RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3446
(166 letters)
>gnl|CDD|187547 cd05236, FAR-N_SDR_e, fatty acyl CoA reductases (FARs), extended
(e) SDRs. SDRs are Rossmann-fold NAD(P)H-binding
proteins, many of which may function as fatty acyl CoA
reductases (FAR), acting on medium and long chain fatty
acids, and have been reported to be involved in diverse
processes such as biosynthesis of insect pheromones,
plant cuticular wax production, and mammalian wax
biosynthesis. In Arabidopsis thaliana, proteins with
this particular architecture have also been identified
as the MALE STERILITY 2 (MS2) gene product, which is
implicated in male gametogenesis. Mutations in MS2
inhibit the synthesis of exine (sporopollenin),
rendering plants unable to reduce pollen wall fatty
acids to corresponding alcohols. This N-terminal domain
shares the catalytic triad (but not the upstream Asn)
and characteristic NADP-binding motif of the extended
SDR family. 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 = 320
Score = 104 bits (261), Expect = 2e-27
Identities = 43/90 (47%), Positives = 59/90 (65%)
Query: 77 REIRQLKLFLRLKTEVPHFLEKISAVAGDVSLPGLGLSETDRELLRTNVNVIFHGAATVR 136
RE+ + KLF R + P F KI + GD+S P LGLS+ D + L VN+I H AATV
Sbjct: 47 RELLKDKLFDRGRNLNPLFESKIVPIEGDLSEPNLGLSDEDLQTLIEEVNIIIHCAATVT 106
Query: 137 FDEKIQLAVAINVLGVRAMLELAREIRQLK 166
FDE++ A++INVLG +LELA+ ++LK
Sbjct: 107 FDERLDEALSINVLGTLRLLELAKRCKKLK 136
Score = 103 bits (260), Expect = 2e-27
Identities = 41/86 (47%), Positives = 56/86 (65%)
Query: 1 LFLRLKTEVPHFLEKISAVAGDVSLPGLGLSETDRELLRTNVNVIFHGAATVRFDEKIQL 60
LF R + P F KI + GD+S P LGLS+ D + L VN+I H AATV FDE++
Sbjct: 54 LFDRGRNLNPLFESKIVPIEGDLSEPNLGLSDEDLQTLIEEVNIIIHCAATVTFDERLDE 113
Query: 61 AVAINVLGVRAMLELAREIRQLKLFL 86
A++INVLG +LELA+ ++LK F+
Sbjct: 114 ALSINVLGTLRLLELAKRCKKLKAFV 139
>gnl|CDD|219687 pfam07993, NAD_binding_4, Male sterility protein. This family
represents the C-terminal region of the male sterility
protein in a number of arabidopsis and drosophila. A
sequence-related jojoba acyl CoA reductase is also
included.
Length = 245
Score = 96.9 bits (242), Expect = 3e-25
Identities = 43/95 (45%), Positives = 58/95 (61%), Gaps = 5/95 (5%)
Query: 71 AMLELAREIRQLKLFLRLKTEVPHFLEKISAVAGDVSLPGLGLSETDRELLRTNVNVIFH 130
A+ L +E+ + LF RLK LE+I VAGD+S P LGLS+ D + L V+VI H
Sbjct: 37 ALERLRQELLKYGLFDRLKA-----LERIIPVAGDLSEPNLGLSDEDFQELAEEVDVIIH 91
Query: 131 GAATVRFDEKIQLAVAINVLGVRAMLELAREIRQL 165
AATV F E A NVLG R +L LA+++++L
Sbjct: 92 NAATVNFVEPYSDLRATNVLGTREVLRLAKQMKKL 126
Score = 91.9 bits (229), Expect = 2e-23
Identities = 35/75 (46%), Positives = 47/75 (62%)
Query: 8 EVPHFLEKISAVAGDVSLPGLGLSETDRELLRTNVNVIFHGAATVRFDEKIQLAVAINVL 67
+ LE+I VAGD+S P LGLS+ D + L V+VI H AATV F E A NVL
Sbjct: 52 DRLKALERIIPVAGDLSEPNLGLSDEDFQELAEEVDVIIHNAATVNFVEPYSDLRATNVL 111
Query: 68 GVRAMLELAREIRQL 82
G R +L LA+++++L
Sbjct: 112 GTREVLRLAKQMKKL 126
>gnl|CDD|187546 cd05235, SDR_e1, extended (e) SDRs, subgroup 1. This family
consists of an SDR module of multidomain proteins
identified as putative polyketide sythases fatty acid
synthases (FAS), and nonribosomal peptide synthases,
among others. However, unlike the usual ketoreductase
modules of FAS and polyketide synthase, these domains
are related to the extended SDRs, and have canonical
NAD(P)-binding motifs and an active site tetrad.
