+ + GA +IL A I++ + L K + LG
Sbjct: 217 EDVAEALQELGGA---KLILATAPNA-KAISALVGGLAPR--GKLLI-----------LG 259
Query: 299 LVPGLVK-NAFDLLKSNFESGELCKTNTIRWGFFMPIPYAVKEINKFIERGQIKPVIDSK 357
V + L+ +I G+ ++ KF ++P+++
Sbjct: 260 AAGEPVAVSPLQLIM---------GRKSIH-GWPSGTALDSEDTLKFSALHGVRPMVE-T 308
Query: 358 YNFCELPTAFEKVQQGHLRGKIILN 382
+ + A++++ G R +++L
Sbjct: 309 FPLEKANEAYDRMMSGKARFRVVLT 333
>gnl|CDD|182701 PRK10754, PRK10754, quinone oxidoreductase, NADPH-dependent;
Provisional.
Length = 327
Score = 56.3 bits (136), Expect = 6e-09
Identities = 64/239 (26%), Positives = 97/239 (40%), Gaps = 33/239 (13%)
Query: 31 QISSYGGADELQFNDNVKTPILKSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQLET 90
+ +GG + LQ + +V VE KA+ +N ID + G
Sbjct: 6 EFHKHGGPEVLQAVEFTPAD-PAENEVQVENKAIGINYIDTYIRSG-------------- 50
Query: 91 CSVEPVLEFPLTLGRDFCGKIVAKGPRVTDLNIDD-VVYGVIQPHKQGSFSKL--ILADS 147
+ P P LG + G + G V + + D VVY G++S + + AD
Sbjct: 51 --LYPPPSLPSGLGTEAAGVVSKVGSGVKHIKVGDRVVYA---QSALGAYSSVHNVPADK 105
Query: 148 ALVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRVLVLGASGGVGTMAVQ 207
A + P IS E+AA GLT + L+ T + P D++ L A+GGVG +A Q
Sbjct: 106 AAI--LPDAISFEQAAASFLKGLTVYYLLRKTYE---IKP-DEQFLFHAAAGGVGLIACQ 159
Query: 208 LLKAWDIEVVTTCSGDAK-DLVTSLNPNLVIDYNE---PEAMHSIAGAGPYDVILDAAG 262
KA +++ T K VI+Y E E + I G V+ D+ G
Sbjct: 160 WAKALGAKLIGTVGSAQKAQRAKKAGAWQVINYREENIVERVKEITGGKKVRVVYDSVG 218
>gnl|CDD|176248 cd08288, MDR_yhdh, Yhdh putative quinone oxidoreductases. Yhdh
putative quinone oxidoreductases (QOR). QOR catalyzes
the conversion of a quinone + NAD(P)H to a hydroquinone
+ NAD(P)+. Quinones are cyclic diones derived from
aromatic compounds. Membrane bound QOR actin the
respiratory chains of bacteria and mitochondria, while
soluble QOR acts to protect from toxic quinones (e.g.
DT-diaphorase) or as a soluble eye-lens protein in some
vertebrates (e.g. zeta-crystalin). QOR reduces quinones
through a semi-quinone intermediate via a
NAD(P)H-dependent single electron transfer. QOR is a
member of the medium chain dehydrogenase/reductase
family, but lacks the zinc-binding sites of the
prototypical alcohol dehydrogenases of this group.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 324
Score = 55.6 bits (135), Expect = 1e-08
Identities = 59/199 (29%), Positives = 85/199 (42%), Gaps = 38/199 (19%)
Query: 52 LKSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQLETCSVEPVLEFPLTLGRDFCGKI 111
L DV VE+ ++N D + G G +V FPL G D G +
Sbjct: 25 LPEGDVTVEVHYSTLNYKDGLAITGKGGIVR---------------TFPLVPGIDLAGTV 69
Query: 112 V-------AKGPRVTDLNIDDVV--YGVIQPHKQGSFSKLILADSALVHKKPSNISDEEA 162
V G RV V+ +GV + H G +++ + + P +S +A
Sbjct: 70 VESSSPRFKPGDRV-------VLTGWGVGERHW-GGYAQRARVKADWLVPLPEGLSARQA 121
Query: 163 AGVLYTGLTAWSALQITAAL--GLVYPRDKRVLVLGASGGVGTMAVQLLKAWDIEVV-TT 219
+ G TA L + A G V P D VLV GA+GGVG++AV LL EVV +T
Sbjct: 122 MAIGTAGFTA--MLCVMALEDHG-VTPGDGPVLVTGAAGGVGSVAVALLARLGYEVVAST 178
Query: 220 CSGDAKDLVTSLNPNLVID 238
+ D + SL + +ID
Sbjct: 179 GRPEEADYLRSLGASEIID 197
>gnl|CDD|176219 cd08258, Zn_ADH4, Alcohol dehydrogenases of the MDR family. This
group shares the zinc coordination sites of the
zinc-dependent alcohol dehydrogenases. The medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of an
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 306
Score = 55.4 bits (134), Expect = 1e-08
Identities = 50/201 (24%), Positives = 74/201 (36%), Gaps = 53/201 (26%)
Query: 47 VKTPILKSKDVLVEMKAVSVNPIDV-AMLGGYGNVVLNSLRQLETCSVEPVLEFPLTLGR 105
V P +VL+++ A + D+ G Y V E P+ LG
Sbjct: 19 VPEPEPGPGEVLIKVAAAGICGSDLHIYKGDYDPV-----------------ETPVVLGH 61
Query: 106 DFCGKIVAKGPRVTDLNIDDVVYGVIQ------------------PHKQ-------GSFS 140
+F G IV GP V + D V PH++ G F+
Sbjct: 62 EFSGTIVEVGPDVEGWKVGDRVVSETTFSTCGRCPYCRRGDYNLCPHRKGIGTQADGGFA 121
Query: 141 KLILADSALVHKKPSNISDEEAAGVLYTGLTAWSALQITAAL--GLVYPRDKRVLVLGAS 198
+ +L +H+ P N+S E AA LT A+ + A + P D V+V G
Sbjct: 122 EYVLVPEESLHELPENLSLEAAA------LTEPLAVAVHAVAERSGIRPGD-TVVVFG-P 173
Query: 199 GGVGTMAVQLLKAWDIEVVTT 219
G +G +A Q+ K VV
Sbjct: 174 GPIGLLAAQVAKLQGATVVVV 194
>gnl|CDD|219758 pfam08240, ADH_N, Alcohol dehydrogenase GroES-like domain. This is
the catalytic domain of alcohol dehydrogenases. Many of
them contain an inserted zinc binding domain. This
domain has a GroES-like structure.
Length = 108
Score = 51.1 bits (123), Expect = 3e-08
Identities = 22/79 (27%), Positives = 33/79 (41%), Gaps = 18/79 (22%)
Query: 56 DVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQLETCSVEPVLEFPLTLGRDFCGKIVAKG 115
+VLV +KA + D+ + G P ++ PL LG + G + G
Sbjct: 3 EVLVRVKAAGICGSDLHIYRGE----------------PPPVKLPLILGHEGAGIVEEVG 46
Query: 116 PRVTDLNIDDVVYGVIQPH 134
P VT L + D V V+ P
Sbjct: 47 PGVTGLKVGDRV--VVYPL 63
>gnl|CDD|176197 cd08235, iditol_2_DH_like, L-iditol 2-dehydrogenase. Putative
L-iditol 2-dehydrogenase based on annotation of some
members in this subgroup. L-iditol 2-dehydrogenase
catalyzes the NAD+-dependent conversion of L-iditol to
L-sorbose in fructose and mannose metabolism. This
enzyme is related to sorbitol dehydrogenase, alcohol
dehydrogenase, and other medium chain
dehydrogenase/reductases. The zinc-dependent alcohol
dehydrogenase (ADH-Zn)-like family of proteins is a
diverse group of proteins related to the first
identified member, class I mammalian ADH. This group is
also called the medium chain dehydrogenases/reductase
family (MDR) to highlight its broad range of activities
and to distinguish from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal GroES-like catalytic
domain. The MDR group contains a host of activities,
including the founding alcohol dehydrogenase (ADH),
quinone reductase, sorbitol dehydrogenase, formaldehyde
dehydrogenase, butanediol DH, ketose reductase, cinnamyl
reductase, and numerous others. The zinc-dependent
alcohol dehydrogenases (ADHs) catalyze the
NAD(P)(H)-dependent interconversion of alcohols to
aldehydes or ketones. Active site zinc has a catalytic
role, while structural zinc aids in stability. ADH-like
proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
generally have 2 tightly bound zinc atoms per subunit.
The active site zinc is coordinated by a histidine, two
cysteines, and a water molecule. The second zinc seems
to play a structural role, affects subunit interactions,
and is typically coordinated by 4 cysteines.
Length = 343
Score = 53.0 bits (128), Expect = 8e-08
Identities = 80/371 (21%), Positives = 125/371 (33%), Gaps = 94/371 (25%)
Query: 46 NVKTPILKSKDVLVEMKAVSVNPIDVAML-GGYGNVVLNSLRQLETCSVEPVLEFPLTLG 104
V P +VLV+++A + DV + GG+ ++ + P LG
Sbjct: 16 EVPVPEPGPGEVLVKVRACGICGTDVKKIRGGHTDL-----------------KPPRILG 58
Query: 105 RDFCGKIVAKGPRVTDLNIDDVVYGVIQPH---------KQGSFS-------KLILADSA 148
+ G+IV G VT + D V + PH +G+ + L D
Sbjct: 59 HEIAGEIVEVGDGVTGFKVGDRV--FVAPHVPCGECHYCLRGNENMCPNYKKFGNLYDGG 116
Query: 149 L---------------VHKKPSNISDEEAAGV--LYTGLTAWSALQITAALGLVYPRDKR 191
V K P N+S EEAA V L + A I
Sbjct: 117 FAEYVRVPAWAVKRGGVLKLPDNVSFEEAALVEPLACCINAQRKAGIKP--------GDT 168
Query: 192 VLVLGASGGVGTMAVQLLKAWDIEVVTTC--SGDAKDLVTSLNPNLVIDYNEPEAMHSI- 248
VLV+GA G +G + L KA V + + L + ID E + + +
Sbjct: 169 VLVIGA-GPIGLLHAMLAKASGARKVIVSDLNEFRLEFAKKLGADYTIDAAEEDLVEKVR 227
Query: 249 ---AGAGPYDVILDAAGIPLDQINSYLPFLKT-GKFSKFVTLRSPFLKNTDSLGLVPGLV 304
G G DV++ A G P + L ++ G+ F K +
Sbjct: 228 ELTDGRG-ADVVIVATGSP-EAQAQALELVRKGGRILFF----GGLPKGSTV-------- 273
Query: 305 KNAFDLLKSNFESGELCKTNTIRWGFFMPIPYAVKEINKFIERGQI--KPVIDSKYNFCE 362
D + E+ T + P KE + I G+I K +I ++ +
Sbjct: 274 --NIDP--NLIHYREITITGSYAAS-----PEDYKEALELIASGKIDVKDLITHRFPLED 324
Query: 363 LPTAFEKVQQG 373
+ AFE G
Sbjct: 325 IEEAFELAADG 335
>gnl|CDD|223991 COG1063, Tdh, Threonine dehydrogenase and related Zn-dependent
dehydrogenases [Amino acid transport and metabolism /
General function prediction only].
Length = 350
Score = 52.4 bits (126), Expect = 2e-07
Identities = 69/374 (18%), Positives = 113/374 (30%), Gaps = 84/374 (22%)
Query: 35 YGGADELQFNDNVKTPILKSKDVLVEMKAVSVNPIDV-AMLGGYGNVVLNSLRQLETCSV 93
Y G +++ + PI DVL+ + A + D+ GG V
Sbjct: 7 YVGGGDVRLEE-PPPPIPGPGDVLIRVTATGICGSDLHIYRGGEP-------------FV 52
Query: 94 EPVLEFPLTLGRDFCGKIVAKGPRVTDLNIDDVV-------------------------- 127
P LG +F G++V G V + D V
Sbjct: 53 PPGDII---LGHEFVGEVVEVG-VVRGFKVGDRVVVEPNIPCGHCRYCRAGEYNLCENPG 108
Query: 128 ---YGVIQPHKQGSFSKLILADSALVHKK-PSNISDEEAAGV-LYTGLTAWSALQITAAL 182
Y + G F++ + + K P I +E AA TA+ AA+
Sbjct: 109 FYGYAGLGGGIDGGFAEYVRVPADFNLAKLPDGIDEEAAALTEPLA--TAYHGHAERAAV 166
Query: 183 GLVYPRDKRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAK--DLVTSLNPNLVIDYN 240
V+V+GA G +G +A+ L K VV + +L V+
Sbjct: 167 ----RPGGTVVVVGA-GPIGLLAIALAKLLGASVVIVVDRSPERLELAKEAGGADVVVNP 221
Query: 241 ----EPEAMHSIAGAGPYDVILDAAGIP--LDQINSYLPFLKT-------GKFSKFVTLR 287
+ + G DV+++A G P LDQ L T G +
Sbjct: 222 SEDDAGAEILELTGGRGADVVIEAVGSPPALDQALEALRPGGTVVVVGVYGGEDIPLPAG 281
Query: 288 SPFLKNTDSLGLVPGLVKNAFDLLKSNFESGELCKTNTIRWGFFMPIPYAVKEINKFIER 347
K G + + F+ +L + I + + + + E
Sbjct: 282 LVVSKELTLRGSLRPSGREDFERAL------DLLASGKIDPEKLITHRLPLDDAAEAYEL 335
Query: 348 ------GQIKPVID 355
IK V+
Sbjct: 336 FADRKEEAIKVVLK 349
>gnl|CDD|176251 cd08291, ETR_like_1, 2-enoyl thioester reductase (ETR) like
proteins, child 1. 2-enoyl thioester reductase (ETR)
like proteins. ETR catalyzes the NADPH-dependent
conversion of trans-2-enoyl acyl carrier
protein/coenzyme A (ACP/CoA) to acyl-(ACP/CoA) in fatty
acid synthesis. 2-enoyl thioester reductase activity has
been linked in Candida tropicalis as essential in
maintaining mitiochondrial respiratory function. This
ETR family is a part of the medium chain
dehydrogenase/reductase family, but lack the zinc
coordination sites characteristic of the 2-enoyl
thioester reductase (ETR) like proteins. ETR catalyzes
the NADPH-dependent dependent conversion of
trans-2-enoyl acyl carrier protein/coenzyme A (ACP/CoA)
to acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl
thioester reductase activity has been linked in Candida
tropicalis as essential in maintaining mitiochondrial
respiratory function. This ETR family is a part of the
medium chain dehydrogenase/reductase family, but lack
the zinc coordination sites characteristic of the
alcohol dehydrogenases in this family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. The N-terminal catalytic domain has a
distant homology to GroES. These proteins typically
form dimers (typically higher plants, mammals) or
tetramers (yeast, bacteria), and have 2 tightly bound
zinc atoms per subunit, a catalytic zinc at the active
site and a structural zinc in a lobe of the catalytic
domain. NAD(H) binding occurs in the cleft between the
catalytic and coenzyme-binding domains at the active
site, and coenzyme binding induces a conformational
closing of this cleft. Coenzyme binding typically
precedes and contributes to substrate binding. Candida
tropicalis enoyl thioester reductase (Etr1p) catalyzes
the NADPH-dependent reduction of trans-2-enoyl
thioesters in mitochondrial fatty acid synthesis. Etr1p
forms homodimers, with each subunit containing a
nucleotide-binding Rossmann fold domain and a catalytic
domain.
Length = 324
Score = 51.5 bits (124), Expect = 3e-07
Identities = 43/182 (23%), Positives = 71/182 (39%), Gaps = 43/182 (23%)
Query: 47 VKTPILKSKDVLVEMKAVSVNPIDVA-MLGGYGNVVLNSLRQLETCSVEPVLEFPLTLGR 105
+ P +VL++++A +NP D+ + G YG S + L P+ G
Sbjct: 23 PEVPEPGPGEVLIKVEAAPINPSDLGFLKGQYG-----STKAL-----------PVPPGF 66
Query: 106 DFCGKIVAKGP----------RVTDLNIDDVVYGVIQPHKQGSFSKLILADSALVHKKPS 155
+ G +VA G RV G++++ +AD+ P
Sbjct: 67 EGSGTVVAAGGGPLAQSLIGKRVA-----------FLAGSYGTYAEYAVADAQQCLPLPD 115
Query: 156 NISDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRVLVLGASGGVGTMAVQLLKAWDIE 215
+S E+ A LTA L+ G K V+ A+ +G M V+L KA I+
Sbjct: 116 GVSFEQGASSFVNPLTALGMLETAREEG-----AKAVVHTAAASALGRMLVRLCKADGIK 170
Query: 216 VV 217
V+
Sbjct: 171 VI 172
>gnl|CDD|176194 cd08232, idonate-5-DH, L-idonate 5-dehydrogenase. L-idonate
5-dehydrogenase (L-ido 5-DH ) catalyzes the conversion
of L-lodonate to 5-ketogluconate in the metabolism of
L-Idonate to 6-P-gluconate. In E. coli, this GntII
pathway is a subsidiary pathway to the canonical GntI
system, which also phosphorylates and transports
gluconate. L-ido 5-DH is found in an operon with a
regulator indR, transporter idnT, 5-keto-D-gluconate
5-reductase, and Gnt kinase. L-ido 5-DH is a
zinc-dependent alcohol dehydrogenase-like protein. The
alcohol dehydrogenase ADH-like family of proteins is a
diverse group of proteins related to the first
identified member, class I mammalian ADH. This group is
also called the medium chain dehydrogenases/reductase
family (MDR) which displays a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases(~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal GroES-like catalytic
domain. The MDR group contains a host of activities,
including the founding alcohol dehydrogenase (ADH),
quinone reductase, sorbitol dehydrogenase, formaldehyde
dehydrogenase, butanediol DH, ketose reductase, cinnamyl
reductase, and numerous others. The zinc-dependent
alcohol dehydrogenases (ADHs) catalyze the
NAD(P)(H)-dependent interconversion of alcohols to
aldehydes or ketones. ADH-like proteins typically form
dimers (typically higher plants, mammals) or tetramers
(yeast, bacteria), and generally have 2 tightly bound
zinc atoms per subunit. The active site zinc is
coordinated by a histidine, two cysteines, and a water
molecule. The second zinc seems to play a structural
role, affects subunit interactions, and is typically
coordinated by 4 cysteines.
Length = 339
Score = 51.5 bits (124), Expect = 3e-07
Identities = 60/267 (22%), Positives = 95/267 (35%), Gaps = 68/267 (25%)
Query: 37 GADELQFNDNVKTPILKSKDVLVEMKAVSVNPIDVAML--GGYGNVVLNSLRQLETCSVE 94
A +L+ + P +V V + A + D+ GG+G V L R+
Sbjct: 5 AAGDLRV-EERPAPEPGPGEVRVRVAAGGICGSDLHYYQHGGFGTVRL---RE------- 53
Query: 95 PVLEFPLTLGRDFCGKIVAKGPRVTDLNIDDVV--------------------------- 127
P+ LG + G + A GP VT L V
Sbjct: 54 -----PMVLGHEVSGVVEAVGPGVTGLAPGQRVAVNPSRPCGTCDYCRAGRPNLCLNMRF 108
Query: 128 YG--VIQPHKQGSFSKLILADSALVHKKPSNISDEEAA-----GVLYTGLTAWSALQITA 180
G + PH QG F + ++ D++ P +S AA V A A+
Sbjct: 109 LGSAMRFPHVQGGFREYLVVDASQCVPLPDGLSLRRAALAEPLAV------ALHAVNRAG 162
Query: 181 ALGLVYPRDKRVLVLGASGGVGTMAVQLLK---AWDIEVVTTCSGDAKDLVTSLNPNLVI 237
L KRVLV GA G +G + V + A +I V T + + ++ + +
Sbjct: 163 DL-----AGKRVLVTGA-GPIGALVVAAARRAGAAEI-VATDLADAPLAVARAMGADETV 215
Query: 238 DYNEPEAMHSIAGAGPYDVILDAAGIP 264
+ A G +DV+ +A+G P
Sbjct: 216 NLARDPLAAYAADKGDFDVVFEASGAP 242
>gnl|CDD|215721 pfam00107, ADH_zinc_N, Zinc-binding dehydrogenase.