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 = 290
Score = 56.5 bits (137), Expect = 4e-10
Identities = 33/88 (37%), Positives = 44/88 (50%), Gaps = 7/88 (7%)
Query: 75 LAREIRQLKLFLRLKTEVPHFLEKISAVAGDVSLPGLGLSETDRELLRTNVNVIFHGAAT 134
L R I LK L L +I V GD+S P LGLS+ D + L V+VI H A
Sbjct: 41 LERLIDNLK-EYGLNLWDELELSRIKVVVGDLSKPNLGLSDDDYQELAEEVDVIIHNGAN 99
Query: 135 VRF---DEKIQLAVAINVLGVRAMLELA 159
V + E++ NVLG + +L+LA
Sbjct: 100 VNWVYPYEEL---KPANVLGTKELLKLA 124
Score = 56.1 bits (136), Expect = 5e-10
Identities = 27/68 (39%), Positives = 38/68 (55%), Gaps = 6/68 (8%)
Query: 12 FLEKISAVAGDVSLPGLGLSETDRELLRTNVNVIFHGAATVRF---DEKIQLAVAINVLG 68
L +I V GD+S P LGLS+ D + L V+VI H A V + E++ NVLG
Sbjct: 60 ELSRIKVVVGDLSKPNLGLSDDDYQELAEEVDVIIHNGANVNWVYPYEEL---KPANVLG 116
Query: 69 VRAMLELA 76
+ +L+LA
Sbjct: 117 TKELLKLA 124
>gnl|CDD|233557 TIGR01746, Thioester-redct, thioester reductase domain. This model
includes the terminal domain from the fungal alpha
aminoadipate reductase enzyme (also known as
aminoadipate semialdehyde dehydrogenase) which is
involved in the biosynthesis of lysine , as well as the
reductase-containing component of the myxochelin
biosynthetic gene cluster, MxcG. The mechanism of
reduction involves activation of the substrate by
adenylation and transfer to a covalently-linked
pantetheine cofactor as a thioester. This thioester is
then reduced to give an aldehyde (thus releasing the
product) and a regenerated pantetheine thiol. (In
myxochelin biosynthesis this aldehyde is further reduced
to an alcohol or converted to an amine by an
aminotransferase.) This is a fundamentally different
reaction than beta-ketoreductase domains of polyketide
synthases which act at a carbonyl two carbons removed
from the thioester and forms an alcohol as a product.
This domain is invariably found at the C-terminus of the
proteins which contain it (presumably because it results
in the release of the product). The majority of hits to
this model are non-ribosomal peptide synthetases in
which this domain is similarly located proximal to a
thiolation domain (pfam00550). In some cases this domain
is found at the end of a polyketide synthetase enzyme,
but is unlike ketoreductase domains which are found
before the thiolase domains. Exceptions to this observed
relationship with the thiolase domain include three
proteins which consist of stand-alone reductase domains
(GP|466833 from M. leprae, GP|435954 from Anabaena and
OMNI|NTL02SC1199 from Strep. coelicolor) and one protein
(OMNI|NTL01NS2636 from Nostoc) which contains N-terminal
homology with a small group of hypothetical proteins but
no evidence of a thiolation domain next to the putative
reductase domain. Below the noise cutoff to this model
are proteins containing more distantly related
ketoreductase and dehydratase/epimerase domains. It has
been suggested that a NADP-binding motif can be found in
the N-terminal portion of this domain that may form a
Rossman-type fold.