Length = 131
Score = 48.5 bits (116), Expect = 3e-07
Identities = 26/84 (30%), Positives = 38/84 (45%), Gaps = 6/84 (7%)
Query: 200 GVGTMAVQLLKAW-DIEVVTTCSGDAK-DLVTSLNPNLVIDYNEP---EAMHSIAGAGPY 254
GVG AVQL KA V+ + K +L L + VI+Y + E + + G
Sbjct: 1 GVGLAAVQLAKALGAARVIAVDRSEEKLELAKELGADHVINYRDEDFVERVRELTGGRGV 60
Query: 255 DVILDAAGIPLDQINSYLPFLKTG 278
DV++D G P + L L+ G
Sbjct: 61 DVVIDCVGAP-ATLEQALELLRPG 83
>gnl|CDD|176204 cd08242, MDR_like, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group contains members identified as related to
zinc-dependent alcohol dehydrogenase and other members
of the MDR family, including threonine dehydrogenase.
The medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group includes
various activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has a
catalytic role, while structural zinc aids in stability.
ADH-like proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and generally have 2 tightly bound zinc atoms per
subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 319
Score = 51.1 bits (123), Expect = 4e-07
Identities = 54/235 (22%), Positives = 83/235 (35%), Gaps = 63/235 (26%)
Query: 57 VLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQLETCSVEPVLEFPLTLGRDFCGKIVAKGP 116
LV + + D+ + GY FP G +F G IV +GP
Sbjct: 27 ALVRVLLAGICNTDLEIYKGYYP-------------------FPGVPGHEFVG-IVEEGP 66
Query: 117 -------RVT-DLNIDD-----------------VVYGVIQPHKQGSFSKLILADSALVH 151
RV ++NI V G++ + G+F++ + +H
Sbjct: 67 EAELVGKRVVGEINIACGRCEYCRRGLYTHCPNRTVLGIVD--RDGAFAEYLTLPLENLH 124
Query: 152 KKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYPR-DKRVLVLGASGGVGTMAVQLLK 210
P + DE+A V L A AL+I V +V VLG G +G + Q+L
Sbjct: 125 VVPDLVPDEQA--VFAEPLAA--ALEILE---QVPITPGDKVAVLGD-GKLGLLIAQVLA 176
Query: 211 AWDIEVVTTCSGDAK-DLVTSLNPNLVIDYNEPEAMHSIAGAGPYDVILDAAGIP 264
+VV K L L V+ G +DV+++A G P
Sbjct: 177 LTGPDVVLVGRHSEKLALARRLGVETVLPDEAESEG------GGFDVVVEATGSP 225
>gnl|CDD|176190 cd05288, PGDH, Prostaglandin dehydrogenases. Prostaglandins and
related eicosanoids are metabolized by the oxidation of
the 15(S)-hydroxyl group of the NAD+-dependent (type I
15-PGDH) 15-prostaglandin dehydrogenase (15-PGDH)
followed by reduction by NADPH/NADH-dependent (type II
15-PGDH) delta-13 15-prostaglandin reductase (13-PGR) to
15-keto-13,14,-dihydroprostaglandins. 13-PGR is a
bifunctional enzyme, since it also has leukotriene B(4)
12-hydroxydehydrogenase activity. These 15-PGDH and
related enzymes are members of the medium chain
dehydrogenase/reductase family. The medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES.
Length = 329
Score = 50.2 bits (121), Expect = 6e-07
Identities = 55/241 (22%), Positives = 86/241 (35%), Gaps = 67/241 (27%)
Query: 168 TGLTAWSALQITAALGLVYPRDKRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAK-D 226
TGLTA+ L + V+V A+G VG++ Q+ K VV D K
Sbjct: 129 TGLTAYFGLTEIGKPK----PGETVVVSAAAGAVGSVVGQIAKLLGARVVGIAGSDEKCR 184
Query: 227 LVTSLNPNL----VIDYNEPEAMHSIAGAGP--YDV--------ILDAAGIPLDQINSYL 272
+ L I+Y P+ ++ A P DV ILDAA L +N
Sbjct: 185 WLVE---ELGFDAAINYKTPDLAEALKEAAPDGIDVYFDNVGGEILDAA---LTLLN--- 235
Query: 273 PFLKTGKFSKFVTLRSPFLKNTDSLGLV-------PGLVKNAFDLLKSNFESGELCKTNT 325
K + G + P KN +++ K T
Sbjct: 236 ------KGGRIAL-----------CGAISQYNATEPPGPKNLGNIIT---------KRLT 269
Query: 326 IRWGFFMP-----IPYAVKEINKFIERGQIKPVIDSKYNFCELPTAFEKVQQGHLRGKII 380
++ GF + P A+ E+ K++ G++K D P AF + G GK++
Sbjct: 270 MQ-GFIVSDYADRFPEALAELAKWLAEGKLKYREDVVEGLENAPEAFLGLFTGKNTGKLV 328
Query: 381 L 381
+
Sbjct: 329 V 329
>gnl|CDD|166155 PLN02514, PLN02514, cinnamyl-alcohol dehydrogenase.
Length = 357
Score = 49.4 bits (118), Expect = 1e-06
Identities = 55/212 (25%), Positives = 85/212 (40%), Gaps = 42/212 (19%)
Query: 99 FPLTLGRDFCGKIVAKGPRVTDLNIDDVV-YGVI-------QPHK--------------- 135
+P+ G + G++V G V+ + D+V GVI P K
Sbjct: 63 YPMVPGHEVVGEVVEVGSDVSKFTVGDIVGVGVIVGCCGECSPCKSDLEQYCNKRIWSYN 122
Query: 136 ---------QGSFSKLILADSALVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVY 186
QG F+ ++ D V K P ++ E+AA +L G+T +S L GL
Sbjct: 123 DVYTDGKPTQGGFASAMVVDQKFVVKIPEGMAPEQAAPLLCAGVTVYSPLS---HFGLKQ 179
Query: 187 PRDKRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAK--DLVTSLNPNLVIDYNEPEA 244
R +LG GGVG M V++ KA V S D K + + L + + ++
Sbjct: 180 S-GLRGGILGL-GGVGHMGVKIAKAMGHHVTVISSSDKKREEALEHLGADDYLVSSDAAE 237
Query: 245 MHSIAGAGPYDVILDAAGIPLDQINSYLPFLK 276
M A + D I+D + + YL LK
Sbjct: 238 MQEAADS--LDYIIDTVPV-FHPLEPYLSLLK 266
>gnl|CDD|176222 cd08261, Zn_ADH7, Alcohol dehydrogenases of the MDR family. This
group contains members identified as related to
zinc-dependent alcohol dehydrogenase and other members
of the MDR family. The medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group includes
various activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has a
catalytic role, while structural zinc aids in stability.
ADH-like proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and generally have 2 tightly bound zinc atoms per
subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 337
Score = 48.7 bits (117), Expect = 2e-06
Identities = 57/248 (22%), Positives = 92/248 (37%), Gaps = 56/248 (22%)
Query: 47 VKTPILKSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQLETCSVEPVLEFPLTLGRD 106
+ P+ + +VLV +K V + D+ + G R P +P LG +
Sbjct: 17 IPEPVPGAGEVLVRVKRVGICGSDLHIYHG---------RN-------PFASYPRILGHE 60
Query: 107 FCGKIVAKGPRVTDLNIDDVVY------------------------GVIQPHKQGSFSKL 142
G++V G V L + D V V+ H+ G F++
Sbjct: 61 LSGEVVEVGEGVAGLKVGDRVVVDPYISCGECYACRKGRPNCCENLQVLGVHRDGGFAEY 120
Query: 143 ILADSALVHKKPSNISDEEAAGV--LYTGLTAWSALQITAALGLVYPRDKRVLVLGASGG 200
I+ A P +S ++AA V L G A +TA VLV+GA G
Sbjct: 121 IVV-PADALLVPEGLSLDQAALVEPLAIGAHAVRRAGVTA--------GDTVLVVGA-GP 170
Query: 201 VGTMAVQLLKAWDIEVVTTCSGDAK-DLVTSLNPNLVI---DYNEPEAMHSIAGAGPYDV 256
+G +Q+ KA V+ D + + L + I D + + + DV
Sbjct: 171 IGLGVIQVAKARGARVIVVDIDDERLEFARELGADDTINVGDEDVAARLRELTDGEGADV 230
Query: 257 ILDAAGIP 264
++DA G P
Sbjct: 231 VIDATGNP 238
>gnl|CDD|176193 cd08231, MDR_TM0436_like, Hypothetical enzyme TM0436 resembles the
zinc-dependent alcohol dehydrogenases (ADH). This group
contains the hypothetical TM0436 alcohol dehydrogenase
from Thermotoga maritima, proteins annotated as
5-exo-alcohol dehydrogenase, and other members of the
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
MDR, which contains the zinc-dependent alcohol
dehydrogenase (ADH-Zn) and related proteins, is a
diverse group of proteins related to the first
identified member, class I mammalian ADH. MDRs display
a broad range of activities and are distinguished from
the smaller short chain dehydrogenases (~ 250 amino
acids vs. the ~ 350 amino acids of the MDR). The MDR
proteins have 2 domains: a C-terminal NAD(P)
binding-Rossmann fold domain of a beta-alpha form and an
N-terminal catalytic domain with distant homology to
GroES. The MDR group contains a host of activities,
including the founding alcohol dehydrogenase (ADH),
quinone reductase, sorbitol dehydrogenase, formaldehyde
dehydrogenase, butanediol DH, ketose reductase, cinnamyl
reductase, and numerous others. The zinc-dependent
alcohol dehydrogenases (ADHs) catalyze the
NAD(P)(H)-dependent interconversion of alcohols to
aldehydes or ketones. Active site zinc has a catalytic
role, while structural zinc aids in stability.
Length = 361
Score = 46.5 bits (111), Expect = 1e-05
Identities = 62/265 (23%), Positives = 90/265 (33%), Gaps = 69/265 (26%)
Query: 47 VKTPILKSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQLETCSVEPVLEFPLTLGRD 106
V P L+ VLV ++ V DV + G P + P+ LG +
Sbjct: 18 VPLPDLEPGAVLVRVRLAGVCGSDVHTVAG----------------RRPRVPLPIILGHE 61
Query: 107 FCGKIVAKGPRVTDLNI-------DDVVYGVI---------------------------- 131
G++VA G VT D V + V
Sbjct: 62 GVGRVVALGGGVTTDVAGEPLKVGDRVTWSVGAPCGRCYRCLVGDPTKCENRKKYGHEAS 121
Query: 132 --QPHKQGSFSKLI--LADSALVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYP 187
PH G +++ I +A+V + P N+ DE AA T +AL G V
Sbjct: 122 CDDPHLSGGYAEHIYLPPGTAIV-RVPDNVPDEVAAPANCALATVLAALD---RAGPV-G 176
Query: 188 RDKRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDA--KDLVTSLNPNLVIDYNEP--- 242
V+V GA G +G AV K V G +L + ID +E
Sbjct: 177 AGDTVVVQGA-GPLGLYAVAAAKLAGARRVIVIDGSPERLELAREFGADATIDIDELPDP 235
Query: 243 ---EAMHSIAGAGPYDVILDAAGIP 264
+ I G DV+++A+G P
Sbjct: 236 QRRAIVRDITGGRGADVVIEASGHP 260
>gnl|CDD|176223 cd08262, Zn_ADH8, Alcohol dehydrogenases of the MDR family. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 341
Score = 45.0 bits (107), Expect = 3e-05
Identities = 51/196 (26%), Positives = 81/196 (41%), Gaps = 36/196 (18%)
Query: 100 PLTLGRDFCGKIVAKGP----------RVTDL---NIDDVVYGVI--QPHKQGSFSKLIL 144
+ LG +FCG++V GP RVT L I P G +++ +L
Sbjct: 64 DIVLGHEFCGEVVDYGPGTERKLKVGTRVTSLPLLLCGQGASCGIGLSPEAPGGYAEYML 123
Query: 145 ADSALVHKKPSNISDEEAAGV--LYTGLTAWSALQITAALGLVYPRDKRVLVLGASGGVG 202
AL+ + P +S E+AA L GL A ++T + LV+G G +G
Sbjct: 124 LSEALLLRVPDGLSMEDAALTEPLAVGLHAVRRARLTP--------GEVALVIGC-GPIG 174
Query: 203 TMAVQLLKAWDIE--VVTTCSGDAKDLVTSLNPNLVIDYNE--PEAMHSI----AGAGPY 254
+ LKA + V + S + + L ++ ++V+D P A + AG
Sbjct: 175 LAVIAALKARGVGPIVASDFSPERRALALAMGADIVVDPAADSPFAAWAAELARAGGPKP 234
Query: 255 DVILDAAGIP--LDQI 268
VI + G P + QI
Sbjct: 235 AVIFECVGAPGLIQQI 250
>gnl|CDD|176249 cd08289, MDR_yhfp_like, Yhfp putative quinone oxidoreductases.
yhfp putative quinone oxidoreductases (QOR). QOR
catalyzes the conversion of a quinone + NAD(P)H to a
hydroquinone + NAD(P)+. Quinones are cyclic diones
derived from aromatic compounds. Membrane bound QOR
actin the respiratory chains of bacteria and
mitochondria, while soluble QOR acts to protect from
toxic quinones (e.g. DT-diaphorase) or as a soluble
eye-lens protein in some vertebrates (e.g.
zeta-crystalin). QOR reduces quinones through a
semi-quinone intermediate via a NAD(P)H-dependent single
electron transfer. QOR is a member of the medium chain
dehydrogenase/reductase family, but lacks the
zinc-binding sites of the prototypical alcohol
dehydrogenases of this group. NAD(P)(H)-dependent
oxidoreductases are the major enzymes in the
interconversion of alcohols and aldehydes, or ketones.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation. ADH
is a member of the medium chain alcohol dehydrogenase
family (MDR), which has a NAD(P)(H)-binding domain in a
Rossmann fold of a beta-alpha form. The NAD(H)-binding
region is comprised of 2 structurally similar halves,
each of which contacts a mononucleotide. A GxGxxG motif
after the first mononucleotide contact half allows the
close contact of the coenzyme with the ADH backbone.
The N-terminal catalytic domain has a distant homology
to GroES. These proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and have 2 tightly bound zinc atoms per
subunit, a catalytic zinc at the active site, and a
structural zinc in a lobe of the catalytic domain.
NAD(H) binding occurs in the cleft between the catalytic
and coenzyme-binding domains at the active site, and
coenzyme binding induces a conformational closing of
this cleft. Coenzyme binding typically precedes and
contributes to substrate binding. In human ADH
catalysis, the zinc ion helps coordinate the alcohol,
followed by deprotonation of a histidine, the ribose of
NAD, a serine, then the alcohol, which allows the
transfer of a hydride to NAD+, creating NADH and a
zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 326
Score = 44.6 bits (106), Expect = 4e-05
Identities = 49/149 (32%), Positives = 68/149 (45%), Gaps = 13/149 (8%)
Query: 96 VLEFPLTLGRDFCGKIV-AKGPRVTDLNIDDVV---YGVIQPHKQGSFSKLILADSALVH 151
V +P G D G +V + PR D+V+ Y + H G +S+ + V
Sbjct: 54 VKRYPFIPGIDLAGTVVESNDPRFKPG--DEVIVTSYDLGVSH-HGGYSEYARVPAEWVV 110
Query: 152 KKPSNISDEEAAGVLYTGLTAWSALQITAAL--GLVYPRDKRVLVLGASGGVGTMAVQLL 209
P ++ +EA + G TA AL I GL P VLV GA+GGVG++AV +L
Sbjct: 111 PLPKGLTLKEAMILGTAGFTA--ALSIHRLEENGLT-PEQGPVLVTGATGGVGSLAVSIL 167
Query: 210 KAWDIEVV-TTCSGDAKDLVTSLNPNLVI 237
EVV +T DA D + L VI
Sbjct: 168 AKLGYEVVASTGKADAADYLKKLGAKEVI 196
>gnl|CDD|166227 PLN02586, PLN02586, probable cinnamyl alcohol dehydrogenase.
Length = 360
Score = 44.1 bits (104), Expect = 7e-05
Identities = 42/156 (26%), Positives = 76/156 (48%), Gaps = 14/156 (8%)
Query: 137 GSFSKLILADSALVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRVLVLG 196
G +S +I+ D V + P N+ + A +L G+T +S ++ G+ P K + V G
Sbjct: 136 GGYSDMIVVDQHFVLRFPDNLPLDAGAPLLCAGITVYSPMKY---YGMTEP-GKHLGVAG 191
Query: 197 ASGGVGTMAVQLLKAW--DIEVVTTCSGDAKDLVTSLNPNLVIDYNEPEAMHSIAGAGPY 254
GG+G +AV++ KA+ + V+++ S + + L + + +PE M A G
Sbjct: 192 L-GGLGHVAVKIGKAFGLKVTVISSSSNKEDEAINRLGADSFLVSTDPEKMK--AAIGTM 248
Query: 255 DVILDAAGIPLDQINSYLPFLKTGKFS-KFVTLRSP 289
D I+D + +++ P L K + K +TL P
Sbjct: 249 DYIIDT----VSAVHALGPLLGLLKVNGKLITLGLP 280
>gnl|CDD|176230 cd08269, Zn_ADH9, Alcohol dehydrogenases of the MDR family. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability.
Length = 312
Score = 41.2 bits (97), Expect = 6e-04
Identities = 45/168 (26%), Positives = 67/168 (39%), Gaps = 21/168 (12%)
Query: 109 GKIVAKGPRVTDLNIDDVVYGVIQPHKQGSFSKLILADSALVHKKPSNISDEEAAG-VLY 167
G++VA GP V L + D V G+ G+F++ LAD+ PS + + G L
Sbjct: 61 GRVVALGPGVRGLAVGDRVAGLSG----GAFAEYDLADADHAVPLPSLLDGQAFPGEPLG 116
Query: 168 TGLTAWSALQITAALGLVYPRDKRVLVLGASGGVGTMAVQLLKAWDIEVVTTCS--GDAK 225
L + I A K V V+GA G +G + +QL A V
Sbjct: 117 CALNVFRRGWIRAG--------KTVAVIGA-GFIGLLFLQLAAAAGARRVIAIDRRPARL 167
Query: 226 DLVTSLNPNLVIDYNEP---EAMHSIAGAGPYDVILDAAG--IPLDQI 268
L L V+ + E + + G DV+++A G PLD
Sbjct: 168 ALARELGATEVVTDDSEAIVERVRELTGGAGADVVIEAVGHQWPLDLA 215
>gnl|CDD|176252 cd08292, ETR_like_2, 2-enoyl thioester reductase (ETR) like
proteins, child 2. 2-enoyl thioester reductase (ETR)
like proteins. ETR catalyzes the NADPH-dependent
conversion of trans-2-enoyl acyl carrier
protein/coenzyme A (ACP/CoA) to acyl-(ACP/CoA) in fatty
acid synthesis. 2-enoyl thioester reductase activity has
been linked in Candida tropicalis as essential in
maintaining mitiochondrial respiratory function. This
ETR family is a part of the medium chain
dehydrogenase/reductase family, but lack the zinc
coordination sites characteristic of the 2-enoyl
thioester reductase (ETR) like proteins. ETR catalyzes
the NADPH-dependent dependent conversion of
trans-2-enoyl acyl carrier protein/coenzyme A (ACP/CoA)
to acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl
thioester reductase activity has been linked in Candida
tropicalis as essential in maintaining mitiochondrial
respiratory function. This ETR family is a part of the
medium chain dehydrogenase/reductase family, but lack
the zinc coordination sites characteristic of the
alcohol dehydrogenases in this family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. The N-terminal catalytic domain has a
distant homology to GroES. These proteins typically
form dimers (typically higher plants, mammals) or
tetramers (yeast, bacteria), and have 2 tightly bound
zinc atoms per subunit, a catalytic zinc at the active
site, and a structural zinc in a lobe of the catalytic
domain. NAD(H) binding occurs in the cleft between the
catalytic and coenzyme-binding domains, at the active
site, and coenzyme binding induces a conformational
closing of this cleft. Coenzyme binding typically
precedes and contributes to substrate binding. Candida
tropicalis enoyl thioester reductase (Etr1p) catalyzes
the NADPH-dependent reduction of trans-2-enoyl
thioesters in mitochondrial fatty acid synthesis. Etr1p
forms homodimers, with each subunit containing a
nucleotide-binding Rossmann fold domain and a catalytic
domain.