Length = 367
Score = 55.9 bits (135), Expect = 7e-10
Identities = 29/66 (43%), Positives = 39/66 (59%), Gaps = 6/66 (9%)
Query: 14 EKISAVAGDVSLPGLGLSETDRELLRTNVNVIFHGAATVRF---DEKIQLAVAINVLGVR 70
E+I VAGD+S P LGLS+ + E L NV+ I H A V + +++ A NVLG R
Sbjct: 61 ERIEVVAGDLSEPRLGLSDAEWERLAENVDTIVHNGALVNWVYPYSELRGA---NVLGTR 117
Query: 71 AMLELA 76
+L LA
Sbjct: 118 EVLRLA 123
Score = 55.9 bits (135), Expect = 7e-10
Identities = 29/66 (43%), Positives = 39/66 (59%), Gaps = 6/66 (9%)
Query: 97 EKISAVAGDVSLPGLGLSETDRELLRTNVNVIFHGAATVRF---DEKIQLAVAINVLGVR 153
E+I VAGD+S P LGLS+ + E L NV+ I H A V + +++ A NVLG R
Sbjct: 61 ERIEVVAGDLSEPRLGLSDAEWERLAENVDTIVHNGALVNWVYPYSELRGA---NVLGTR 117
Query: 154 AMLELA 159
+L LA
Sbjct: 118 EVLRLA 123
>gnl|CDD|187573 cd05263, MupV_like_SDR_e, Pseudomonas fluorescens MupV-like,
extended (e) SDRs. This subgroup of extended SDR family
domains have the characteristic active site tetrad and a
well-conserved NAD(P)-binding motif. This subgroup is
not well characterized, its members are annotated as
having a variety of putative functions. One
characterized member is Pseudomonas fluorescens MupV a
protein involved in the biosynthesis of Mupirocin, a
polyketide-derived antibiotic. 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 = 293
Score = 55.5 bits (134), Expect = 9e-10
Identities = 22/100 (22%), Positives = 41/100 (41%), Gaps = 9/100 (9%)
Query: 74 ELAREIRQLKLFLRLKTEV---------PHFLEKISAVAGDVSLPGLGLSETDRELLRTN 124
L ++ + +R ++ +++ + GD++ P LGLS L
Sbjct: 17 RLLENGFKVLVLVRSESLGEAHERIEEAGLEADRVRVLEGDLTQPNLGLSAAASRELAGK 76
Query: 125 VNVIFHGAATVRFDEKIQLAVAINVLGVRAMLELAREIRQ 164
V+ + H AA+ F + A N+ G +LELA +
Sbjct: 77 VDHVIHCAASYDFQAPNEDAWRTNIDGTEHVLELAARLDI 116
Score = 55.5 bits (134), Expect = 1e-09
Identities = 21/84 (25%), Positives = 35/84 (41%)
Query: 2 FLRLKTEVPHFLEKISAVAGDVSLPGLGLSETDRELLRTNVNVIFHGAATVRFDEKIQLA 61
E +++ + GD++ P LGLS L V+ + H AA+ F + A
Sbjct: 37 AHERIEEAGLEADRVRVLEGDLTQPNLGLSAAASRELAGKVDHVIHCAASYDFQAPNEDA 96
Query: 62 VAINVLGVRAMLELAREIRQLKLF 85
N+ G +LELA + +
Sbjct: 97 WRTNIDGTEHVLELAARLDIQRFH 120
>gnl|CDD|215279 PLN02503, PLN02503, fatty acyl-CoA reductase 2.