Length = 324
Score = 40.8 bits (96), Expect = 6e-04
Identities = 59/226 (26%), Positives = 90/226 (39%), Gaps = 37/226 (16%)
Query: 46 NVKTPILKSKDVLVEMKAVSVNPIDV-AMLGGYGNVVLNSLRQLETCSVEPVLEFPLTLG 104
V P + +VLV ++ D+ + G YG +P L P G
Sbjct: 20 EVPKPTPGAGEVLVRTTLSPIHNHDLWTIRGTYG--------------YKPEL--PAIGG 63
Query: 105 RDFCGKIVAKGPRVTDLNIDD--VVYGVIQPHKQGSFSKLILADSALVHKKPSNISDEEA 162
+ G + A G V L + V V G++++ +A + + P ISDE A
Sbjct: 64 SEAVGVVDAVGEGVKGLQVGQRVAVAPV-----HGTWAEYFVAPADGLVPLPDGISDEVA 118
Query: 163 AGVLYTGLTAWSALQITAALGLVYPRDKRVLVLGASGG-VGTMAVQLLKAWDIEVVTTCS 221
A ++ L+A L LG V P L+ A+GG VG + L A I V+
Sbjct: 119 AQLIAMPLSALMLLD---FLG-VKPGQ--WLIQNAAGGAVGKLVAMLAAARGINVINLVR 172
Query: 222 GDA--KDLVTSLNPNLVIDYNEP---EAMHSIAGAGPYDVILDAAG 262
DA +L +L V+ +P + + AG P V LD+ G
Sbjct: 173 RDAGVAEL-RALGIGPVVSTEQPGWQDKVREAAGGAPISVALDSVG 217
>gnl|CDD|176244 cd08284, FDH_like_2, Glutathione-dependent formaldehyde
dehydrogenase related proteins, child 2.
Glutathione-dependent formaldehyde dehydrogenases (FDHs)
are members of the zinc-dependent/medium chain alcohol
dehydrogenase family. Formaldehyde dehydrogenase (FDH)
is a member of the zinc-dependent/medium chain alcohol
dehydrogenase family. FDH converts formaldehyde and NAD
to formate and NADH. The initial step in this process
the spontaneous formation of a
S-(hydroxymethyl)glutathione adduct from formaldehyde
and glutathione, followed by FDH-mediated oxidation (and
detoxification) of the adduct to S-formylglutathione.
These tetrameric FDHs have a catalytic zinc that resides
between the catalytic and NAD(H)binding domains and a
structural zinc in a lobe of the catalytic domain. The
medium chain alcohol dehydrogenase family (MDR) has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The N-terminal region typically has an
all-beta catalytic domain. These proteins typically form
dimers (typically higher plants, mammals) or tetramers
(yeast, bacteria), and have 2 tightly bound zinc atoms
per subunit.
Length = 344
Score = 40.7 bits (96), Expect = 7e-04
Identities = 37/145 (25%), Positives = 52/145 (35%), Gaps = 44/145 (30%)
Query: 102 TLGRDFCGKIVAKGPRVTDLNIDDVVYG--VIQ--------------------------P 133
LG +F G++V GP V L + D V I P
Sbjct: 56 VLGHEFVGEVVEVGPEVRTLKVGDRVVSPFTIACGECFYCRRGQSGRCAKGGLFGYAGSP 115
Query: 134 HKQGSFSKLI---LADSALVHKKPSNISDEEA---AGVLYTGLTAWSALQITAALGLVYP 187
+ G+ ++ + AD L+ K P +SDE A +L TG + A V P
Sbjct: 116 NLDGAQAEYVRVPFADGTLL-KLPDGLSDEAALLLGDILPTG---YFG----AKRAQVRP 167
Query: 188 RDKRVLVLGASGGVGTMAVQLLKAW 212
V V+G G VG AV +
Sbjct: 168 -GDTVAVIGC-GPVGLCAVLSAQVL 190
>gnl|CDD|187575 cd05265, SDR_a1, atypical (a) SDRs, subgroup 1. Atypical SDRs in
this subgroup are poorly defined and have been
identified putatively as isoflavones reductase, sugar
dehydratase, mRNA binding protein etc. Atypical SDRs are
distinct from classical SDRs. Members of this subgroup
retain the canonical active site triad (though not the
upstream Asn found in most SDRs) but have an unusual
putative glycine-rich NAD(P)-binding motif, GGXXXXG, in
the usual location. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta reductase
(BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 250
Score = 39.6 bits (93), Expect = 0.001
Identities = 18/73 (24%), Positives = 35/73 (47%), Gaps = 6/73 (8%)
Query: 190 KRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAKDLVTSLNP---NLVIDYNEPEAMH 246
++L++G + +G V+ L A +V G K L ++V D N+ +A+
Sbjct: 1 MKILIIGGTRFIGKALVEELLAAGHDVTVFNRGRTKP---DLPEGVEHIVGDRNDRDALE 57
Query: 247 SIAGAGPYDVILD 259
+ G +DV++D
Sbjct: 58 ELLGGEDFDVVVD 70
>gnl|CDD|177834 PLN02178, PLN02178, cinnamyl-alcohol dehydrogenase.
Length = 375
Score = 38.9 bits (90), Expect = 0.003
Identities = 40/157 (25%), Positives = 70/157 (44%), Gaps = 13/157 (8%)
Query: 136 QGSFSKLILADSALVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRVLVL 195
QG +S +I+ D V P + + A +L G+T +S ++ G+ KR+ V
Sbjct: 129 QGGYSDVIVVDHRFVLSIPDGLPSDSGAPLLCAGITVYSPMKY---YGMTKESGKRLGVN 185
Query: 196 GASGGVGTMAVQLLKAWD--IEVVTTCSGDAKDLVTSLNPNLVIDYNEPEAMHSIAGAGP 253
G GG+G +AV++ KA+ + V++ S ++ + L + + + + M G
Sbjct: 186 GL-GGLGHIAVKIGKAFGLRVTVISRSSEKEREAIDRLGADSFLVTTDSQKMKE--AVGT 242
Query: 254 YDVILDAAGIPLDQINSYLPFLKTGKFS-KFVTLRSP 289
D I+D ++ LP K S K V L P
Sbjct: 243 MDFIIDTVSAE----HALLPLFSLLKVSGKLVALGLP 275
>gnl|CDD|182371 PRK10309, PRK10309, galactitol-1-phosphate dehydrogenase;
Provisional.
Length = 347
Score = 38.3 bits (89), Expect = 0.006
Identities = 45/197 (22%), Positives = 82/197 (41%), Gaps = 40/197 (20%)
Query: 99 FPLTLGRDFCGKIVAKGPRVTDLNIDDVV------------------------YGVIQPH 134
+P+TLG +F G + A G V DL+ D V Y I
Sbjct: 53 YPITLGHEFSGYVEAVGSGVDDLHPGDAVACVPLLPCFTCPECLRGFYSLCAKYDFIGSR 112
Query: 135 KQGSFSKLILADSALVHKKPSNISDEEAAGV--LYTGLTAWSALQITAALGLVYPRDKRV 192
+ G ++ I+ + P+++ E+ A + + GL A+ Q K V
Sbjct: 113 RDGGNAEYIVVKRKNLFALPTDMPIEDGAFIEPITVGLHAFHLAQGC--------EGKNV 164
Query: 193 LVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAKDLVTSLNPNLVIDYNEPE----AMHSI 248
+++GA G +G +A+Q A + VT +++ L + + + +N E + S+
Sbjct: 165 IIIGA-GTIGLLAIQCAVALGAKSVTAIDINSEKLALAKSLGAMQTFNSREMSAPQIQSV 223
Query: 249 AGAGPYD-VILDAAGIP 264
+D +IL+ AG+P
Sbjct: 224 LRELRFDQLILETAGVP 240
>gnl|CDD|176243 cd08283, FDH_like_1, Glutathione-dependent formaldehyde
dehydrogenase related proteins, child 1. Members
identified as glutathione-dependent formaldehyde
dehydrogenase(FDH), a member of the
zinc-dependent/medium chain alcohol dehydrogenase
family. FDH converts formaldehyde and NAD(P) to formate
and NAD(P)H. The initial step in this process the
spontaneous formation of a S-(hydroxymethyl)glutathione
adduct from formaldehyde and glutathione, followed by
FDH-mediated oxidation (and detoxification) of the
adduct to S-formylglutathione. MDH family uses NAD(H)
as a cofactor in the interconversion of alcohols and
aldehydes, or ketones. Like many zinc-dependent alcohol
dehydrogenases (ADH) of the medium chain alcohol
dehydrogenase/reductase family (MDR), these FDHs form
dimers, with 4 zinc ions per dimer. The medium chain
alcohol dehydrogenase family (MDR) has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The N-terminal region typically has an
all-beta catalytic domain. These proteins typically form
dimers (typically higher plants, mammals) or tetramers
(yeast, bacteria), and have 2 tightly bound zinc atoms
per subunit.
Length = 386
Score = 37.9 bits (89), Expect = 0.007
Identities = 62/274 (22%), Positives = 94/274 (34%), Gaps = 81/274 (29%)
Query: 45 DNVKTP-ILKSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQLETCSVEPVLEFPLTL 103
+ V P I D +V + A ++ D+ + GY P ++ L
Sbjct: 15 EEVPDPKIEDPTDAIVRVTATAICGSDLHLYHGYI----------------PGMKKGDIL 58
Query: 104 GRDFCGKIVAKGPRVTDLNIDD--VVYGVI-------------------QPHK------- 135
G +F G + GP V +L + D VV I P
Sbjct: 59 GHEFMGVVEEVGPEVRNLKVGDRVVVPFTIACGECFYCKRGLYSQCDNTNPSAEMAKLYG 118
Query: 136 -------------------QGSFSKLILADSALVHKKPSNISDEEAAGVLYTGLTAWSAL 176
Q + ++ AD K P ++SDE+A + T + A
Sbjct: 119 HAGAGIFGYSHLTGGYAGGQAEYVRVPFADVGPF-KIPDDLSDEKALFLSDILPTGYHA- 176
Query: 177 QITAALGLVYPRDKRVLVLGASGGVGTMAVQ---LLKAWDIEVVTTCSGDAKDLVTSLNP 233
A L V P D V V G G VG A + LL A + + + ++ S
Sbjct: 177 ---AELAEVKPGDT-VAVWGC-GPVGLFAARSAKLLGAERVIAIDRV-PERLEMARSHLG 230
Query: 234 NLVIDYNE----PEAMHSI-AGAGPYDVILDAAG 262
I++ E EA+ + G GP DV +DA G
Sbjct: 231 AETINFEEVDDVVEALRELTGGRGP-DVCIDAVG 263
>gnl|CDD|176184 cd05281, TDH, Threonine dehydrogenase. L-threonine dehydrogenase
(TDH) catalyzes the zinc-dependent formation of
2-amino-3-ketobutyrate from L-threonine via NAD(H)-
dependent oxidation. THD is a member of the
zinc-requiring, medium chain NAD(H)-dependent alcohol
dehydrogenase family (MDR). MDRs have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes, or ketones. The N-terminal region typically
has an all-beta catalytic domain. These proteins
typically form dimers (typically higher plants, mammals)
or tetramers (yeast, bacteria) and have 2 tightly bound
zinc atoms per subunit. Sorbitol and aldose reductase
are NAD(+) binding proteins of the polyol pathway, which
interconverts glucose and fructose.
Length = 341
Score = 37.2 bits (87), Expect = 0.010
Identities = 56/269 (20%), Positives = 93/269 (34%), Gaps = 95/269 (35%)
Query: 47 VKTPILKSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQLETCSVEPVLEFPLTLGRD 106
V P +VL+++ A S+ DV + Y + Q ++P PL G +
Sbjct: 18 VPVPKPGPGEVLIKVLAASICGTDVHI---Y---EWDEWAQ---SRIKP----PLIFGHE 64
Query: 107 FCGKIVAKGPRVTDLNIDDVV---------------------------YGVIQPHKQGSF 139
F G++V G VT + + D V GV G F
Sbjct: 65 FAGEVVEVGEGVTRVKVGDYVSAETHIVCGKCYQCRTGNYHVCQNTKILGV---DTDGCF 121
Query: 140 SKLILADSALVHKKPSNISDEEAA----------GVLYTGLTAWSALQITAALGLVYPRD 189
++ ++ + K +I E A+ VL ++
Sbjct: 122 AEYVVVPEENLWKNDKDIPPEIASIQEPLGNAVHTVLAGDVSG----------------- 164
Query: 190 KRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAKDLVTSLNP-----------NLVID 238
K VL+ G G +G MA+ + KA +G + + + NP ++VI+
Sbjct: 165 KSVLITGC-GPIGLMAIAVAKA---------AGASLVIASDPNPYRLELAKKMGADVVIN 214
Query: 239 YNE---PEAMHSIAGAGPYDVILDAAGIP 264
E E G G DV+L+ +G P
Sbjct: 215 PREEDVVEVKSVTDGTGV-DVVLEMSGNP 242
>gnl|CDD|223774 COG0702, COG0702, Predicted nucleoside-diphosphate-sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 275
Score = 36.8 bits (85), Expect = 0.014
Identities = 16/64 (25%), Positives = 27/64 (42%), Gaps = 2/64 (3%)
Query: 190 KRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAKDLVTSLNPNLVI-DYNEPEAMHSI 248
++LV GA+G VG V+ L A EV + +V+ D +P+++
Sbjct: 1 MKILVTGATGFVGGAVVRELLARGHEVRAAVRNPEAAAALAGGVEVVLGDLRDPKSLV-A 59
Query: 249 AGAG 252
G
Sbjct: 60 GAKG 63
>gnl|CDD|180817 PRK07060, PRK07060, short chain dehydrogenase; Provisional.
Length = 245
Score = 36.6 bits (85), Expect = 0.014
Identities = 24/79 (30%), Positives = 35/79 (44%), Gaps = 6/79 (7%)
Query: 190 KRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAKDLVTSLNPN----LVIDYNEPEAM 245
K VLV GAS G+G L VV + +A L L +D + A+
Sbjct: 10 KSVLVTGASSGIGRACAVALAQRGARVVAA-ARNAAALDRLAGETGCEPLRLDVGDDAAI 68
Query: 246 HSI-AGAGPYDVILDAAGI 263
+ A AG +D +++ AGI
Sbjct: 69 RAALAAAGAFDGLVNCAGI 87
>gnl|CDD|176181 cd05278, FDH_like, Formaldehyde dehydrogenases. Formaldehyde
dehydrogenase (FDH) is a member of the
zinc-dependent/medium chain alcohol dehydrogenase
family. Formaldehyde dehydrogenase (aka ADH3) may be
the ancestral form of alcohol dehydrogenase, which
evolved to detoxify formaldehyde. This CD contains
glutathione dependant FDH, glutathione independent FDH,
and related alcohol dehydrogenases. FDH converts
formaldehyde and NAD(P) to formate and NAD(P)H. The
initial step in this process the spontaneous formation
of a S-(hydroxymethyl)glutathione adduct from
formaldehyde and glutathione, followed by FDH-mediated
oxidation (and detoxification) of the adduct to
S-formylglutathione. Unlike typical FDH, Pseudomonas
putida aldehyde-dismutating FDH (PFDH) is
glutathione-independent. The medium chain alcohol
dehydrogenase family (MDR) have a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit.
Length = 347
Score = 36.5 bits (85), Expect = 0.020
Identities = 67/323 (20%), Positives = 108/323 (33%), Gaps = 80/323 (24%)
Query: 95 PVLEFPLTLGRDFCGKIVAKGPRVTDLNIDDVV---------------YGVIQPH----- 134
P + + LG +F G++V G V L D V G H
Sbjct: 50 PGAKHGMILGHEFVGEVVEVGSDVKRLKPGDRVSVPCITFCGRCRFCRRGYHA-HCENGL 108
Query: 135 --------KQGSFSKLIL---ADSALVHKKPSNISDEEA---AGVLYTGLTAWSALQITA 180
G ++ + AD L K P + DE+A + +L TG A
Sbjct: 109 WGWKLGNRIDGGQAEYVRVPYADMNLA-KIPDGLPDEDALMLSDILPTGFHG-------A 160
Query: 181 ALGLVYPRDKRVLVLGASGGVGTMAV---QLLKAWDIEVVTTCSGDAKDLVTSLNPNLVI 237
L + P V V+GA G VG AV +LL A I V + + + DL +I
Sbjct: 161 ELAGIKPGST-VAVIGA-GPVGLCAVAGARLLGAARIIAVDS-NPERLDLAKEAGATDII 217
Query: 238 DYNEPEAMHSIAG--AGP-YDVILDAAGIP--LDQINSYLPFLKTGKFSKFVTLRSPFLK 292
+ + + I G D +++A G +Q +K + + + K
Sbjct: 218 NPKNGDIVEQILELTGGRGVDCVIEAVGFEETFEQA------VKVVRPGGTIANVGVYGK 271
Query: 293 NTDSLGLVPGLVKNAFDLLKSNFESGELCKTNTIRWGFFMPIPYAVKEINKFIERGQIKP 352
L KN T + G P+ + E+ IE G+I P
Sbjct: 272 PDPLPLLGEWFGKNL-----------------TFKTGLV-PVRARMPELLDLIEEGKIDP 313
Query: 353 --VIDSKYNFCELPTAFEKVQQG 373
+I ++ ++ A+
Sbjct: 314 SKLITHRFPLDDILKAYRLFDNK 336
>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 314
Score = 36.1 bits (83), Expect = 0.025
Identities = 14/75 (18%), Positives = 24/75 (32%)
Query: 190 KRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAKDLVTSLNPNLVIDYNEPEAMHSIA 249
R+LV G +G +G+ V+ L A +V V+ +
Sbjct: 1 MRILVTGGAGFIGSHLVERLLAAGHDVRGLDRLRDGLDPLLSGVEFVVLDLTDRDLVDEL 60
Query: 250 GAGPYDVILDAAGIP 264
G D ++ A
Sbjct: 61 AKGVPDAVIHLAAQS 75
>gnl|CDD|187564 cd05254, dTDP_HR_like_SDR_e, dTDP-6-deoxy-L-lyxo-4-hexulose
reductase and related proteins, extended (e) SDRs.
dTDP-6-deoxy-L-lyxo-4-hexulose reductase, an extended
SDR, synthesizes dTDP-L-rhamnose from
alpha-D-glucose-1-phosphate, providing the precursor of
L-rhamnose, an essential cell wall component of many
pathogenic bacteria. This subgroup has the
characteristic active site tetrad and NADP-binding
motif. This subgroup also contains human MAT2B, the
regulatory subunit of methionine adenosyltransferase
(MAT); MAT catalyzes S-adenosylmethionine synthesis. The
human gene encoding MAT2B encodes two major splicing
variants which are induced in human cell liver cancer
and regulate HuR, an mRNA-binding protein which
stabilizes the mRNA of several cyclins, to affect cell
proliferation. Both MAT2B variants include this extended
SDR domain. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 280
Score = 35.7 bits (83), Expect = 0.026
Identities = 20/73 (27%), Positives = 33/73 (45%), Gaps = 8/73 (10%)
Query: 191 RVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAKDLVTSLNPNLVIDYNEPEAMHSIAG 250
++L+ GA+G +G V+LLK EV+ T A +D +P+A+
Sbjct: 1 KILITGATGMLGRALVRLLKERGYEVIGTGRSRASL--------FKLDLTDPDAVEEAIR 52
Query: 251 AGPYDVILDAAGI 263
DVI++ A
Sbjct: 53 DYKPDVIINCAAY 65
>gnl|CDD|180054 PRK05396, tdh, L-threonine 3-dehydrogenase; Validated.
Length = 341
Score = 36.0 bits (84), Expect = 0.029
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 100 PLTLGRDFCGKIVAKGPRVTDLNIDDVVYG 129
P+ +G +F G++V G VT + D V G
Sbjct: 58 PMVVGHEFVGEVVEVGSEVTGFKVGDRVSG 87
>gnl|CDD|187609 cd05351, XR_like_SDR_c, xylulose reductase-like, classical (c)
SDRs. Members of this subgroup include proteins
identified as L-xylulose reductase (XR) and carbonyl
reductase; they are members of the SDR family. XR,
catalyzes the NADP-dependent reduction of L-xyulose and
other sugars. Tetrameric mouse carbonyl reductase is
involved in the metabolism of biogenic and xenobiotic
carbonyl compounds. This subgroup also includes
tetrameric chicken liver D-erythrulose reductase, which
catalyzes the reduction of D-erythrulose to D-threitol.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRS are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes have a 3-glycine N-terminal NAD(P)(H)-binding
pattern (typically, TGxxxGxG in classical SDRs and
TGxxGxxG in extended SDRs), while substrate binding is
in the C-terminal region. A critical catalytic Tyr
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering), is often found in a
conserved YXXXK pattern. In addition to the Tyr and Lys,
there is often an upstream Ser (Ser-138, 15-PGDH
numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser).
Length = 244
Score = 35.5 bits (82), Expect = 0.033
Identities = 30/116 (25%), Positives = 50/116 (43%), Gaps = 20/116 (17%)
Query: 188 RDKRVLVLGASGGVGTMAVQLLKAWDIEV--VTTCSGDAKDLV---TSLNPNLVIDYNEP 242
KR LV GA G+G V+ L V V+ D LV + P + +D ++
Sbjct: 6 AGKRALVTGAGKGIGRATVKALAKAGARVVAVSRTQADLDSLVRECPGIEP-VCVDLSDW 64
Query: 243 EAMH-SIAGAGPYDVILDAAGIPLDQINSYLPFLKTGK------FSKFVTLRSPFL 291
+A ++ GP D++++ A + + Q PFL+ K F V +R+
Sbjct: 65 DATEEALGSVGPVDLLVNNAAVAILQ-----PFLEVTKEAFDRSFD--VNVRAVIH 113
>gnl|CDD|176201 cd08239, THR_DH_like, L-threonine dehydrogenase (TDH)-like.
MDR/AHD-like proteins, including a protein annotated as
a threonine dehydrogenase. L-threonine dehydrogenase
(TDH) catalyzes the zinc-dependent formation of
2-amino-3-ketobutyrate from L-threonine via
NAD(H)-dependent oxidation. The zinc-dependent alcohol
dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent
interconversion of alcohols to aldehydes or ketones.
Zinc-dependent ADHs are medium chain
dehydrogenase/reductase type proteins (MDRs) and have a
NAD(P)(H)-binding domain in a Rossmann fold of an
beta-alpha form. The N-terminal region typically has an
all-beta catalytic domain. In addition to alcohol
dehydrogenases, this group includes quinone reductase,
sorbitol dehydrogenase, formaldehyde dehydrogenase,
butanediol DH, ketose reductase, cinnamyl reductase, and
numerous others. These proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 339
Score = 35.4 bits (82), Expect = 0.040
Identities = 44/191 (23%), Positives = 74/191 (38%), Gaps = 41/191 (21%)
Query: 104 GRDFCGKIVAKGPRVTDLNIDDVV----------------------------YGVIQPHK 135
G + G +VA GP VT + D V YG +
Sbjct: 59 GHEPAGVVVAVGPGVTHFRVGDRVMVYHYVGCGACRNCRRGWMQLCTSKRAAYGWNRD-- 116
Query: 136 QGSFSKLILADSALVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRVLVL 195
G ++ +L + P ++S + A +L TA+ AL+ G VLV+
Sbjct: 117 -GGHAEYMLVPEKTLIPLPDDLSFADGALLLCGIGTAYHALRRVGVSG-----RDTVLVV 170
Query: 196 GASGGVGTMAVQLLKAWDIEVV--TTCSGDAKDLVTSLNPNLVID--YNEPEAMHSIAGA 251
GA G VG A+ L +A E V S + +L +L + VI+ ++ + + +
Sbjct: 171 GA-GPVGLGALMLARALGAEDVIGVDPSPERLELAKALGADFVINSGQDDVQEIRELTSG 229
Query: 252 GPYDVILDAAG 262
DV ++ +G
Sbjct: 230 AGADVAIECSG 240
>gnl|CDD|181298 PRK08219, PRK08219, short chain dehydrogenase; Provisional.
Length = 227
Score = 34.9 bits (81), Expect = 0.040
Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 6/77 (7%)
Query: 192 VLVLGASGGVGT-MAVQLLKAWDIEVVTTCSGDAKDLVTSLNPN---LVIDYNEPEAMHS 247
L+ GAS G+G +A +L + + + +L L P +D +PEA+ +
Sbjct: 6 ALITGASRGIGAAIARELAPTHTLLLGGRPAERLDELAAEL-PGATPFPVDLTDPEAIAA 64
Query: 248 -IAGAGPYDVILDAAGI 263
+ G DV++ AG+
Sbjct: 65 AVEQLGRLDVLVHNAGV 81
>gnl|CDD|130269 TIGR01202, bchC, 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide
A dehydrogenase. [Biosynthesis of cofactors, prosthetic
groups, and carriers, Chlorophyll and
bacteriochlorphyll].
Length = 308
Score = 34.4 bits (79), Expect = 0.068
Identities = 41/193 (21%), Positives = 66/193 (34%), Gaps = 31/193 (16%)
Query: 95 PVLEFPLTLGRDFCGKIVAKGPRVTDLNIDDVV------YGVIQPHKQGSFSKLILADSA 148
P + +PL G + G++V GP D V Y ++ G+ +L+ S
Sbjct: 54 PGMGYPLVPGYESVGRVVEAGPDTGFRPGDRVFVPGSNCYEDVRGLFGGASKRLVTPASR 113
Query: 149 LVHKKPSNISDEEAAGVLYTGLTAWSALQITA--ALGLVYPRDKRVLVLGASGGVGTMAV 206
+ P + A + AL TA A+ + L++G G +G +
Sbjct: 114 VCRLDP--ALGPQGALL---------ALAATARHAVAGAEVKVLPDLIVG-HGTLGRLLA 161
Query: 207 QLLKAWDIEVVTTCSGDAKDLVTSLNPNLVIDYNEPEAMHSIAGAG-PYDVILDAAGIPL 265
+L KA V NP E + Y I DA+G P
Sbjct: 162 RLTKAAGGSPPA---------VWETNPRRRDGATGYEVLDPEKDPRRDYRAIYDASGDP- 211
Query: 266 DQINSYLPFLKTG 278
I++ + L G
Sbjct: 212 SLIDTLVRRLAKG 224
>gnl|CDD|235703 PRK06125, PRK06125, short chain dehydrogenase; Provisional.
Length = 259
Score = 34.2 bits (79), Expect = 0.069
Identities = 26/95 (27%), Positives = 41/95 (43%), Gaps = 14/95 (14%)
Query: 188 RDKRVLVLGASGGVGTMAVQLLKAWDIEVVTTC-SGD----AKDLVTSLNP----NLVID 238
KRVL+ GAS G+G A + A + D + + + +D
Sbjct: 6 AGKRVLITGASKGIGAAAAEAFAAEGCHLHLVARDADALEALAADLRAAHGVDVAVHALD 65
Query: 239 YNEPEAMHSIAG-AGPYDVILDAAG-IP---LDQI 268
+ PEA +A AG D++++ AG IP LD +
Sbjct: 66 LSSPEAREQLAAEAGDIDILVNNAGAIPGGGLDDV 100
>gnl|CDD|181288 PRK08204, PRK08204, hypothetical protein; Provisional.
Length = 449
Score = 34.2 bits (79), Expect = 0.11
Identities = 27/95 (28%), Positives = 42/95 (44%), Gaps = 17/95 (17%)
Query: 129 GVIQPHKQGSFSKLILADSALVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYPR 188
GV Q H G L+ D LVH +++SD+E + +G + +I +G YP
Sbjct: 232 GVEQLHDAG----LLGPDLNLVH--GNDLSDDELKLLADSGGSFSVTPEIEMMMGHGYPV 285
Query: 189 DKRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGD 223
R+L G +G ++VVT+ GD
Sbjct: 286 TGRLLAHGVRPSLG-----------VDVVTSTGGD 309
>gnl|CDD|132492 TIGR03451, mycoS_dep_FDH, S-(hydroxymethyl)mycothiol dehydrogenase.
Members of this protein family are mycothiol-dependent
formaldehyde dehydrogenase (EC 1.2.1.66). This protein
is found, so far, only in the Actinobacteria
(Mycobacterium sp., Streptomyces sp., Corynebacterium
sp., and related species), where mycothione replaces
glutathione [Cellular processes, Detoxification].
Length = 358
Score = 34.0 bits (78), Expect = 0.12
Identities = 56/212 (26%), Positives = 78/212 (36%), Gaps = 53/212 (25%)
Query: 98 EFPLTLGRDFCGKIVAKGPRVTDLNIDDVVY-------GVIQPHKQG----------SFS 140
EFP LG + G + A G VTD+ D V G + K+G +
Sbjct: 53 EFPFLLGHEAAGVVEAVGEGVTDVAPGDYVVLNWRAVCGQCRACKRGRPWYCFDTHNATQ 112
Query: 141 KLILADS---------------ALVHK----KPSNISDEEAAGVLYTGLTA-WSALQITA 180
K+ L D LVH K +D AAG+L G+ A A T
Sbjct: 113 KMTLTDGTELSPALGIGAFAEKTLVHAGQCTKVDPAADPAAAGLLGCGVMAGLGAAVNTG 172
Query: 181 ALGLVYPRDKRVLVLGASGGVGTMAV---QLLKAWDIEVVTTCSGDAKDL--VTSLNPNL 235
+ R V V+G GGVG A+ L A I V D + L
Sbjct: 173 GVK----RGDSVAVIGC-GGVGDAAIAGAALAGASKIIAVDI---DDRKLEWAREFGATH 224
Query: 236 VIDYNEP---EAMHSIAGAGPYDVILDAAGIP 264
++ + EA+ ++ G DV++DA G P
Sbjct: 225 TVNSSGTDPVEAIRALTGGFGADVVIDAVGRP 256
>gnl|CDD|216461 pfam01370, Epimerase, NAD dependent epimerase/dehydratase family.
This family of proteins utilise NAD as a cofactor. The
proteins in this family use nucleotide-sugar substrates
for a variety of chemical reactions.
Length = 233
Score = 33.4 bits (77), Expect = 0.14
Identities = 17/83 (20%), Positives = 32/83 (38%), Gaps = 1/83 (1%)
Query: 192 VLVLGASGGVGTMAVQLLKAWDIEVVT-TCSGDAKDLVTSLNPNLVIDYNEPEAMHSIAG 250
+LV G +G +G+ V+ L EV+ ++ L T D +P+A+ +
Sbjct: 1 ILVTGGTGFIGSHLVRRLLQEGYEVIVLGRRRRSESLNTGRIRFHEGDLTDPDALERLLA 60
Query: 251 AGPYDVILDAAGIPLDQINSYLP 273
D ++ A + P
Sbjct: 61 EVQPDAVIHLAAQSGVGASFEDP 83
>gnl|CDD|212497 cd11731, Lin1944_like_SDR_c, Lin1944 and related proteins,
classical (c) SDRs. Lin1944 protein from Listeria
Innocua is a classical SDR, it contains a glycine-rich
motif similar to the canonical motif of the SDR
NAD(P)-binding site. However, the typical SDR active
site residues are absent in this subgroup of proteins of
undetermined function. SDRs are a functionally diverse
family of oxidoreductases that have a single domain with
a structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human prostaglandin dehydrogenase
(PGDH) numbering). In addition to the Tyr and Lys, there
is often an upstream Ser (Ser-138, PGDH numbering)
and/or an Asn (Asn-107, PGDH numbering) contributing to
the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 198
Score = 32.9 bits (76), Expect = 0.15
Identities = 12/27 (44%), Positives = 18/27 (66%)
Query: 192 VLVLGASGGVGTMAVQLLKAWDIEVVT 218
++V+GA+G +G QLL A EV+T
Sbjct: 1 IIVIGATGTIGLAVAQLLSAHGHEVIT 27
>gnl|CDD|237218 PRK12825, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 249
Score = 33.3 bits (77), Expect = 0.16
Identities = 24/89 (26%), Positives = 44/89 (49%), Gaps = 16/89 (17%)
Query: 190 KRVLVLGASGGVGT-MAVQLLKA-WDIEVVTTCSG--DAKDLVTSLNPN------LVIDY 239
+ LV GA+ G+G +A++L +A D+ VV S A++LV ++ + D
Sbjct: 7 RVALVTGAARGLGRAIALRLARAGADV-VVHYRSDEEAAEELVEAVEALGRRAQAVQADV 65
Query: 240 NEPEAMHSIAGA-----GPYDVILDAAGI 263
+ A+ + A G D++++ AGI
Sbjct: 66 TDKAALEAAVAAAVERFGRIDILVNNAGI 94
>gnl|CDD|182229 PRK10083, PRK10083, putative oxidoreductase; Provisional.
Length = 339
Score = 33.2 bits (76), Expect = 0.19
Identities = 35/127 (27%), Positives = 56/127 (44%), Gaps = 29/127 (22%)
Query: 89 ETCSVEPVLE----FPLTLGR-DFCGKIVAKGPRVTDLNIDDVVYGVIQPHKQGSFSKLI 143
E +V+PV+ +P ++G+ + C +V V GV H+ G FS+
Sbjct: 79 ERVAVDPVISCGHCYPCSIGKPNVCTSLV--------------VLGV---HRDGGFSEYA 121
Query: 144 LADSALVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRVLVLGASGGVGT 203
+ + H+ P I+D+ A V + A +T G +D L+ GA G VG
Sbjct: 122 VVPAKNAHRIPDAIADQYAVMVEPFTIAA----NVTGRTG-PTEQDV-ALIYGA-GPVGL 174
Query: 204 MAVQLLK 210
VQ+LK
Sbjct: 175 TIVQVLK 181
>gnl|CDD|237747 PRK14530, PRK14530, adenylate kinase; Provisional.
Length = 215
Score = 32.8 bits (75), Expect = 0.20
Identities = 17/38 (44%), Positives = 23/38 (60%), Gaps = 3/38 (7%)
Query: 188 RDKRVLVLGASG-GVGTMAVQLLKAWDIEVVTTCSGDA 224
R+L+LGA G G GT + L + + +E VTT GDA
Sbjct: 2 SQPRILLLGAPGAGKGTQSSNLAEEFGVEHVTT--GDA 37
>gnl|CDD|222146 pfam13460, NAD_binding_10, NADH(P)-binding.
Length = 182
Score = 32.7 bits (75), Expect = 0.20
Identities = 20/86 (23%), Positives = 34/86 (39%), Gaps = 5/86 (5%)
Query: 192 VLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAKDLVTSLNPNLVIDYNEPEAMHS-IAG 250
+ V+GA+G G V+ L A +V +K + P + D + + +AG
Sbjct: 1 IAVIGATGKTGRRLVKELLARGHQVTALSRNPSKAPAPGVTP-VQKDLFDLADLAEALAG 59
Query: 251 AGPYDVILDAAGIPLDQINSYLPFLK 276
D ++DA G D + L
Sbjct: 60 V---DAVVDAFGARPDDSDGVKHLLD 82
>gnl|CDD|235631 PRK05866, PRK05866, short chain dehydrogenase; Provisional.
Length = 293
Score = 32.8 bits (75), Expect = 0.26
Identities = 11/30 (36%), Positives = 15/30 (50%)
Query: 188 RDKRVLVLGASGGVGTMAVQLLKAWDIEVV 217
KR+L+ GAS G+G A + VV
Sbjct: 39 TGKRILLTGASSGIGEAAAEQFARRGATVV 68
>gnl|CDD|216527 pfam01488, Shikimate_DH, Shikimate / quinate 5-dehydrogenase. This
family contains both shikimate and quinate
dehydrogenases. Shikimate 5-dehydrogenase catalyzes the
conversion of shikimate to 5-dehydroshikimate. This
reaction is part of the shikimate pathway which is
involved in the biosynthesis of aromatic amino acids.
Quinate 5-dehydrogenase catalyzes the conversion of
quinate to 5-dehydroquinate. This reaction is part of
the quinate pathway where quinic acid is exploited as a
source of carbon in prokaryotes and microbial
eukaryotes. Both the shikimate and quinate pathways
share two common pathway metabolites 3-dehydroquinate
and dehydroshikimate.
Length = 133
Score = 31.5 bits (72), Expect = 0.27
Identities = 18/86 (20%), Positives = 36/86 (41%), Gaps = 10/86 (11%)
Query: 188 RDKRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGD---AKDLVTSLN-PNLVIDYNEPE 243
+ K+VL++GA G + +A + L + + +T + AK+L + +E E
Sbjct: 11 KGKKVLLIGA-GEMARLAAKHLLSKGAKKITIANRTLEKAKELAEEFPVGGEALPLDELE 69
Query: 244 AMHSIAGAGPYDVILDAAGIPLDQIN 269
+ D+++ A P I
Sbjct: 70 ELL-----AEADIVISATSAPTPIIT 90
>gnl|CDD|176192 cd08230, glucose_DH, Glucose dehydrogenase. Glucose dehydrogenase
(GlcDH), a member of the medium chain
dehydrogenase/zinc-dependent alcohol dehydrogenase-like
family, catalyzes the NADP(+)-dependent oxidation of
glucose to gluconate, the first step in the
Entner-Doudoroff pathway, an alternative to or
substitute for glycolysis or the pentose phosphate
pathway. The medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossman fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has a
catalytic role, while structural zinc aids in stability.
Length = 355
Score = 32.6 bits (75), Expect = 0.29
Identities = 24/83 (28%), Positives = 36/83 (43%), Gaps = 15/83 (18%)
Query: 190 KRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAKDLVTSLNPNLV----IDY----NE 241
+R LVLGA G +G +A LL+ EV D ++V Y
Sbjct: 174 RRALVLGA-GPIGLLAALLLRLRGFEVYVLNRRDP----PDPKADIVEELGATYVNSSKT 228
Query: 242 PEAMHSIAGAGPYDVILDAAGIP 264
P A + G +D+I++A G+P
Sbjct: 229 PVAEVKLVG--EFDLIIEATGVP 249
>gnl|CDD|187654 cd08951, DR_C-13_KR_SDR_c_like, daunorubicin C-13 ketoreductase
(KR), classical (c)-like SDRs. Daunorubicin is a
clinically important therapeutic compound used in some
cancer treatments. Daunorubicin C-13 ketoreductase is
member of the classical SDR family with a canonical
glycine-rich NAD(P)-binding motif, but lacking a
complete match to the active site tetrad characteristic
of this group. The critical Tyr, plus the Lys and
upstream Asn are present, but the catalytic Ser is
replaced, generally by Gln. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human prostaglandin dehydrogenase
(PGDH) numbering). In addition to the Tyr and Lys, there
is often an upstream Ser (Ser-138, PGDH numbering)
and/or an Asn (Asn-107, PGDH numbering) contributing to
the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type KRs have a TGXXXGX(1-2)G
NAD(P)-binding motif. Some atypical SDRs have lost
catalytic activity and/or have an unusual NAD(P)-binding
motif and missing or unusual active site residues.
Reactions catalyzed within the SDR family include
isomerization, decarboxylation, epimerization, C=N bond
reduction, dehydratase activity, dehalogenation,
Enoyl-CoA reduction, and carbonyl-alcohol
oxidoreduction.
Length = 260
Score = 32.5 bits (74), Expect = 0.31
Identities = 28/118 (23%), Positives = 44/118 (37%), Gaps = 19/118 (16%)
Query: 187 PRDKRVLVLGASGGVGTMAVQLLKAWDIEVVTTC-----SGDAKDLVTSLNPNLVIDYNE 241
P KR+ + G+S G+G A + L EVV + DAK L+ D +
Sbjct: 5 PPMKRIFITGSSDGLGLAAARTLLHQGHEVVLHARSQKRAADAKAACPGAAGVLIGDLSS 64
Query: 242 PEAMHSIA----GAGPYDVILDAAGIPLDQINSYLPFLKT----GKFSKFVTLRSPFL 291
+A G +D ++ AGI P KT V + +P++
Sbjct: 65 LAETRKLADQVNAIGRFDAVIHNAGILSG------PNRKTPDTGIPAMVAVNVLAPYV 116
>gnl|CDD|183714 PRK12742, PRK12742, oxidoreductase; Provisional.
Length = 237
Score = 32.0 bits (73), Expect = 0.35
Identities = 24/90 (26%), Positives = 38/90 (42%), Gaps = 10/90 (11%)
Query: 188 RDKRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGD---AKDLVTSLNPNLV-IDYNEPE 243
K+VLVLG S G+G V+ V T +G A+ L V D + +
Sbjct: 5 TGKKVLVLGGSRGIGAAIVRRFVTDGANVRFTYAGSKDAAERLAQETGATAVQTDSADRD 64
Query: 244 AMHS-IAGAGPYDVILDAAGI-----PLDQ 267
A+ + +G D+++ AGI L+
Sbjct: 65 AVIDVVRKSGALDILVVNAGIAVFGDALEL 94
>gnl|CDD|187612 cd05354, SDR_c7, classical (c) SDR, subgroup 7. These proteins are
members of the classical SDR family, with a canonical
active site triad (and also an active site Asn) and a
typical Gly-rich NAD-binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRS are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr and Lys, as
well as Asn (or Ser). Some SDR family members, including
17 beta-hydroxysteroid dehydrogenase contain an
additional helix-turn-helix motif that is not generally
found among SDRs.
Length = 235
Score = 32.0 bits (73), Expect = 0.35
Identities = 26/83 (31%), Positives = 40/83 (48%), Gaps = 7/83 (8%)
Query: 188 RDKRVLVLGASGGVGTMAVQ-LLKAWDIEVVTTCS--GDAKDLVTSLNPN---LVIDYNE 241
+DK VLV GA+ G+G V+ LL +V G A LV L +D +
Sbjct: 2 KDKTVLVTGANRGIGKAFVESLLAHGAKKVYAAVRDPGSAAHLVAKYGDKVVPLRLDVTD 61
Query: 242 PEAMHSIAGAGP-YDVILDAAGI 263
PE++ + A DV+++ AG+
Sbjct: 62 PESIKAAAAQAKDVDVVINNAGV 84
>gnl|CDD|185200 PRK15300, PRK15300, fimbrial protein StiA; Provisional.