Length = 605
Score = 53.7 bits (129), Expect = 5e-09
Identities = 27/78 (34%), Positives = 44/78 (56%)
Query: 13 LEKISAVAGDVSLPGLGLSETDRELLRTNVNVIFHGAATVRFDEKIQLAVAINVLGVRAM 72
L K+ V G+V LGL + + V+VI + AA FDE+ +A+ IN G +
Sbjct: 191 LSKLVPVVGNVCESNLGLEPDLADEIAKEVDVIINSAANTTFDERYDVAIDINTRGPCHL 250
Query: 73 LELAREIRQLKLFLRLKT 90
+ A++ ++LKLFL++ T
Sbjct: 251 MSFAKKCKKLKLFLQVST 268
Score = 47.2 bits (112), Expect = 8e-07
Identities = 30/101 (29%), Positives = 49/101 (48%), Gaps = 5/101 (4%)
Query: 71 AMLELAREIRQLKLFLRL-----KTEVPHFLEKISAVAGDVSLPGLGLSETDRELLRTNV 125
A+ L E+ +LF L K+ L K+ V G+V LGL + + V
Sbjct: 161 AIERLKNEVIDAELFKCLQETHGKSYQSFMLSKLVPVVGNVCESNLGLEPDLADEIAKEV 220
Query: 126 NVIFHGAATVRFDEKIQLAVAINVLGVRAMLELAREIRQLK 166
+VI + AA FDE+ +A+ IN G ++ A++ ++LK
Sbjct: 221 DVIINSAANTTFDERYDVAIDINTRGPCHLMSFAKKCKKLK 261
>gnl|CDD|215538 PLN02996, PLN02996, fatty acyl-CoA reductase.
Length = 491
Score = 52.0 bits (125), Expect = 2e-08
Identities = 26/78 (33%), Positives = 49/78 (62%), Gaps = 1/78 (1%)
Query: 14 EKISAVAGDVSLPGLGLSETD-RELLRTNVNVIFHGAATVRFDEKIQLAVAINVLGVRAM 72
EK++ V GD+S LG+ +++ RE + ++++ + AAT FDE+ +A+ IN LG +
Sbjct: 84 EKVTPVPGDISYDDLGVKDSNLREEMWKEIDIVVNLAATTNFDERYDVALGINTLGALNV 143
Query: 73 LELAREIRQLKLFLRLKT 90
L A++ ++K+ L + T
Sbjct: 144 LNFAKKCVKVKMLLHVST 161
Score = 51.6 bits (124), Expect = 2e-08
Identities = 40/123 (32%), Positives = 63/123 (51%), Gaps = 17/123 (13%)
Query: 54 FDEKIQLAVAINV----LGVRA------MLELAREIRQLKLFLRLKTEVPHFL-----EK 98
F EKI L V NV L +RA L E+ LF L+ ++ L EK
Sbjct: 27 FVEKI-LRVQPNVKKLYLLLRASDAKSATQRLHDEVIGKDLFKVLREKLGENLNSLISEK 85
Query: 99 ISAVAGDVSLPGLGLSETD-RELLRTNVNVIFHGAATVRFDEKIQLAVAINVLGVRAMLE 157
++ V GD+S LG+ +++ RE + ++++ + AAT FDE+ +A+ IN LG +L
Sbjct: 86 VTPVPGDISYDDLGVKDSNLREEMWKEIDIVVNLAATTNFDERYDVALGINTLGALNVLN 145
Query: 158 LAR 160
A+
Sbjct: 146 FAK 148
>gnl|CDD|225857 COG3320, COG3320, Putative dehydrogenase domain of multifunctional
non-ribosomal peptide synthetases and related enzymes
[Secondary metabolites biosynthesis, transport, and
catabolism].