Length = 179
Score = 31.6 bits (71), Expect = 0.47
Identities = 32/134 (23%), Positives = 53/134 (39%), Gaps = 11/134 (8%)
Query: 52 LKSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQLETCSVEPVLEFPLTLGRDFCGKI 111
L K + V + A++++P +A G V + L + C+V+ +TL +F
Sbjct: 3 LSLKTLTVALAAITLSPAALADTAKDGTVHITGLIKQNACTVK-TDSVEVTLQEEFASLF 61
Query: 112 VAKGPRVTDL-------NIDDVVYGVIQPHKQGSF---SKLILADSALVHKKPSNISDEE 161
A G D N D VY +Q +G+ IL + I D+
Sbjct: 62 TAAGQTAGDTDFTIELENCDANVYSSVQARFEGTLDGTDATILKNEDDAENIGVQILDKT 121
Query: 162 AAGVLYTGLTAWSA 175
+ + + L AWSA
Sbjct: 122 STPMTFNDLQAWSA 135
>gnl|CDD|187549 cd05238, Gne_like_SDR_e, Escherichia coli Gne (a
nucleoside-diphosphate-sugar 4-epimerase)-like, extended
(e) SDRs. Nucleoside-diphosphate-sugar 4-epimerase has
the characteristic active site tetrad and NAD-binding
motif of the extended SDR, and is related to more
specifically defined epimerases such as UDP-glucose 4
epimerase (aka UDP-galactose-4-epimerase), which
catalyzes the NAD-dependent conversion of UDP-galactose
to UDP-glucose, the final step in Leloir galactose
synthesis. This subgroup includes Escherichia coli
055:H7 Gne, a UDP-GlcNAc 4-epimerase, essential for O55
antigen synthesis. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 305
Score = 31.6 bits (72), Expect = 0.54
Identities = 23/81 (28%), Positives = 36/81 (44%), Gaps = 14/81 (17%)
Query: 191 RVLVLGASGGVGT-MAVQLLKAWDIEVVTTCSGDAKDLVTSLNPN-------LVIDYNEP 242
+VL+ GASG VG +A +LL E + D+V+ P+ + D P
Sbjct: 2 KVLITGASGFVGQRLAERLLSDVPNERLILI-----DVVSPKAPSGAPRVTQIAGDLAVP 56
Query: 243 EAMHSIAGAGPYDVILDAAGI 263
+ ++A G DV+ A I
Sbjct: 57 ALIEALA-NGRPDVVFHLAAI 76
>gnl|CDD|235139 PRK03612, PRK03612, spermidine synthase; Provisional.
Length = 521
Score = 31.7 bits (73), Expect = 0.58
Identities = 20/42 (47%), Positives = 27/42 (64%), Gaps = 10/42 (23%)
Query: 184 LVYP------RDKRVLVLGASGGVGTMAV-QLLKAWDIEVVT 218
LV+P R +RVLVLG GG G +A+ ++LK D+E VT
Sbjct: 287 LVHPAMAASARPRRVLVLG--GGDG-LALREVLKYPDVEQVT 325
>gnl|CDD|187586 cd05325, carb_red_sniffer_like_SDR_c, carbonyl reductase
sniffer-like, classical (c) SDRs. Sniffer is an
NADPH-dependent carbonyl reductase of the classical SDR
family. Studies in Drosophila melanogaster implicate
Sniffer in the prevention of neurodegeneration due to
aging and oxidative-stress. This subgroup also includes
Rhodococcus sp. AD45 IsoH, which is an NAD-dependent
1-hydroxy-2-glutathionyl-2-methyl-3-butene dehydrogenase
involved in isoprene metabolism, Aspergillus nidulans
StcE encoded by a gene which is part of a proposed
sterigmatocystin biosynthesis gene cluster, Bacillus
circulans SANK 72073 BtrF encoded by a gene found in the
butirosin biosynthesis gene cluster, and Aspergillus
parasiticus nor-1 involved in the biosynthesis of
aflatoxins. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes catalyze a wide range of activities including
the metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 233
Score = 31.5 bits (72), Expect = 0.62
Identities = 34/136 (25%), Positives = 55/136 (40%), Gaps = 38/136 (27%)
Query: 192 VLVLGASGGVG-TMAVQLLKAWDIEVVTTC--SGDAKDL--VTSLNPNLVI---DYNEP- 242
VL+ GAS G+G + QLL + V+ TC A +L + + + L I D +
Sbjct: 1 VLITGASRGIGLELVRQLLARGNNTVIATCRDPSAATELAALGASHSRLHILELDVTDEI 60
Query: 243 -EAMHSIA---GAGPYDVILDAAGI-------------------------PLDQINSYLP 273
E+ ++A G DV+++ AGI PL ++LP
Sbjct: 61 AESAEAVAERLGDAGLDVLINNAGILHSYGPASEVDSEDLLEVFQVNVLGPLLLTQAFLP 120
Query: 274 FLKTGKFSKFVTLRSP 289
L G +K + + S
Sbjct: 121 LLLKGARAKIINISSR 136
>gnl|CDD|187594 cd05333, BKR_SDR_c, beta-Keto acyl carrier protein reductase (BKR),
involved in Type II FAS, classical (c) SDRs. This
subgroup includes the Escherichai coli K12 BKR, FabG.
BKR catalyzes the NADPH-dependent reduction of ACP in
the first reductive step of de novo fatty acid synthesis
(FAS). FAS consists of four elongation steps, which are
repeated to extend the fatty acid chain through the
addition of two-carbo units from malonyl acyl-carrier
protein (ACP): condensation, reduction, dehydration, and
a final reduction. Type II FAS, typical of plants and
many bacteria, maintains these activities on discrete
polypeptides, while type I FAS utilizes one or two
multifunctional polypeptides. BKR resembles enoyl
reductase, which catalyzes the second reduction step in
FAS. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) NAD(P)(H) binding
region and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRS are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes have a 3-glycine N-terminal NAD(P)(H) binding
pattern: TGxxxGxG in classical SDRs. Extended SDRs have
additional elements in the C-terminal region, and
typically have a TGXXGXXG cofactor binding motif.
Complex (multidomain) SDRs such as ketoreductase domains
of fatty acid synthase have a GGXGXXG NAD(P) binding
motif and an altered active site motif (YXXXN). Fungal
type type ketoacyl reductases have a TGXXXGX(1-2)G
NAD(P)-binding motif. Some atypical SDRs have lost
catalytic activity and/or have an unusual NAD(P) binding
motif and missing or unusual active site residues.
Reactions catalyzed within the SDR family include
isomerization, decarboxylation, epimerization, C=N bond
reduction, dehydratase activity, dehalogenation,
Enoyl-CoA reduction, and carbonyl-alcohol
oxidoreduction. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr-151 and
Lys-155, and well as Asn-111 (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is not
generally found among SDRs.
Length = 240
Score = 31.4 bits (72), Expect = 0.64
Identities = 26/91 (28%), Positives = 40/91 (43%), Gaps = 13/91 (14%)
Query: 190 KRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSG-----DAKDLVTSLNPN---LVIDYNE 241
K LV GAS G+G L A +V T + + + +L N L D ++
Sbjct: 1 KVALVTGASRGIGRAIALRLAAEGAKVAVTDRSEEAAAETVEEIKALGGNAAALEADVSD 60
Query: 242 PEAMHS-----IAGAGPYDVILDAAGIPLDQ 267
EA+ + A GP D++++ AGI D
Sbjct: 61 REAVEALVEKVEAEFGPVDILVNNAGITRDN 91
>gnl|CDD|240360 PTZ00325, PTZ00325, malate dehydrogenase; Provisional.
Length = 321
Score = 31.6 bits (72), Expect = 0.72
Identities = 28/86 (32%), Positives = 36/86 (41%), Gaps = 16/86 (18%)
Query: 191 RVLVLGASGGVGTMAVQLLK---------AWDIEVVTTCSGDAKDLVTSLNPNLVIDYNE 241
+V VLGA+GG+G LLK +DI G A DL P V Y +
Sbjct: 10 KVAVLGAAGGIGQPLSLLLKQNPHVSELSLYDI---VGAPGVAADLSHIDTPAKVTGYAD 66
Query: 242 PEAMHSIA-GAGPYDVILDAAGIPLD 266
E GA D++L AG+P
Sbjct: 67 GELWEKALRGA---DLVLICAGVPRK 89
>gnl|CDD|233220 TIGR00978, asd_EA, aspartate-semialdehyde dehydrogenase
(non-peptidoglycan organisms). Two closely related
families of aspartate-semialdehyde dehydrogenase are
found. They differ by a deep split in phylogenetic and
percent identity trees and in gap patterns. Separate
models are built for the two types in order to exclude
the USG-1 protein, found in several species, which is
specifically related to the Bacillus subtilis type of
aspartate-semialdehyde dehydrogenase. Members of this
type are found primarily in organisms that lack
peptidoglycan [Amino acid biosynthesis, Aspartate
family].
Length = 341
Score = 31.3 bits (71), Expect = 0.73
Identities = 13/36 (36%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 191 RVLVLGASGGVGTMAVQLLKAW-DIEVVTTCSGDAK 225
RV VLGA+G VG V+LL E+ +
Sbjct: 2 RVAVLGATGLVGQKFVKLLAKHPYFELAKVVASPRS 37
>gnl|CDD|187656 cd08953, KR_2_SDR_x, ketoreductase (KR), subgroup 2, complex (x)
SDRs. Ketoreductase, a module of the multidomain
polyketide synthase (PKS), has 2 subdomains, each
corresponding to a SDR family monomer. The C-terminal
subdomain catalyzes the NADPH-dependent reduction of the
beta-carbonyl of a polyketide to a hydroxyl group, a
step in the biosynthesis of polyketides, such as
erythromycin. The N-terminal subdomain, an interdomain
linker, is a truncated Rossmann fold which acts to
stabilizes the catalytic subdomain. Unlike typical SDRs,
the isolated domain does not oligomerize but is composed
of 2 subdomains, each resembling an SDR monomer. The
active site resembles that of typical SDRs, except that
the usual positions of the catalytic Asn and Tyr are
swapped, so that the canonical YXXXK motif changes to
YXXXN. Modular PKSs are multifunctional structures in
which the makeup recapitulates that found in (and may
have evolved from) FAS. Polyketide synthesis also
proceeds via the addition of 2-carbon units as in fatty
acid synthesis. The complex SDR NADP-binding motif,
GGXGXXG, is often present, but is not strictly conserved
in each instance of the module. This subfamily includes
both KR domains of the Bacillus subtilis Pks J,-L, and
PksM, and all three KR domains of PksN, components of
the megacomplex bacillaene synthase, which synthesizes
the antibiotic bacillaene. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human prostaglandin dehydrogenase
(PGDH) numbering). In addition to the Tyr and Lys, there
is often an upstream Ser (Ser-138, PGDH numbering)
and/or an Asn (Asn-107, PGDH numbering) contributing to
the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type KRs have a TGXXXGX(1-2)G
NAD(P)-binding motif. Some atypical SDRs have lost
catalytic activity and/or have an unusual NAD(P)-binding
motif and missing or unusual active site residues.
Reactions catalyzed within the SDR family include
isomerization, decarboxylation, epimerization, C=N bond
reduction, dehydratase activity, dehalogenation,
Enoyl-CoA reduction, and carbonyl-alcohol
oxidoreduction.
Length = 436
Score = 31.6 bits (72), Expect = 0.78
Identities = 18/81 (22%), Positives = 29/81 (35%), Gaps = 7/81 (8%)
Query: 144 LADSALVHKKPSNISDEEAAGVLYTGLTAWSA------LQITAALGLVYPRDKRVLVLGA 197
+ AL + + ++ AA V Y + L AA LV G
Sbjct: 154 ASAEALARELAAELAAPGAAEVRYRDGLRYVQTLEPLPLPAGAAASAPLKPGGVYLVTGG 213
Query: 198 SGGVGTM-AVQLLKAWDIEVV 217
+GG+G A L + + +V
Sbjct: 214 AGGIGRALARALARRYGARLV 234
>gnl|CDD|176245 cd08285, NADP_ADH, NADP(H)-dependent alcohol dehydrogenases. This
group is predominated by atypical alcohol
dehydrogenases; they exist as tetramers and exhibit
specificity for NADP(H) as a cofactor in the
interconversion of alcohols and aldehydes, or ketones.
Like other zinc-dependent alcohol dehydrogenases (ADH)
of the medium chain alcohol dehydrogenase/reductase
family (MDR), tetrameric ADHs have a catalytic zinc that
resides between the catalytic and NAD(H)binding domains;
however, they do not have and a structural zinc in a
lobe of the catalytic domain. The medium chain alcohol
dehydrogenase family (MDR) has a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit.
Length = 351
Score = 31.1 bits (71), Expect = 0.88
Identities = 44/191 (23%), Positives = 60/191 (31%), Gaps = 61/191 (31%)
Query: 50 PILKSKDVLVEMKAVSVNPIDVAML-GGYGNVVLNSLRQLETCSVEPVLEFPLTLGRDFC 108
P+ D +V AV+ DV + GG P + LG +
Sbjct: 20 PVCGPNDAIVRPTAVAPCTSDVHTVWGGA-----------------PGERHGMILGHEAV 62
Query: 109 GKIVAKGPRVTDLNIDD-VVYGVIQPH--------------------------KQGSFSK 141
G + G V D D V+ I P K G F++
Sbjct: 63 GVVEEVGSEVKDFKPGDRVIVPAITPDWRSVAAQRGYPSQSGGMLGGWKFSNFKDGVFAE 122
Query: 142 LIL---ADSALVHKKPSNISDEEAA---GVLYTGLTAWSALQITAALGLVYPRDKRVLVL 195
AD+ L P ++DE+A ++ TG I LG V V
Sbjct: 123 YFHVNDADANLAP-LPDGLTDEQAVMLPDMMSTGFHGAELANIK--LG------DTVAVF 173
Query: 196 GASGGVGTMAV 206
G G VG MAV
Sbjct: 174 GI-GPVGLMAV 183
>gnl|CDD|178321 PLN02719, PLN02719, triacylglycerol lipase.
Length = 518
Score = 31.2 bits (70), Expect = 0.89
Identities = 30/109 (27%), Positives = 41/109 (37%), Gaps = 33/109 (30%)
Query: 228 VTSLNPNLVIDYNEPEAMHSIAGAGPYDVILDAAGIPLDQINSYLPFLKT---------- 277
V + +P L ++ P+A+ +AG P+ +PLD S PFLK
Sbjct: 370 VVAKSPGLFLNERAPQALMKLAGGLPWCYSHVGEMLPLDHQKS--PFLKPTVDLSTAHNL 427
Query: 278 -----------GKFSKFVTLRSPFLKNTDSLGLVPGLVKNAFDLLKSNF 315
GK +FV S G P LV A D LK +F
Sbjct: 428 EALLHLLDGYHGKGQRFVL----------SSGRDPALVNKASDFLKDHF 466
>gnl|CDD|181126 PRK07806, PRK07806, short chain dehydrogenase; Provisional.
Length = 248
Score = 30.8 bits (70), Expect = 0.91
Identities = 10/30 (33%), Positives = 14/30 (46%)
Query: 188 RDKRVLVLGASGGVGTMAVQLLKAWDIEVV 217
K LV G+S G+G ++L VV
Sbjct: 5 PGKTALVTGSSRGIGADTAKILAGAGAHVV 34
>gnl|CDD|224016 COG1091, RfbD, dTDP-4-dehydrorhamnose reductase [Cell envelope
biogenesis, outer membrane].
Length = 281
Score = 30.7 bits (70), Expect = 1.0
Identities = 19/103 (18%), Positives = 40/103 (38%), Gaps = 19/103 (18%)
Query: 191 RVLVLGASGGVGT-MAVQLLKAWDIEVVTTCSGD------AKDLVTSLNPNLVI------ 237
++L+ GA+G +GT + L +++ D +++ P++VI
Sbjct: 2 KILITGANGQLGTELRRALPGEFEVIATDRAELDITDPDAVLEVIRETRPDVVINAAAYT 61
Query: 238 ----DYNEPEAMHSIAGAGPYDV--ILDAAGIPLDQINSYLPF 274
+EPE ++ G ++ G L I++ F
Sbjct: 62 AVDKAESEPELAFAVNATGAENLARAAAEVGARLVHISTDYVF 104
>gnl|CDD|226133 COG3605, PtsP, Signal transduction protein containing GAF and PtsI
domains [Signal transduction mechanisms].
Length = 756
Score = 31.2 bits (71), Expect = 1.1
Identities = 19/66 (28%), Positives = 30/66 (45%), Gaps = 6/66 (9%)
Query: 175 ALQITAALGLVYPRDKRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAKDLVTSLNPN 234
A ++ AA L YPRD+ V+ G + A + +A I V A +V S+
Sbjct: 334 ARELGAAELLEYPRDRLRGVVLEDGAANSHAAIVARAMGIPTV----MGAAGIVPSVLNG 389
Query: 235 --LVID 238
L++D
Sbjct: 390 DALIVD 395
>gnl|CDD|176218 cd08256, Zn_ADH2, Alcohol dehydrogenases of the MDR family. This
group has the characteristic catalytic and structural
zinc-binding sites of the zinc-dependent alcohol
dehydrogenases of the MDR family. The medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability.
Length = 350
Score = 30.8 bits (70), Expect = 1.2
Identities = 29/150 (19%), Positives = 53/150 (35%), Gaps = 44/150 (29%)
Query: 47 VKTPILKSKDVLVEMKAVSVNPIDVAMLGG----YGNVVLNSLRQLETCSVEPVLEFPLT 102
V P ++LV+++A + D+ G +G+ + P ++ P+
Sbjct: 17 VPVPRPGPGEILVKVEACGICAGDIKCYHGAPSFWGDE-----------NQPPYVKPPMI 65
Query: 103 LGRDFCGKIVAKGPRVTDLNI---DDVV-----------------YGVIQPHKQGSFSK- 141
G +F G++V G + + D V+ Y + Q H F
Sbjct: 66 PGHEFVGRVVELGEGAEERGVKVGDRVISEQIVPCWNCRFCNRGQYWMCQKHDLYGFQNN 125
Query: 142 --------LILADSALVHKKPSNISDEEAA 163
+ A+VHK P +I E+A
Sbjct: 126 VNGGMAEYMRFPKEAIVHKVPDDIPPEDAI 155
>gnl|CDD|240643 cd12166, 2-Hacid_dh_7, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 300
Score = 30.6 bits (70), Expect = 1.2
Identities = 9/29 (31%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 189 DKRVLVLGASGGVGTMAVQLLKAWDIEVV 217
D+RVL++G G +G + L +++ V
Sbjct: 132 DRRVLIVGY-GSIGRAIERRLAPFEVRVT 159
>gnl|CDD|180604 PRK06523, PRK06523, short chain dehydrogenase; Provisional.
Length = 260
Score = 30.6 bits (70), Expect = 1.2
Identities = 13/30 (43%), Positives = 15/30 (50%)
Query: 190 KRVLVLGASGGVGTMAVQLLKAWDIEVVTT 219
KR LV G + G+G V L VVTT
Sbjct: 10 KRALVTGGTKGIGAATVARLLEAGARVVTT 39
>gnl|CDD|218026 pfam04321, RmlD_sub_bind, RmlD substrate binding domain.
L-rhamnose is a saccharide required for the virulence of
some bacteria. Its precursor, dTDP-L-rhamnose, is
synthesised by four different enzymes the final one of
which is RmlD. The RmlD substrate binding domain is
responsible for binding a sugar nucleotide.
Length = 284
Score = 30.7 bits (70), Expect = 1.2
Identities = 26/102 (25%), Positives = 42/102 (41%), Gaps = 24/102 (23%)
Query: 192 VLVLGASGGVGTMAVQLLKAWDIEVVTTCSGD--------AKDLVTSLNPNLVIDYN--- 240
+LV GA+G +G +LL +EVV + LV P++V+ N
Sbjct: 1 ILVTGANGQLGRELTRLLAERGVEVVALDRPELDLTDPEAVAALVREARPDVVV--NAAA 58
Query: 241 ---------EPEAMHSIAGAGPYDV--ILDAAGIPLDQINSY 271
EPE +++ GP ++ A G PL I++
Sbjct: 59 YTAVDKAESEPELAYAVNALGPGNLAEACAARGAPLIHISTD 100
>gnl|CDD|215378 PLN02702, PLN02702, L-idonate 5-dehydrogenase.
Length = 364
Score = 30.9 bits (70), Expect = 1.3
Identities = 64/253 (25%), Positives = 88/253 (34%), Gaps = 62/253 (24%)
Query: 48 KTPILKSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQLETCSVEPVLEFPLTLGRDF 107
K P L DV V MKAV + DV + L+ + V++ P+ +G +
Sbjct: 35 KLPPLGPHDVRVRMKAVGICGSDV-----------HYLKTMRCADF--VVKEPMVIGHEC 81
Query: 108 CGKIVAKGPRVTDLNIDDVV------------------YGVI-------QPHKQGSFSKL 142
G I G V L + D V Y + P GS +
Sbjct: 82 AGIIEEVGSEVKHLVVGDRVALEPGISCWRCNLCKEGRYNLCPEMKFFATPPVHGSLANQ 141
Query: 143 ILADSALVHKKPSNISDEEAAGV--LYTGLTAWSALQITAALGLVYPRDKRVLVLGAS-- 198
++ + L K P N+S EE A L G+ A I + VLV+GA
Sbjct: 142 VVHPADLCFKLPENVSLEEGAMCEPLSVGVHACRRANIGP--------ETNVLVMGAGPI 193
Query: 199 GGVGTMAVQLLKAWDIEVVTTCS---GDAKDL------VTSLNPNLVIDYNEPEAMHSIA 249
G V +A + A I +V AK L + S N V E E +
Sbjct: 194 GLVTMLAARAFGAPRIVIVDVDDERLSVAKQLGADEIVLVSTNIEDVES--EVEEIQKAM 251
Query: 250 GAGPYDVILDAAG 262
G G DV D G
Sbjct: 252 G-GGIDVSFDCVG 263
>gnl|CDD|240636 cd12159, 2-Hacid_dh_2, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 303
Score = 30.7 bits (70), Expect = 1.3
Identities = 10/30 (33%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 188 RDKRVLVLGASGGVGTMAVQLLKAWDIEVV 217
R V ++GA GG+G + LL + +V+
Sbjct: 124 RGSTVAIVGA-GGIGRALIPLLAPFGAKVI 152
>gnl|CDD|215522 PLN02968, PLN02968, Probable N-acetyl-gamma-glutamyl-phosphate
reductase.
Length = 381
Score = 30.6 bits (69), Expect = 1.5
Identities = 29/108 (26%), Positives = 40/108 (37%), Gaps = 25/108 (23%)
Query: 189 DKRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAK----------DLVTSLNPNLV-- 236
KR+ VLGASG G +LL +T + D K L+T PNLV
Sbjct: 38 KKRIFVLGASGYTGAEVRRLLANHPDFEITVMTADRKAGQSFGSVFPHLITQDLPNLVAV 97
Query: 237 --IDYNEPEAM----------HSIAGAGPYDVILDA-AGIPLDQINSY 271
D+++ +A+ I I+D A L I Y
Sbjct: 98 KDADFSDVDAVFCCLPHGTTQEIIKALPKDLKIVDLSADFRLRDIAEY 145
>gnl|CDD|223959 COG1028, FabG, Dehydrogenases with different specificities (related
to short-chain alcohol dehydrogenases) [Secondary
metabolites biosynthesis, transport, and catabolism /
General function prediction only].
Length = 251
Score = 30.2 bits (68), Expect = 1.6
Identities = 12/40 (30%), Positives = 17/40 (42%), Gaps = 1/40 (2%)
Query: 189 DKRVLVLGASGGVG-TMAVQLLKAWDIEVVTTCSGDAKDL 227
K LV GAS G+G +A L + VV + +
Sbjct: 5 GKVALVTGASSGIGRAIARALAREGARVVVAARRSEEEAA 44
>gnl|CDD|187569 cd05259, PCBER_SDR_a, phenylcoumaran benzylic ether reductase
(PCBER) like, atypical (a) SDRs. PCBER and
pinoresinol-lariciresinol reductases are NADPH-dependent
aromatic alcohol reductases, and are atypical members of
the SDR family. Other proteins in this subgroup are
identified as eugenol synthase. These proteins contain
an N-terminus characteristic of NAD(P)-binding proteins
and a small C-terminal domain presumed to be involved in
substrate binding, but they do not have the conserved
active site Tyr residue typically found in SDRs.
Numerous other members have unknown functions. The
glycine rich NADP-binding motif in this subgroup is of 2
forms: GXGXXG and G[GA]XGXXG; it tends to be atypical
compared with the forms generally seen in classical or
extended SDRs. The usual SDR active site tetrad is not
present, but a critical active site Lys at the usual SDR
position has been identified in various members, though
other charged and polar residues are found at this
position in this subgroup. Atypical SDR-related proteins
retain the Rossmann fold of the SDRs, but have limited
sequence identity and generally lack the catalytic
properties of the archetypical members. Atypical SDRs
include biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 282
Score = 30.3 bits (69), Expect = 1.6
Identities = 20/86 (23%), Positives = 37/86 (43%), Gaps = 10/86 (11%)
Query: 191 RVLVLGASGGVGTMAVQ-LLKAWDIE--VVTTCSGDAKDLVTSLNPNLV-IDYNEPEAMH 246
++ + GA+G +G V LL + V+T S + + +V +DY E++
Sbjct: 1 KIAIAGATGTLGGPIVSALLASPGFTVTVLTRPSSTSSNEFQPSGVKVVPVDYASHESLV 60
Query: 247 SI-AGAGPYDVILDAAGI--PLDQIN 269
+ G D ++ A G DQ+
Sbjct: 61 AALKG---VDAVISALGGAAIGDQLK 83
>gnl|CDD|224833 COG1922, WecG, Teichoic acid biosynthesis proteins [Cell envelope
biogenesis, outer membrane].
Length = 253
Score = 30.3 bits (69), Expect = 1.6
Identities = 22/82 (26%), Positives = 35/82 (42%), Gaps = 15/82 (18%)
Query: 189 DKRVLVLGASGGVGTMAVQLLKA-W-DIEVVTTCSGDAKDLVTSLNPNLVIDYNEPEAMH 246
KRV +LG GV A L+A + +++V + G E +
Sbjct: 108 GKRVFLLGGKPGVAEQAAAKLRAKYPGLKIVGSHDGYFDPE------------EEEAIVE 155
Query: 247 SIAGAGPYDVILDAAGIPLDQI 268
IA +GP D++L G+P +I
Sbjct: 156 RIAASGP-DILLVGMGVPRQEI 176
>gnl|CDD|187540 cd05229, SDR_a3, atypical (a) SDRs, subgroup 3. These atypical SDR
family members of unknown function have a glycine-rich
NAD(P)-binding motif consensus that is very similar to
the extended SDRs, GXXGXXG. Generally, this group has
poor conservation of the active site tetrad, However,
individual sequences do contain matches to the YXXXK
active site motif, and generally Tyr or Asn in place of
the upstream Ser found in most SDRs. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 302
Score = 30.0 bits (68), Expect = 1.7
Identities = 12/29 (41%), Positives = 19/29 (65%), Gaps = 2/29 (6%)
Query: 192 VLVLGASGGVGT-MAVQLLKA-WDIEVVT 218
VLGASG +G +A +L + WD+ +V+
Sbjct: 2 AHVLGASGPIGREVARELRRRGWDVRLVS 30
>gnl|CDD|240664 cd12188, SDH, Saccharopine Dehydrogenase NAD-binding and catalytic
domains. Saccharopine Dehydrogenase (SDH) catalyzes the
final step in the reversible NAD-dependent oxidative
deamination of saccharopine to alpha-ketoglutarate and
lysine, in the alpha-aminoadipate pathway of L-lysine
biosynthesis. SHD is structurally related to formate
dehydrogenase and similar enzymes, having a 2-domain
structure in which a Rossmann-fold NAD(P)-binding domain
is inserted within the linear sequence of a catalytic
domain of related structure.
Length = 351
Score = 30.3 bits (69), Expect = 1.8
Identities = 17/46 (36%), Positives = 22/46 (47%), Gaps = 8/46 (17%)
Query: 177 QITAALGLVYPRDKRVLVLGASGGVGTMAVQLLKA-------WDIE 215
+ AL R R LV+GA G G+ AV LL+A WD+
Sbjct: 172 DVKKALATG-GRKPRALVIGALGRCGSGAVDLLEAAGIEVTKWDMA 216
>gnl|CDD|223247 COG0169, AroE, Shikimate 5-dehydrogenase [Amino acid transport and
metabolism].
Length = 283
Score = 29.9 bits (68), Expect = 2.0
Identities = 29/138 (21%), Positives = 47/138 (34%), Gaps = 15/138 (10%)
Query: 178 ITAALGLVYPRDKRVLVLGASGGVGT---MAVQLLKAWDIEVVTTCSGDAKDLVTSLNPN 234
+ V KRVL+LGA GG A+ A I VV A++L
Sbjct: 115 LKEFGLPVDVTGKRVLILGA-GGAARAVAFALAEAGAKRITVVNRTRERAEELADLFGEL 173
Query: 235 LVIDYNEPEAMHSIAGAGPYDVILDAAGIPLD-QINSYLPFLKTGKFSKFVT------LR 287
E A+ + G D++++A + + + V L
Sbjct: 174 GA--AVEAAALADLEGLEEADLLINATPVGMAGPEGDSPVPAELLPKGAIVYDVVYNPLE 231
Query: 288 SPFLKNTDSLGL--VPGL 303
+P L+ + G + GL
Sbjct: 232 TPLLREARAQGAKTIDGL 249
>gnl|CDD|176224 cd08263, Zn_ADH10, Alcohol dehydrogenases of the MDR family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 367
Score = 30.0 bits (68), Expect = 2.1
Identities = 22/62 (35%), Positives = 32/62 (51%), Gaps = 5/62 (8%)
Query: 150 VHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRVLVLGASGGVGTMAVQLL 209
+ P ++ E+A + G TA+ AL V P + V V+G GGVG+ A+QL
Sbjct: 153 LAPLPESLDYTESAVLGCAGFTAYGAL---KHAADVRPGET-VAVIGV-GGVGSSAIQLA 207
Query: 210 KA 211
KA
Sbjct: 208 KA 209
>gnl|CDD|180343 PRK05993, PRK05993, short chain dehydrogenase; Provisional.
Length = 277
Score = 30.0 bits (68), Expect = 2.2
Identities = 16/68 (23%), Positives = 30/68 (44%), Gaps = 4/68 (5%)
Query: 187 PRDKRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAKDLVTSLNPNL---VIDYNEPE 243
+ +L+ G S G+G + L++ V TC +D+ L +DY EPE
Sbjct: 2 DMKRSILITGCSSGIGAYCARALQSDGWRVFATCR-KEEDVAALEAEGLEAFQLDYAEPE 60
Query: 244 AMHSIAGA 251
++ ++
Sbjct: 61 SIAALVAQ 68
>gnl|CDD|237460 PRK13656, PRK13656, trans-2-enoyl-CoA reductase; Provisional.
Length = 398
Score = 29.8 bits (68), Expect = 2.2
Identities = 13/28 (46%), Positives = 16/28 (57%), Gaps = 2/28 (7%)
Query: 177 QI--TAALGLVYPRDKRVLVLGASGGVG 202
QI A G + K+VLV+GAS G G
Sbjct: 27 QIEYVKAQGPIANGPKKVLVIGASSGYG 54
>gnl|CDD|188169 TIGR01829, AcAcCoA_reduct, acetoacetyl-CoA reductase. This model
represent acetoacetyl-CoA reductase, a member of the
family short-chain-alcohol dehydrogenases. Note that,
despite the precision implied by the enzyme name, the
reaction of EC 1.1.1.36 is defined more generally as
(R)-3-hydroxyacyl-CoA + NADP+ = 3-oxoacyl-CoA + NADPH.
Members of this family may act in the biosynthesis of
poly-beta-hydroxybutyrate (e.g. Rhizobium meliloti) and
related poly-beta-hydroxyalkanoates. Note that the
member of this family from Azospirillum brasilense,
designated NodG, appears to lack acetoacetyl-CoA
reductase activity and to act instead in the production
of nodulation factor. This family is downgraded to
subfamily for this NodG. Other proteins designated NodG,
as from Rhizobium, belong to related but distinct
protein families.
Length = 242
Score = 29.7 bits (67), Expect = 2.3
Identities = 23/88 (26%), Positives = 31/88 (35%), Gaps = 14/88 (15%)
Query: 193 LVLGASGGVGTMAVQLLKAWDIEVVTTCSGD------------AKDLVTSLNPNLVIDYN 240
LV G GG+GT Q L V C + A + V +
Sbjct: 4 LVTGGMGGIGTAICQRLAKDGYRVAANCGPNEERAEAWLQEQGALGFDFRVVEGDVSSFE 63
Query: 241 EPEAM--HSIAGAGPYDVILDAAGIPLD 266
+A A GP DV+++ AGI D
Sbjct: 64 SCKAAVAKVEAELGPIDVLVNNAGITRD 91
>gnl|CDD|235340 PRK05086, PRK05086, malate dehydrogenase; Provisional.
Length = 312
Score = 29.6 bits (67), Expect = 2.4
Identities = 27/87 (31%), Positives = 42/87 (48%), Gaps = 21/87 (24%)
Query: 191 RVLVLGASGGVGTMAVQLLKA----------WDIEVVTTCSGDAKDLV---TSLNPNLVI 237
+V VLGA+GG+G LLK +DI VT G A DL T++ +
Sbjct: 2 KVAVLGAAGGIGQALALLLKTQLPAGSELSLYDIAPVT--PGVAVDLSHIPTAVK---IK 56
Query: 238 DYNEPEAMHSIAGAGPYDVILDAAGIP 264
++ + ++ GA DV+L +AG+
Sbjct: 57 GFSGEDPTPALEGA---DVVLISAGVA 80
>gnl|CDD|184076 PRK13479, PRK13479, 2-aminoethylphosphonate--pyruvate transaminase;
Provisional.
Length = 368
Score = 29.9 bits (68), Expect = 2.5
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 180 AALGLVYPRDKRVLVLGASGGVGTMAVQLLKAWDIEVVT 218
AA+G + PRD +VLV +G G Q+ + I V
Sbjct: 71 AAIGSLVPRDGKVLVP-DNGAYGARIAQIAEYLGIAHVV 108
>gnl|CDD|212496 cd11730, Tthb094_like_SDR_c, Tthb094 and related proteins,
classical (c) SDRs. Tthb094 from Thermus Thermophilus
is a classical SDR which binds NADP. Members of this
subgroup contain the YXXXK active site characteristic of
SDRs. Also, an upstream Asn residue of the canonical
catalytic tetrad is partially conserved in this subgroup
of proteins of undetermined function. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human prostaglandin
dehydrogenase (PGDH) numbering). In addition to the Tyr
and Lys, there is often an upstream Ser (Ser-138, PGDH
numbering) and/or an Asn (Asn-107, PGDH numbering)
contributing to the active site; while substrate binding
is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P)-binding motif and missing or
unusual active site residues. Reactions catalyzed within
the SDR family include isomerization, decarboxylation,
epimerization, C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 206
Score = 29.4 bits (66), Expect = 2.7
Identities = 21/77 (27%), Positives = 34/77 (44%), Gaps = 8/77 (10%)
Query: 192 VLVLGASGGVGTMAVQLLKA--WDIEVV----TTCSGDAKDLVTSLNPNLVIDYNEPEAM 245
L+LGA+GG+G + L W + + +G A ++ P V E A+
Sbjct: 1 ALILGATGGIGRALARALAGRGWRLLLSGRDAGALAGLAAEVGALARPADVAAELEVWAL 60
Query: 246 HSIAGAGPYDVILDAAG 262
GP D+++ AAG
Sbjct: 61 --AQELGPLDLLVYAAG 75
>gnl|CDD|187554 cd05243, SDR_a5, atypical (a) SDRs, subgroup 5. This subgroup
contains atypical SDRs, some of which are identified as
putative NAD(P)-dependent epimerases, one as a putative
NAD-dependent epimerase/dehydratase. Atypical SDRs are
distinct from classical SDRs. Members of this subgroup
have a glycine-rich NAD(P)-binding motif that is very
similar to the extended SDRs, GXXGXXG, and binds NADP.
Generally, this subgroup has poor conservation of the
active site tetrad; however, individual sequences do
contain matches to the YXXXK active site motif, the
upstream Ser, and there is a highly conserved Asp in
place of the usual active site Asn throughout the
subgroup. Atypical SDRs generally lack the catalytic
residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta reductase
(BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 203
Score = 29.1 bits (66), Expect = 2.7
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 191 RVLVLGASGGVGTMAVQLLKAWDIEVV 217
+VLV+GA+G VG V+ L +V
Sbjct: 1 KVLVVGATGKVGRHVVRELLDRGYQVR 27
>gnl|CDD|216573 pfam01564, Spermine_synth, Spermine/spermidine synthase. Spermine
and spermidine are polyamines. This family includes
spermidine synthase that catalyzes the fifth (last) step
in the biosynthesis of spermidine from arginine, and
spermine synthase.
Length = 240
Score = 29.2 bits (66), Expect = 2.8
Identities = 19/85 (22%), Positives = 34/85 (40%), Gaps = 12/85 (14%)
Query: 183 GLVYPRDKRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAK--DLVTSLNPNLVIDYN 240
+P K+VL++G GG G +++K +E +T D K + P+L ++
Sbjct: 70 LCSHPNPKKVLIIG--GGDGGALREVVKHPSVEKITLVEIDEKVIEFSKKFLPSLAGGFD 127
Query: 241 EPEA--------MHSIAGAGPYDVI 257
+P +DVI
Sbjct: 128 DPRVKVVIGDGFKFLKDYLVEFDVI 152
>gnl|CDD|180617 PRK06550, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 235
Score = 29.2 bits (66), Expect = 2.8
Identities = 25/90 (27%), Positives = 40/90 (44%), Gaps = 8/90 (8%)
Query: 189 DKRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAKDLVTSLNPNLVIDYNEP-EAMHS 247
K VL+ GA+ G+G + A +V D DL + + L +D ++ E +
Sbjct: 5 TKTVLITGAASGIGLAQARAFLAQGAQVYGVDKQDKPDLSGNFH-FLQLDLSDDLEPLFD 63
Query: 248 IAGAGPYDVILDAAGIPLDQINSYLPFLKT 277
+ D++ + AGI LD Y P L T
Sbjct: 64 WVPS--VDILCNTAGI-LDD---YKPLLDT 87
>gnl|CDD|176238 cd08277, liver_alcohol_DH_like, Liver alcohol dehydrogenase.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. There are 7 vertebrate ADH 7
classes, 6 of which have been identified in humans.
Class III, glutathione-dependent formaldehyde
dehydrogenase, has been identified as the primordial
form and exists in diverse species, including plants,
micro-organisms, vertebrates, and invertebrates. Class
I, typified by liver dehydrogenase, is an evolving
form. Gene duplication and functional specialization of
ADH into ADH classes and subclasses created numerous
forms in vertebrates. For example, the A, B and C
(formerly alpha, beta, gamma) human class I subunits
have high overall structural similarity, but differ in
the substrate binding pocket and therefore in substrate
specificity. In human ADH catalysis, the zinc ion helps
coordinate the alcohol, followed by deprotonation of a
histidine (His-51), the ribose of NAD, a serine
(Ser-48) , then the alcohol, which allows the transfer
of a hydride to NAD+, creating NADH and a zinc-bound
aldehyde or ketone. In yeast and some bacteria, the
active site zinc binds an aldehyde, polarizing it, and
leading to the reverse reaction. ADH is a member of the
medium chain alcohol dehydrogenase family (MDR), which
has a NAD(P)(H)-binding domain in a Rossmann fold of an
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES.
These proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
have 2 tightly bound zinc atoms per subunit, a catalytic
zinc at the active site and a structural zinc in a lobe
of the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
Length = 365
Score = 29.6 bits (67), Expect = 3.1
Identities = 19/75 (25%), Positives = 31/75 (41%), Gaps = 17/75 (22%)
Query: 53 KSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQLETCSVEPVLEFPLTLGRDFCGKIV 112
K+ +V ++M A SV D+ + G+ FP+ LG + G +
Sbjct: 26 KANEVRIKMLATSVCHTDILAIEGF-----------------KATLFPVILGHEGAGIVE 68
Query: 113 AKGPRVTDLNIDDVV 127
+ G VT+L D V
Sbjct: 69 SVGEGVTNLKPGDKV 83
>gnl|CDD|133448 cd01080, NAD_bind_m-THF_DH_Cyclohyd, NADP binding domain of
methylene-tetrahydrofolate dehydrogenase/cyclohydrolase.
NADP binding domain of the Methylene-Tetrahydrofolate
Dehydrogenase/cyclohydrolase (m-THF DH/cyclohydrolase)
bifunctional enzyme. Tetrahydrofolate is a versatile
carrier of activated one-carbon units. The major
one-carbon folate donors are N-5 methyltetrahydrofolate,
N5,N10-m-THF, and N10-formayltetrahydrofolate. The
oxidation of metabolic intermediate m-THF to m-THF
requires the enzyme m-THF DH. In addition, most DHs also
have an associated cyclohydrolase activity which
catalyzes its hydrolysis to N10-formyltetrahydrofolate.
m-THF DH is typically found as part of a multifunctional
protein in eukaryotes. NADP-dependent m-THF DH in
mammals, birds and yeast are components of a
trifunctional enzyme with DH, cyclohydrolase, and
synthetase activities. Certain eukaryotic cells also
contain homodimeric bifunctional DH/cyclodrolase form.