Length = 382
Score = 49.3 bits (118), Expect = 2e-07
Identities = 27/80 (33%), Positives = 38/80 (47%), Gaps = 7/80 (8%)
Query: 4 RLKTEVPHFL-------EKISAVAGDVSLPGLGLSETDRELLRTNVNVIFHGAATVRFDE 56
RL+ + +++ VAGD++ P LGLSE + L NV++I H AA V
Sbjct: 43 RLEKTFDLYRHWDELSADRVEVVAGDLAEPDLGLSERTWQELAENVDLIIHNAALVNHVF 102
Query: 57 KIQLAVAINVLGVRAMLELA 76
NVLG +L LA
Sbjct: 103 PYSELRGANVLGTAEVLRLA 122
Score = 49.3 bits (118), Expect = 2e-07
Identities = 27/80 (33%), Positives = 38/80 (47%), Gaps = 7/80 (8%)
Query: 87 RLKTEVPHFL-------EKISAVAGDVSLPGLGLSETDRELLRTNVNVIFHGAATVRFDE 139
RL+ + +++ VAGD++ P LGLSE + L NV++I H AA V
Sbjct: 43 RLEKTFDLYRHWDELSADRVEVVAGDLAEPDLGLSERTWQELAENVDLIIHNAALVNHVF 102
Query: 140 KIQLAVAINVLGVRAMLELA 159
NVLG +L LA
Sbjct: 103 PYSELRGANVLGTAEVLRLA 122
>gnl|CDD|235962 PRK07201, PRK07201, short chain dehydrogenase; Provisional.
Length = 657
Score = 41.9 bits (99), Expect = 6e-05
Identities = 25/69 (36%), Positives = 41/69 (59%), Gaps = 5/69 (7%)
Query: 14 EKISAVAGDVSLPGLGLSETDRELLRTNVNVIFHGAAT--VRFDEKIQLAVAINVLGVRA 71
+++ + GD++ PGLGLSE D L +++ + H AA + DE+ Q A NV G R
Sbjct: 51 DRVVPLVGDLTEPGLGLSEADIAEL-GDIDHVVHLAAIYDLTADEEAQRAA--NVDGTRN 107
Query: 72 MLELAREIR 80
++ELA ++
Sbjct: 108 VVELAERLQ 116
Score = 41.9 bits (99), Expect = 6e-05
Identities = 25/69 (36%), Positives = 41/69 (59%), Gaps = 5/69 (7%)
Query: 97 EKISAVAGDVSLPGLGLSETDRELLRTNVNVIFHGAAT--VRFDEKIQLAVAINVLGVRA 154
+++ + GD++ PGLGLSE D L +++ + H AA + DE+ Q A NV G R
Sbjct: 51 DRVVPLVGDLTEPGLGLSEADIAEL-GDIDHVVHLAAIYDLTADEEAQRAA--NVDGTRN 107
Query: 155 MLELAREIR 163
++ELA ++
Sbjct: 108 VVELAERLQ 116
>gnl|CDD|234212 TIGR03443, alpha_am_amid, L-aminoadipate-semialdehyde dehydrogenase.
Members of this protein family are
L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31),
product of the LYS2 gene. It is also called
alpha-aminoadipate reductase. In fungi, lysine is
synthesized via aminoadipate. Currently, all members of
this family are fungal.
Length = 1389
Score = 37.0 bits (86), Expect = 0.003
Identities = 15/41 (36%), Positives = 20/41 (48%)
Query: 12 FLEKISAVAGDVSLPGLGLSETDRELLRTNVNVIFHGAATV 52
+ +I V GD+S GLS+ L V+VI H A V
Sbjct: 1032 WASRIEVVLGDLSKEKFGLSDEKWSDLTNEVDVIIHNGALV 1072
Score = 37.0 bits (86), Expect = 0.003
Identities = 15/41 (36%), Positives = 20/41 (48%)
Query: 95 FLEKISAVAGDVSLPGLGLSETDRELLRTNVNVIFHGAATV 135
+ +I V GD+S GLS+ L V+VI H A V
Sbjct: 1032 WASRIEVVLGDLSKEKFGLSDEKWSDLTNEVDVIIHNGALV 1072
>gnl|CDD|187580 cd05272, TDH_SDR_e, L-threonine dehydrogenase, extended (e) SDRs.