In bacteria, monofucntional DH, as well as bifunctional
m-THF m-THF DHm-THF DHDH/cyclodrolase are found. In
addition, yeast (S. cerevisiae) also express an
monofunctional DH. This family contains the bifunctional
DH/cyclohydrolase. M-THF DH, like other amino acid
DH-like NAD(P)-binding domains, is a member of the
Rossmann fold superfamily which includes glutamate,
leucine, and phenylalanine DHs, m-THF DH,
methylene-tetrahydromethanopterin DH, m-THF
DH/cyclohydrolase, Shikimate DH-like proteins, malate
oxidoreductases, and glutamyl tRNA reductase. Amino acid
DHs catalyze the deamination of amino acids to keto
acids with NAD(P)+ as a cofactor. The NAD(P)-binding
Rossmann fold superfamily includes a wide variety of
protein families including NAD(P)- binding domains of
alcohol DHs, tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DH, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains.
Length = 168
Score = 28.7 bits (65), Expect = 3.6
Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 1/41 (2%)
Query: 187 PRDKRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAKDL 227
K+V+V+G S VG LL + VT C K+L
Sbjct: 42 LAGKKVVVVGRSNIVGKPLAALLLNRNA-TVTVCHSKTKNL 81
>gnl|CDD|223498 COG0421, SpeE, Spermidine synthase [Amino acid transport and
metabolism].
Length = 282
Score = 29.3 bits (66), Expect = 3.7
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 2/43 (4%)
Query: 183 GLVYPRDKRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAK 225
L +P KRVL++G GG G ++LK +E +T D
Sbjct: 71 LLAHPNPKRVLIIG--GGDGGTLREVLKHLPVERITMVEIDPA 111
>gnl|CDD|130833 TIGR01772, MDH_euk_gproteo, malate dehydrogenase, NAD-dependent.
This model represents the NAD-dependent malate
dehydrogenase found in eukaryotes and certain gamma
proteobacteria. The enzyme is involved in the citric
acid cycle as well as the glyoxalate cycle. Several
isoforms exidt in eukaryotes. In S. cereviseae, for
example, there are cytoplasmic, mitochondrial and
peroxisomal forms. Although malate dehydrogenases have
in some cases been mistaken for lactate dehydrogenases
due to the similarity of these two substrates and the
apparent ease with which evolution can toggle these
activities, critical residues have been identified which
can discriminate between the two activities. At the time
of the creation of this model no hits above the trusted
cutoff contained critical residues typical of lactate
dehydrogenases [Energy metabolism, TCA cycle].
Length = 312
Score = 29.3 bits (66), Expect = 3.7
Identities = 26/84 (30%), Positives = 37/84 (44%), Gaps = 16/84 (19%)
Query: 191 RVLVLGASGGVGTMAVQLLKA---------WDIEVVTTCSGDAKDLVTSLNPNLVIDYNE 241
+V VLGA+GG+G LLK +DI G A DL V ++
Sbjct: 1 KVAVLGAAGGIGQPLSLLLKLQPYVSELSLYDIAGAA---GVAADLSHIPTAASVKGFSG 57
Query: 242 PEAMHSIA-GAGPYDVILDAAGIP 264
E + + GA DV++ AG+P
Sbjct: 58 EEGLENALKGA---DVVVIPAGVP 78
>gnl|CDD|133452 cd05213, NAD_bind_Glutamyl_tRNA_reduct, NADP-binding domain of
glutamyl-tRNA reductase. Glutamyl-tRNA reductase
catalyzes the conversion of glutamyl-tRNA to
glutamate-1-semialdehyde, initiating the synthesis of
tetrapyrrole. Whereas tRNAs are generally associated
with peptide bond formation in protein translation, here
the tRNA activates glutamate in the initiation of
tetrapyrrole biosynthesis in archaea, plants and many
bacteria. In the first step, activated glutamate is
reduced to glutamate-1-semi-aldehyde via the NADPH
dependent glutamyl-tRNA reductase. Glutamyl-tRNA
reductase forms a V-shaped dimer. Each monomer has 3
domains: an N-terminal catalytic domain, a classic
nucleotide binding domain, and a C-terminal dimerization
domain. Although the representative structure 1GPJ lacks
a bound NADPH, a theoretical binding pocket has been
described. (PMID 11172694). Amino acid dehydrogenase
(DH)-like NAD(P)-binding domains are members of the
Rossmann fold superfamily and include glutamate,
leucine, and phenylalanine DHs, methylene
tetrahydrofolate DH, methylene-tetrahydromethanopterin
DH, methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+ as
a cofactor. The NAD(P)-binding Rossmann fold superfamily
includes a wide variety of protein families including
NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DH, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 311
Score = 29.2 bits (66), Expect = 3.8
Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 12/81 (14%)
Query: 188 RDKRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGD---AKDLVTSLNPNLVIDYNE-PE 243
+ K+VLV+GA G +G +A + L A + +T + A++L L N + +E E
Sbjct: 177 KGKKVLVIGA-GEMGELAAKHLAAKGVAEITIANRTYERAEELAKELGGN-AVPLDELLE 234
Query: 244 AMHSIAGAGPYDVILDAAGIP 264
++ DV++ A G P
Sbjct: 235 LLNE------ADVVISATGAP 249
>gnl|CDD|187632 cd05374, 17beta-HSD-like_SDR_c, 17beta hydroxysteroid
dehydrogenase-like, classical (c) SDRs.
17beta-hydroxysteroid dehydrogenases are a group of
isozymes that catalyze activation and inactivation of
estrogen and androgens. SDRs are a functionally diverse
family of oxidoreductases that have a single domain with
a structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH
numbering) contributing to the active site; while
substrate binding is in the C-terminal region, which
determines specificity. The standard reaction mechanism
is a 4-pro-S hydride transfer and proton relay involving
the conserved Tyr and Lys, a water molecule stabilized
by Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P)-binding motif and missing or
unusual active site residues. Reactions catalyzed within
the SDR family include isomerization, decarboxylation,
epimerization, C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 248
Score = 29.1 bits (66), Expect = 3.8
Identities = 25/87 (28%), Positives = 39/87 (44%), Gaps = 12/87 (13%)
Query: 190 KRVLVLGASGGVG-TMAVQLLKAWDIEVVTTC--SGDAKDLVTSLNPN---LVIDYNEPE 243
K VL+ G S G+G +A+ L V+ T + L LN N L +D + E
Sbjct: 1 KVVLITGCSSGIGLALALALAAQGYR-VIATARNPDKLESLGELLNDNLEVLELDVTDEE 59
Query: 244 AMHS-----IAGAGPYDVILDAAGIPL 265
++ + I G DV+++ AG L
Sbjct: 60 SIKAAVKEVIERFGRIDVLVNNAGYGL 86
>gnl|CDD|181044 PRK07577, PRK07577, short chain dehydrogenase; Provisional.
Length = 234
Score = 28.9 bits (65), Expect = 3.8
Identities = 20/83 (24%), Positives = 29/83 (34%), Gaps = 7/83 (8%)
Query: 189 DKRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAKDLVTSLNPNLVIDYNEP----EA 244
+ VLV GA+ G+G L +V+ D L D +
Sbjct: 3 SRTVLVTGATKGIGLALSLRLANLGHQVIGIARSAIDDFPGEL---FACDLADIEQTAAT 59
Query: 245 MHSIAGAGPYDVILDAAGIPLDQ 267
+ I P D I++ GI L Q
Sbjct: 60 LAQINEIHPVDAIVNNVGIALPQ 82
>gnl|CDD|212538 cd11592, Agmatinase_PAH, Agmatinase-like family includes
proclavaminic acid amidinohydrolase. This agmatinase
subfamily contains bacterial and fungal/metazoan
enzymes, including proclavaminic acid amidinohydrolase
(PAH, EC 3.5.3.22) and Pseudomonas aeruginosa
guanidinobutyrase (GbuA) and guanidinopropionase (GpuA).
PAH hydrolyzes amidinoproclavaminate to yield
proclavaminate and urea in clavulanic acid biosynthesis.
Clavulanic acid is an effective inhibitor of
beta-lactamases and is used in combination with
amoxicillin to prevent the beta-lactam rings of the
antibiotic from hydrolysis and, thus keeping the
antibiotic biologically active. GbuA hydrolyzes
4-guanidinobutyrate (4-GB) into 4-aminobutyrate and urea
while GpuA hydrolyzes 3-guanidinopropionate (3-GP) into
beta-alanine and urea. Mutation studies show that
significant variations in two active site loops in these
two enzymes may be important for substrate specificity.
This subfamily belongs to the ureohydrolase superfamily,
which includes arginase, agmatinase, proclavaminate
amidinohydrolase, and formiminoglutamase.
Length = 289
Score = 29.0 bits (66), Expect = 4.0
Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 10/50 (20%)
Query: 66 VNPIDVAMLGGYGNVVLN------SLRQLETCSVEPVLE---FPLTLGRD 106
V+P D + G+V + +L Q+E + +L PLTLG D
Sbjct: 59 VDPFDWLKVVDCGDVPVTPGDIEDALEQIEE-AYRAILAAGPRPLTLGGD 107
>gnl|CDD|176467 cd01595, Adenylsuccinate_lyase_like, Adenylsuccinate lyase
(ASL)_like. This group contains ASL, prokaryotic-type
3-carboxy-cis,cis-muconate cycloisomerase (pCMLE), and
related proteins. These proteins are members of the
Lyase class I family. Members of this family for the
most part catalyze similar beta-elimination reactions in
which a C-N or C-O bond is cleaved with the release of
fumarate as one of the products. These proteins are
active as tetramers. The four active sites of the
homotetrameric enzyme are each formed by residues from
three different subunits. ASL catalyzes two steps in the
de novo purine biosynthesis: the conversion of
5-aminoimidazole-(N-succinylocarboxamide) ribotide
(SAICAR) into 5-aminoimidazole-4-carboxamide ribotide
(AICAR) and; the conversion of adenylsuccinate (SAMP)
into adenosine monophosphate (AMP). pCMLE catalyzes the
cyclization of 3-carboxy-cis,cis-muconate (3CM) to
4-carboxy-muconolactone, in the beta-ketoadipate
pathway. ASL deficiency has been linked to several
pathologies including psychomotor retardation with
autistic features, epilepsy and muscle wasting.
Length = 381
Score = 29.0 bits (66), Expect = 4.4
Identities = 14/27 (51%), Positives = 15/27 (55%), Gaps = 2/27 (7%)
Query: 190 KRVLVLGASGGVGTMAVQLLKAWDIEV 216
+RVLV G SG VGT A L EV
Sbjct: 168 ERVLVGGISGAVGTHAS--LGPKGPEV 192
>gnl|CDD|176240 cd08279, Zn_ADH_class_III, Class III alcohol dehydrogenase.
Glutathione-dependent formaldehyde dehydrogenases (FDHs,
Class III ADH) are members of the zinc-dependent/medium
chain alcohol dehydrogenase family. FDH converts
formaldehyde and NAD(P) to formate and NAD(P)H. The
initial step in this process the spontaneous formation
of a S-(hydroxymethyl)glutathione adduct from
formaldehyde and glutathione, followed by FDH-mediated
oxidation (and detoxification) of the adduct to
S-formylglutathione. NAD(P)(H)-dependent oxidoreductases
are the major enzymes in the interconversion of alcohols
and aldehydes or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. Class III ADH are also known as
glutathione-dependent formaldehyde dehydrogenase (FDH),
which convert aldehydes to corresponding carboxylic acid
and alcohol. ADH is a member of the medium chain
alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of an
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
Length = 363
Score = 28.7 bits (65), Expect = 5.2
Identities = 26/75 (34%), Positives = 35/75 (46%), Gaps = 13/75 (17%)
Query: 137 GSFSKLILADSALVHKKPSNISDEEAA----GVLYTGLTAWSALQITAALGLVYPRDKRV 192
G+F++ + A V K +I + AA GV T A+ TA V P D V
Sbjct: 135 GTFAEYTVVPEASVVKIDDDIPLDRAALLGCGVT----TGVGAVVNTAR---VRPGDT-V 186
Query: 193 LVLGASGGVGTMAVQ 207
V+G GGVG A+Q
Sbjct: 187 AVIGC-GGVGLNAIQ 200
>gnl|CDD|187548 cd05237, UDP_invert_4-6DH_SDR_e, UDP-Glcnac (UDP-linked
N-acetylglucosamine) inverting 4,6-dehydratase, extended
(e) SDRs. UDP-Glcnac inverting 4,6-dehydratase was
identified in Helicobacter pylori as the hexameric flaA1
gene product (FlaA1). FlaA1 is hexameric, possesses
UDP-GlcNAc-inverting 4,6-dehydratase activity, and
catalyzes the first step in the creation of a
pseudaminic acid derivative in protein glycosylation.
Although this subgroup has the NADP-binding motif
characteristic of extended SDRs, its members tend to
have a Met substituted for the active site Tyr found in
most SDR families. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 287
Score = 28.7 bits (65), Expect = 5.2
Identities = 18/84 (21%), Positives = 32/84 (38%), Gaps = 11/84 (13%)
Query: 189 DKRVLVLGASGGVG-TMAVQLLKAWDIEVVTTCSGDAK--DLVTSLNPNLVI-------- 237
K +LV G +G +G + Q+LK +++ + K +LV L
Sbjct: 2 GKTILVTGGAGSIGSELVRQILKFGPKKLIVFDRDENKLHELVRELRSRFPHDKLRFIIG 61
Query: 238 DYNEPEAMHSIAGAGPYDVILDAA 261
D + E + D++ AA
Sbjct: 62 DVRDKERLRRAFKERGPDIVFHAA 85
>gnl|CDD|200085 TIGR01214, rmlD, dTDP-4-dehydrorhamnose reductase. This enzyme
catalyzes the last of 4 steps in making dTDP-rhamnose, a
precursor of LPS core antigen, O-antigen, etc [Cell
envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides].
Length = 287
Score = 28.5 bits (64), Expect = 5.5
Identities = 18/71 (25%), Positives = 28/71 (39%), Gaps = 13/71 (18%)
Query: 191 RVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAKDLVTSLNPNLVIDYNEPEAMHSIAG 250
R+L+ GA+G +G VQ L VV D +PEA+ +
Sbjct: 1 RILITGANGQLGRELVQQLSPEGRVVVALTRSQL-------------DLTDPEALERLLR 47
Query: 251 AGPYDVILDAA 261
A D +++ A
Sbjct: 48 AIRPDAVVNTA 58
>gnl|CDD|176226 cd08265, Zn_ADH3, Alcohol dehydrogenases of the MDR family. This
group resembles the zinc-dependent alcohol dehydrogenase
and has the catalytic and structural zinc-binding sites
characteristic of this group. The medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines. Other MDR members have only a catalytic zinc,
and some contain no coordinated zinc.
Length = 384
Score = 28.6 bits (64), Expect = 5.5
Identities = 21/85 (24%), Positives = 35/85 (41%), Gaps = 17/85 (20%)
Query: 47 VKTPILKSKDVLVEMKAVSVNPIDVAML----GGYGNVVLNSLRQLETCSVEPVLEFPLT 102
V P LK ++L+ +KA + D+ + GY +L + EFP+
Sbjct: 44 VPVPNLKPDEILIRVKACGICGSDIHLYETDKDGY---ILYP----------GLTEFPVV 90
Query: 103 LGRDFCGKIVAKGPRVTDLNIDDVV 127
+G +F G + G V + D V
Sbjct: 91 IGHEFSGVVEKTGKNVKNFEKGDPV 115
>gnl|CDD|187578 cd05269, TMR_SDR_a, triphenylmethane reductase (TMR)-like proteins,
NMRa-like, atypical (a) SDRs. TMR is an atypical
NADP-binding protein of the SDR family. It lacks the
active site residues of the SDRs but has a glycine rich
NAD(P)-binding motif that matches the extended SDRs.
Proteins in this subgroup however, are more similar in
length to the classical SDRs. TMR was identified as a
reducer of triphenylmethane dyes, important
environmental pollutants. This subgroup also includes
Escherichia coli NADPH-dependent quinine oxidoreductase
(QOR2), which catalyzes two-electron reduction of
quinone; but is unlikely to play a major role in
protecting against quinone cytotoxicity. Atypical SDRs
are distinct from classical SDRs. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 272
Score = 28.4 bits (64), Expect = 5.6
Identities = 13/25 (52%), Positives = 16/25 (64%)
Query: 193 LVLGASGGVGTMAVQLLKAWDIEVV 217
LV GA+G +GT V+LL A VV
Sbjct: 2 LVTGATGKLGTAVVELLLAKVASVV 26
>gnl|CDD|222171 pfam13489, Methyltransf_23, Methyltransferase domain. This family
appears to be a methyltransferase domain.
Length = 154
Score = 27.8 bits (62), Expect = 6.0
Identities = 21/84 (25%), Positives = 32/84 (38%), Gaps = 13/84 (15%)
Query: 175 ALQITAALGLVYPRDKRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAKDLVTSLNPN 234
++ A L RVL +G G G + +LL+ +V A L+ SL
Sbjct: 9 LARLLARLLPRLKPGGRVLDIG--CGTGILL-RLLRERGFDVTGVDPSPAAVLIFSLF-- 63
Query: 235 LVIDYNEPEAMHSIAGAGPYDVIL 258
D +P + G YD+I
Sbjct: 64 ---DAPDPAVLA-----GKYDLIT 79
>gnl|CDD|131872 TIGR02825, B4_12hDH, leukotriene B4
12-hydroxydehydrogenase/15-oxo-prostaglandin
13-reductase. Leukotriene B4 12-hydroxydehydrogenase is
an NADP-dependent enzyme of arachidonic acid metabolism,
responsible for converting leukotriene B4 to the much
less active metabolite 12-oxo-leukotriene B4. The BRENDA
database lists leukotriene B4 12-hydroxydehydrogenase as
one of the synonyms of 2-alkenal reductase (EC
1.3.1.74), while 1.3.1.48 is 15-oxoprostaglandin
13-reductase.
Length = 325
Score = 28.4 bits (63), Expect = 6.1
Identities = 27/99 (27%), Positives = 45/99 (45%), Gaps = 10/99 (10%)
Query: 169 GLTAW-SALQITAALGLVYPRDKRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAK-D 226
GLTA+ L+I G + V+V A+G VG++ Q+ K +VV D K
Sbjct: 123 GLTAYFGLLEICGVKG-----GETVMVNAAAGAVGSVVGQIAKLKGCKVVGAAGSDEKVA 177
Query: 227 LVTSLNPNLVIDYNEPEAM-HSIAGAGP--YDVILDAAG 262
+ L ++ +Y +++ ++ A P YD D G
Sbjct: 178 YLKKLGFDVAFNYKTVKSLEETLKKASPDGYDCYFDNVG 216
>gnl|CDD|187568 cd05258, CDP_TE_SDR_e, CDP-tyvelose 2-epimerase, extended (e) SDRs.
CDP-tyvelose 2-epimerase is a tetrameric SDR that
catalyzes the conversion of CDP-D-paratose to
CDP-D-tyvelose, the last step in tyvelose biosynthesis.
This subgroup is a member of the extended SDR subfamily,
with a characteristic active site tetrad and NAD-binding
motif. Extended SDRs are distinct from classical SDRs.
In addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 337
Score = 28.4 bits (64), Expect = 6.1
Identities = 8/28 (28%), Positives = 14/28 (50%)
Query: 190 KRVLVLGASGGVGTMAVQLLKAWDIEVV 217
RVL+ G +G +G+ + EV+
Sbjct: 1 MRVLITGGAGFIGSNLARFFLKQGWEVI 28
>gnl|CDD|133043 cd06421, CESA_CelA_like, CESA_CelA_like are involved in the
elongation of the glucan chain of cellulose. Family of
proteins related to Agrobacterium tumefaciens CelA and
Gluconacetobacter xylinus BscA. These proteins are
involved in the elongation of the glucan chain of
cellulose, an aggregate of unbranched polymers of
beta-1,4-linked glucose residues. They are putative
catalytic subunit of cellulose synthase, which is a
glycosyltransferase using UDP-glucose as the substrate.
The catalytic subunit is an integral membrane protein
with 6 transmembrane segments and it is postulated that
the protein is anchored in the membrane at the
N-terminal end.