This subgroup contains members identified as L-threonine
dehydrogenase (TDH). TDH catalyzes the zinc-dependent
formation of 2-amino-3-ketobutyrate from L-threonine via
NAD(H)-dependent oxidation. This group is distinct from
TDHs that are members of the medium chain
dehydrogenase/reductase family. This group has the
NAD-binding motif and active site tetrad of the extended
SDRs. 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 = 308
Score = 33.8 bits (78), Expect = 0.025
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 3/47 (6%)
Query: 41 NVNVIFHGAA--TVRFDEKIQLAVAINVLGVRAMLELAREIRQLKLF 85
+ I H AA + ++ LA +N+ G+ +LELARE L++F
Sbjct: 65 KITWIIHLAALLSAVGEKNPPLAWDVNMNGLHNVLELARE-HNLRIF 110
Score = 32.7 bits (75), Expect = 0.074
Identities = 14/40 (35%), Positives = 22/40 (55%), Gaps = 2/40 (5%)
Query: 124 NVNVIFHGAA--TVRFDEKIQLAVAINVLGVRAMLELARE 161
+ I H AA + ++ LA +N+ G+ +LELARE
Sbjct: 65 KITWIIHLAALLSAVGEKNPPLAWDVNMNGLHNVLELARE 104
>gnl|CDD|212494 cd08946, SDR_e, extended (e) SDRs. 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 = 200
Score = 31.9 bits (73), Expect = 0.095
Identities = 13/52 (25%), Positives = 21/52 (40%), Gaps = 3/52 (5%)
Query: 30 LSETDRELLRTNVNVIFHGAATVRFDEKIQ---LAVAINVLGVRAMLELARE 78
L ++ ++V+ H AA V NV+G +LE AR+
Sbjct: 19 LERGHEVVVIDRLDVVVHLAALVGVPASWDNPDEDFETNVVGTLNLLEAARK 70
Score = 31.9 bits (73), Expect = 0.095
Identities = 13/52 (25%), Positives = 21/52 (40%), Gaps = 3/52 (5%)
Query: 113 LSETDRELLRTNVNVIFHGAATVRFDEKIQ---LAVAINVLGVRAMLELARE 161
L ++ ++V+ H AA V NV+G +LE AR+
Sbjct: 19 LERGHEVVVIDRLDVVVHLAALVGVPASWDNPDEDFETNVVGTLNLLEAARK 70
>gnl|CDD|187535 cd02266, SDR, Short-chain dehydrogenases/reductases (SDR). 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 (KR) 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 = 186
Score = 30.6 bits (69), Expect = 0.25
Identities = 27/94 (28%), Positives = 42/94 (44%), Gaps = 15/94 (15%)
Query: 27 GLGLSETDRELLRTNVNVIFHGAATVR-------FDEKIQLAVAINVLGVRAMLELAREI 79
L + + L+ + +V+ H AA + +I+ A+ NV+G R +LE ARE+
Sbjct: 17 WLASRGSPKVLVVSRRDVVVHNAAILDDGRLIDLTGSRIERAIRANVVGTRRLLEAAREL 76
Query: 80 RQLKLFLRLKTEVPHFLEKISAVAGDVSLPGLGL 113
+ K IS+VAG PGLG
Sbjct: 77 MKAK----RLGRFIL----ISSVAGLFGAPGLGG 102
Score = 29.8 bits (67), Expect = 0.51
Identities = 18/64 (28%), Positives = 32/64 (50%), Gaps = 7/64 (10%)
Query: 110 GLGLSETDRELLRTNVNVIFHGAATVR-------FDEKIQLAVAINVLGVRAMLELAREI 162