Length = 234
Score = 28.3 bits (64), Expect = 6.1
Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 3/44 (6%)
Query: 178 ITAALGLVYPRDK-RVLVL--GASGGVGTMAVQLLKAWDIEVVT 218
+ AAL + YP DK RV VL G + +A +L + +T
Sbjct: 21 LRAALAIDYPHDKLRVYVLDDGRRPELRALAAELGVEYGYRYLT 64
>gnl|CDD|214863 smart00859, Semialdhyde_dh, Semialdehyde dehydrogenase, NAD binding
domain. The semialdehyde dehydrogenase family is found
in N-acetyl-glutamine semialdehyde dehydrogenase (AgrC),
which is involved in arginine biosynthesis, and
aspartate-semialdehyde dehydrogenase, an enzyme involved
in the biosynthesis of various amino acids from
aspartate. This family is also found in yeast and fungal
Arg5,6 protein, which is cleaved into the enzymes
N-acety-gamma-glutamyl-phosphate reductase and
acetylglutamate kinase. These are also involved in
arginine biosynthesis. All proteins in this entry
contain a NAD binding region of semialdehyde
dehydrogenase.
Length = 123
Score = 27.5 bits (62), Expect = 6.4
Identities = 15/79 (18%), Positives = 33/79 (41%), Gaps = 12/79 (15%)
Query: 191 RVLVLGASGGVGTMAVQLLKA---WDIEVVTTCSGDA----KDLVTSLNPNLVIDYNEPE 243
+V ++GA+G VG ++LL +++ + S A + L +V++ + P+
Sbjct: 1 KVAIVGATGYVGQELLRLLAEHPDFELTALAASSRSAGKKVSEAGPHLKGEVVLELDPPD 60
Query: 244 AMHSIAGAGPYDVILDAAG 262
D++ A
Sbjct: 61 FEELAV-----DIVFLALP 74
>gnl|CDD|236057 PRK07578, PRK07578, short chain dehydrogenase; Provisional.
Length = 199
Score = 27.9 bits (63), Expect = 6.5
Identities = 22/76 (28%), Positives = 35/76 (46%), Gaps = 15/76 (19%)
Query: 190 KRVLVLGASGGVGTMAVQLLKAWDIEVVTT--CSGDAKDLVTSLNPNLVIDYNEPEAMHS 247
++LV+GASG +G V L EV+T SGD + +D +P ++ +
Sbjct: 1 MKILVIGASGTIGRAVVAELSK-RHEVITAGRSSGDVQ-----------VDITDPASIRA 48
Query: 248 -IAGAGPYDVILDAAG 262
G D ++ AAG
Sbjct: 49 LFEKVGKVDAVVSAAG 64
>gnl|CDD|180984 PRK07454, PRK07454, short chain dehydrogenase; Provisional.
Length = 241
Score = 28.0 bits (63), Expect = 6.6
Identities = 27/87 (31%), Positives = 39/87 (44%), Gaps = 13/87 (14%)
Query: 190 KRVLVLGASGGVG-TMAVQLLKA-WDIEVVTTCSGDAKDLVTSLNPN------LVIDYNE 241
R L+ GAS G+G A+ KA WD+ +V + L L ID +
Sbjct: 7 PRALITGASSGIGKATALAFAKAGWDLALVARSQDALEALAAELRSTGVKAAAYSIDLSN 66
Query: 242 PEAM-HSIAGA----GPYDVILDAAGI 263
PEA+ IA G DV+++ AG+
Sbjct: 67 PEAIAPGIAELLEQFGCPDVLINNAGM 93
>gnl|CDD|132245 TIGR03201, dearomat_had, 6-hydroxycyclohex-1-ene-1-carbonyl-CoA
dehydrogenase. Members of this protein family are
6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase, an
enzyme in the anaerobic metabolism of aromatic enzymes
by way of benzoyl-CoA, as seen in Thauera aromatica,
Geobacter metallireducens, and Azoarcus sp. The
experimentally characterized form from T. aromatica uses
only NAD+, not NADP+. Note that Rhodopseudomonas
palustris uses a different pathway to perform a similar
degradation of benzoyl-CoA to 3-hydroxpimelyl-CoA.
Length = 349
Score = 28.3 bits (63), Expect = 6.6
Identities = 68/306 (22%), Positives = 102/306 (33%), Gaps = 69/306 (22%)
Query: 30 WQISSYGGADELQFNDNVKTPILKSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQLE 89
W ++ G + V+ P L + DV+V++ V D L Y
Sbjct: 2 WMMTEPG---KPMVKTRVEIPELGAGDVVVKVAGCGVCHTD---LSYYYM---------- 45
Query: 90 TCSVEPVLEFPLTLGRDFCGKIVAKGPRVTDLNIDDVVYGVIQPHKQGSFSKLILADSAL 149
V PL LG + G+++ G V+ + P + K
Sbjct: 46 --GVRTNHALPLALGHEISGRVIQAGAGAASWIGKAVIVPAVIPCGECELCKTGRGTICR 103
Query: 150 VHKKPSN------------------ISDEE--AAGVLYTGLTAWSALQIT----AALGLV 185
K P N + DE AA L + A +T AA+
Sbjct: 104 AQKMPGNDMQGGFASHIVVPAKGLCVVDEARLAAAGLPLEHVSVVADAVTTPYQAAVQAG 163
Query: 186 YPRDKRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAKDLVTSLNPNLVIDYNEPEAM 245
+ V+V+GA GGVG VQ KA VV ID + PE +
Sbjct: 164 LKKGDLVIVIGA-GGVGGYMVQTAKAMGAAVVA------------------IDID-PEKL 203
Query: 246 HSIAGAGPYDVILDAAGIPLDQINSYLPFLKTGKFSKFVTLRSPFLKNTDSLGLVPGLVK 305
+ G G D+ L+ ++ + F+K LRS K + G PG +
Sbjct: 204 EMMKGFGA-DLTLNPKDKSAREVKKLI-----KAFAKARGLRSTGWKIFECSGSKPGQ-E 256
Query: 306 NAFDLL 311
+A LL
Sbjct: 257 SALSLL 262
>gnl|CDD|171820 PRK12936, PRK12936, 3-ketoacyl-(acyl-carrier-protein) reductase
NodG; Reviewed.
Length = 245
Score = 28.3 bits (63), Expect = 6.9
Identities = 25/88 (28%), Positives = 41/88 (46%), Gaps = 12/88 (13%)
Query: 190 KRVLVLGASGGVGTMAVQLLKAWD---------IEVVTTCSGDAKDLVTSLNPNLVIDYN 240
++ LV GASGG+G +LL A +E + + + + V NL D +
Sbjct: 7 RKALVTGASGGIGEEIARLLHAQGAIVGLHGTRVEKLEALAAELGERVKIFPANLS-DRD 65
Query: 241 EPEAMHSIAGA--GPYDVILDAAGIPLD 266
E +A+ A A D++++ AGI D
Sbjct: 66 EVKALGQKAEADLEGVDILVNNAGITKD 93
>gnl|CDD|133446 cd01078, NAD_bind_H4MPT_DH, NADP binding domain of methylene
tetrahydromethanopterin dehydrogenase. Methylene
Tetrahydromethanopterin Dehydrogenase (H4MPT DH) NADP
binding domain. NADP-dependent H4MPT DH catalyzes the
dehydrogenation of methylene- H4MPT and
methylene-tetrahydrofolate (H4F) with NADP+ as cofactor.
H4F and H4MPT are both cofactors that carry the
one-carbon units between the formyl and methyl oxidation
level. H4F and H4MPT are structurally analogous to each
other with respect to the pterin moiety, but each has
distinct side chain. H4MPT is present only in anaerobic
methanogenic archaea and aerobic methylotrophic
proteobacteria. H4MPT seems to have evolved
independently from H4F and functions as a distinct
carrier in C1 metabolism. Amino acid DH-like
NAD(P)-binding domains are members of the Rossmann fold
superfamily and include glutamate, leucine, and
phenylalanine DHs, methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase, Shikimate
DH-like proteins, malate oxidoreductases, and glutamyl
tRNA reductase. Amino acid DHs catalyze the deamination
of amino acids to keto acids with NAD(P)+ as a cofactor.
The NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha-beta-alpha configuration.
NAD binding involves numerous hydrogen and van der Waals
contacts.
Length = 194
Score = 27.7 bits (62), Expect = 7.2
Identities = 15/48 (31%), Positives = 20/48 (41%)
Query: 162 AAGVLYTGLTAWSALQITAALGLVYPRDKRVLVLGASGGVGTMAVQLL 209
+ G T A +A L + K +VLG +G VG A LL
Sbjct: 1 SNGSNTTAAAAVAAAGKALELMGKDLKGKTAVVLGGTGPVGQRAAVLL 48
>gnl|CDD|234595 PRK00048, PRK00048, dihydrodipicolinate reductase; Provisional.
Length = 257
Score = 28.2 bits (64), Expect = 7.4
Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 7/70 (10%)
Query: 191 RVLVLGASGGVGTMAVQLL-KAWDIEVVTTCSGDAKDLVTSLNPNLVIDYNEPEAMHSIA 249
+V V GASG +G ++ + A D+E+V LV V ++ EA+ +A
Sbjct: 3 KVAVAGASGRMGRELIEAVEAAEDLELVAAVDRPGSPLVGQGALG-VAITDDLEAV--LA 59
Query: 250 GAGPYDVILD 259
A DV++D
Sbjct: 60 DA---DVLID 66
>gnl|CDD|187602 cd05344, BKR_like_SDR_like, putative beta-ketoacyl acyl carrier
protein [ACP] reductase (BKR)-like, SDR. This subgroup
resembles the SDR family, but does not have a perfect
match to the NAD-binding motif or the catalytic tetrad
characteristic of the SDRs. It includes the SDRs, Q9HYA2
from Pseudomonas aeruginosa PAO1 and APE0912 from
Aeropyrum pernix K1. BKR catalyzes the NADPH-dependent
reduction of ACP in the first reductive step of de novo
fatty acid synthesis (FAS). FAS consists of four
elongation steps, which are repeated to extend the fatty
acid chain through the addition of two-carbo units from
malonyl acyl-carrier protein (ACP): condensation,
reduction, dehydration, and a final reduction. Type II
FAS, typical of plants and many bacteria, maintains
these activities on discrete polypeptides, while type I
FAS utilizes one or two multifunctional polypeptides.
BKR resembles enoyl reductase, which catalyzes the
second reduction step in FAS. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRS are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes have a 3-glycine N-terminal
NAD(P)(H)-binding pattern (typically, TGxxxGxG in
classical SDRs and TGxxGxxG in extended SDRs), while
substrate binding is in the C-terminal region. A
critical catalytic Tyr residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering), is often found in a conserved YXXXK pattern.
In addition to the Tyr and Lys, there is often an
upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn
(Asn-107, 15-PGDH numbering) or additional Ser,
contributing to the active site. Substrates for these
enzymes include sugars, steroids, alcohols, and aromatic
compounds. The standard reaction mechanism is a proton
relay involving the conserved Tyr and Lys, as well as
Asn (or Ser). Some SDR family members, including 17
beta-hydroxysteroid dehydrogenase contain an additional
helix-turn-helix motif that is not generally found among
SDRs.
Length = 253
Score = 28.0 bits (63), Expect = 7.4
Identities = 12/40 (30%), Positives = 19/40 (47%), Gaps = 3/40 (7%)
Query: 189 DKRVLVLGASGGVG-TMAVQLLKAWDIEVVTTCSGDAKDL 227
K LV AS G+G +A L + V C+ + ++L
Sbjct: 1 GKVALVTAASSGIGLAIARALAREGA--RVAICARNRENL 38
>gnl|CDD|183778 PRK12829, PRK12829, short chain dehydrogenase; Provisional.
Length = 264
Score = 28.1 bits (63), Expect = 7.7
Identities = 24/101 (23%), Positives = 38/101 (37%), Gaps = 16/101 (15%)
Query: 174 SALQITAALGLVYPRDKRVLVLGASGGVG-TMAVQLLKAWDIEVVTTCSGDAKDLVTSLN 232
SA+ + L RVLV G + G+G +A +A V S A +
Sbjct: 1 SAIDLLKPLD-----GLRVLVTGGASGIGRAIAEAFAEAGARVHVCDVSEAALAATAARL 55
Query: 233 PNLVI-----DYNEPEAMHSIAGA-----GPYDVILDAAGI 263
P + D +P + + G DV+++ AGI
Sbjct: 56 PGAKVTATVADVADPAQVERVFDTAVERFGGLDVLVNNAGI 96
>gnl|CDD|182765 PRK10834, PRK10834, vancomycin high temperature exclusion protein;
Provisional.
Length = 239
Score = 27.8 bits (62), Expect = 7.9
Identities = 16/34 (47%), Positives = 18/34 (52%), Gaps = 4/34 (11%)
Query: 239 YNEPEAMHS---IAGAGPYDVILDAAGI-PLDQI 268
YNEP M AG P D++LD AG LD I
Sbjct: 96 YNEPMTMRKDLIAAGVDPSDIVLDYAGFRTLDSI 129
>gnl|CDD|226444 COG3934, COG3934, Endo-beta-mannanase [Carbohydrate transport and
metabolism].
Length = 587
Score = 28.3 bits (63), Expect = 8.1
Identities = 14/37 (37%), Positives = 17/37 (45%)
Query: 297 LGLVPGLVKNAFDLLKSNFESGELCKTNTIRWGFFMP 333
L L PGLVK D K+N E E+ I + F
Sbjct: 510 LVLNPGLVKIGLDTNKANVEYAEIATFGGIEYRRFHV 546
>gnl|CDD|236372 PRK09072, PRK09072, short chain dehydrogenase; Provisional.
Length = 263
Score = 28.0 bits (63), Expect = 8.5
Identities = 11/14 (78%), Positives = 13/14 (92%)
Query: 189 DKRVLVLGASGGVG 202
DKRVL+ GASGG+G
Sbjct: 5 DKRVLLTGASGGIG 18
>gnl|CDD|133451 cd05212, NAD_bind_m-THF_DH_Cyclohyd_like, NAD(P) binding domain of
methylene-tetrahydrofolate dehydrogenase and
methylene-tetrahydrofolate dehydrogenase/cyclohydrolase.
NAD(P) binding domains of methylene-tetrahydrofolate
dehydrogenase (m-THF DH) and m-THF DH/cyclohydrolase
bifunctional enzymes (m-THF DH/cyclohydrolase). M-THF is
a versatile carrier of activated one-carbon units. The
major one-carbon folate donors are N-5
methyltetrahydrofolate, N5,N10-m-THF, and
N10-formayltetrahydrofolate. The oxidation of metabolic
intermediate m-THF to m-THF requires the enzyme m-THF
DH. In addition, most DHs also have an associated
cyclohydrolase activity which catalyzes its hydrolysis
to N10-formyltetrahydrofolate. m-THF DH is typically
found as part of a multifunctional protein in
eukaryotes. NADP-dependent m-THF DH in mammals, birds
and yeast are components of a trifunctional enzyme with
DH, cyclohydrolase, and synthetase activities. Certain
eukaryotic cells also contain homodimeric bifunctional
DH/cyclodrolase form. In bacteria, mono-functional DH,
as well as bifunctional DH/cyclodrolase are found. In
addition, yeast (S. cerevisiae) also express a
monofunctional DH. M-THF DH, like other amino acid
DH-like NAD(P)-binding domains, is a member of the
Rossmann fold superfamily which includes glutamate,
leucine, and phenylalanine DHs, m-THF DH,
methylene-tetrahydromethanopterin DH, m-THF
DH/cyclohydrolase, Shikimate DH-like proteins, malate
oxidoreductases, and glutamyl tRNA reductase. Amino acid
DHs catalyze the deamination of amino acids to keto
acids with NAD(P)+ as a cofactor. The NAD(P)-binding
Rossmann fold superfamily includes a wide variety of
protein families including NAD(P)- binding domains of
alcohol DHs, tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DH, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 140
Score = 27.1 bits (60), Expect = 8.8
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 190 KRVLVLGASGGVGTMAVQLLKAWDIEVVTTCSGDAKDLVTSLN 232
K+VLV+G SG VG +Q L D V +C L + ++
Sbjct: 29 KKVLVVGRSGIVGA-PLQCLLQRDGATVYSCDWKTIQLQSKVH 70
>gnl|CDD|233597 TIGR01850, argC, N-acetyl-gamma-glutamyl-phosphate reductase,
common form. This model represents the more common of
two related families of
N-acetyl-gamma-glutamyl-phosphate reductase, an enzyme
catalyzing the third step or Arg biosynthesis from Glu.
The two families differ by phylogeny, similarity
clustering, and the gap architecture in a multiple
sequence alignment. Bacterial members of this family
tend to be found within Arg biosynthesis operons [Amino
acid biosynthesis, Glutamate family].
Length = 346
Score = 27.9 bits (63), Expect = 9.0
Identities = 16/72 (22%), Positives = 31/72 (43%), Gaps = 4/72 (5%)
Query: 190 KRVLVLGASGGVGTMAVQLLK---AWDIEVVTTCSGDAKDLVTSLNPNLVIDYNEP-EAM 245
+V ++GASG G ++LL +I + + A V+ ++P+L + E +
Sbjct: 1 IKVAIVGASGYTGGELLRLLLNHPEVEITYLVSSRESAGKPVSEVHPHLRGLVDLNLEPI 60
Query: 246 HSIAGAGPYDVI 257
DV+
Sbjct: 61 DVEEILEDADVV 72
>gnl|CDD|177569 PHA03257, PHA03257, Capsid triplex subunit 2; Provisional.
Length = 316
Score = 28.1 bits (63), Expect = 9.2
Identities = 12/39 (30%), Positives = 18/39 (46%), Gaps = 4/39 (10%)
Query: 81 VLNSLRQLETCSVEPVLEFPLT----LGRDFCGKIVAKG 115
+ +L SV L FP+T L R+ K+VA+
Sbjct: 119 IFGGEDRLRLESVGLELLFPMTVPLALARELIAKVVARA 157
>gnl|CDD|129775 TIGR00692, tdh, L-threonine 3-dehydrogenase. This protein is a
tetrameric, zinc-binding, NAD-dependent enzyme of
threonine catabolism. Closely related proteins include
sorbitol dehydrogenase, xylitol dehydrogenase, and
benzyl alcohol dehydrogenase. Eukaryotic examples of
this enzyme have been demonstrated experimentally but do
not appear in database search results.E. coli His-90
modulates substrate specificity and is believed part of
the active site [Energy metabolism, Amino acids and
amines].
Length = 340
Score = 27.9 bits (62), Expect = 9.3
Identities = 39/189 (20%), Positives = 66/189 (34%), Gaps = 45/189 (23%)
Query: 47 VKTPILKSKDVLVEMKAVSVNPIDVAMLGGYGNVVLNSLRQLETCSVEPVLEFPLTLGRD 106
V P +VL+++ A S+ DV + + + ++P P +G +
Sbjct: 16 VPVPEPGPGEVLIKVLATSICGTDVHIY---------NWDEWAQSRIKP----PQVVGHE 62
Query: 107 FCGKIVAKGPRVTDLNIDDVVYG------------------------VIQPHKQGSFSKL 142
G++V GP V + + D V + G F++
Sbjct: 63 VAGEVVGIGPGVEGIKVGDYVSVETHIVCGKCYACRRGQYHVCQNTKIFGVDTDGCFAEY 122
Query: 143 ILADSALVHKKPSNISDEEAAGVLYTGLTAWSALQITAALGLVYPRDKRVLVLGASGGVG 202
+ + + K P +I E A G + L K VLV GA G +G
Sbjct: 123 AVVPAQNIWKNPKSIPPEYATIQEPLGNAVHTVLAGP-------ISGKSVLVTGA-GPIG 174
Query: 203 TMAVQLLKA 211
MA+ + KA
Sbjct: 175 LMAIAVAKA 183
>gnl|CDD|187551 cd05240, UDP_G4E_3_SDR_e, UDP-glucose 4 epimerase (G4E), subgroup
3, extended (e) SDRs. Members of this bacterial
subgroup are identified as possible sugar epimerases,
such as UDP-glucose 4 epimerase. However, while the
NAD(P)-binding motif is fairly well conserved, not all
members retain the canonical active site tetrad of the
extended SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 306
Score = 27.7 bits (62), Expect = 9.3
Identities = 11/28 (39%), Positives = 16/28 (57%), Gaps = 2/28 (7%)
Query: 192 VLVLGASGGVGTMAVQLLKAWD--IEVV 217
+LV GA+GG+G + + L A I V
Sbjct: 1 ILVTGAAGGLGRLLARRLAASPRVIGVD 28
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.320 0.138 0.407
Gapped
Lambda K H
0.267 0.0807 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,668,614
Number of extensions: 1932610
Number of successful extensions: 2305
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2129
Number of HSP's successfully gapped: 247
Length of query: 383
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 284
Effective length of database: 6,546,556
Effective search space: 1859221904
Effective search space used: 1859221904
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 60 (26.7 bits)