L + + L+ + +V+ H AA + +I+ A+ NV+G R +LE ARE+
Sbjct: 17 WLASRGSPKVLVVSRRDVVVHNAAILDDGRLIDLTGSRIERAIRANVVGTRRLLEAAREL 76
Query: 163 RQLK 166
+ K
Sbjct: 77 MKAK 80
>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 314
Score = 29.9 bits (67), Expect = 0.51
Identities = 19/99 (19%), Positives = 35/99 (35%), Gaps = 9/99 (9%)
Query: 67 LGVRAMLELAREIRQLKLFLRLKTEVPHFLEKISAVAGDVSLPGLGLSETDRELLRTNVN 126
+G + L ++ RL+ + L + V D++ + EL + +
Sbjct: 12 IGSHLVERLLAAGHDVRGLDRLRDGLDPLLSGVEFVVLDLTDR-----DLVDELAKGVPD 66
Query: 127 VIFHGAATVRF----DEKIQLAVAINVLGVRAMLELARE 161
+ H AA + +NV G +LE AR
Sbjct: 67 AVIHLAAQSSVPDSNASDPAEFLDVNVDGTLNLLEAARA 105
Score = 29.1 bits (65), Expect = 1.1
Identities = 17/90 (18%), Positives = 30/90 (33%), Gaps = 9/90 (10%)
Query: 1 LFLRLKTEVPHFLEKISAVAGDVSLPGLGLSETDRELLRTNVNVIFHGAATVRF----DE 56
RL+ + L + V D++ + EL + + + H AA
Sbjct: 29 GLDRLRDGLDPLLSGVEFVVLDLTDR-----DLVDELAKGVPDAVIHLAAQSSVPDSNAS 83
Query: 57 KIQLAVAINVLGVRAMLELAREIRQLKLFL 86
+ +NV G +LE AR +
Sbjct: 84 DPAEFLDVNVDGTLNLLEAARAAGVKRFVF 113
>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 = 29.3 bits (66), Expect = 0.87
Identities = 24/88 (27%), Positives = 39/88 (44%), Gaps = 7/88 (7%)
Query: 78 EIRQLKLFLRLKTEVPHFLEKISAVAGDVSLPGLGLSETDRELLRTNVNVIFHGAATV-R 136
+L L + + P +++ +AGD+++P L L +V+FH AA V
Sbjct: 25 PNERLILIDVVSPKAPSGAPRVTQIAGDLAVPAL-----IEALANGRPDVVFHLAAIVSG 79
Query: 137 FDEK-IQLAVAINVLGVRAMLELAREIR 163
E L +NV G R +LE R+
Sbjct: 80 GAEADFDLGYRVNVDGTRNLLEALRKNG 107
Score = 28.1 bits (63), Expect = 2.4
Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 7/75 (9%)
Query: 8 EVPHFLEKISAVAGDVSLPGLGLSETDRELLRTNVNVIFHGAATV-RFDEK-IQLAVAIN 65
+ P +++ +AGD+++P L L +V+FH AA V E L +N
Sbjct: 38 KAPSGAPRVTQIAGDLAVPAL-----IEALANGRPDVVFHLAAIVSGGAEADFDLGYRVN 92
Query: 66 VLGVRAMLELAREIR 80
V G R +LE R+
Sbjct: 93 VDGTRNLLEALRKNG 107
>gnl|CDD|187539 cd05228, AR_FR_like_1_SDR_e, uncharacterized subgroup of aldehyde
reductase and flavonoid reductase related proteins,
extended (e) SDRs. This subgroup contains proteins of
unknown function related to aldehyde reductase and
flavonoid reductase of the extended SDR-type. Aldehyde
reductase I (aka carbonyl reductase) is an NADP-binding
SDR; it has an NADP-binding motif consensus that is
slightly different from the canonical SDR form and lacks
the Asn of the extended SDR active site tetrad. Aldehyde
reductase I catalyzes the NADP-dependent reduction of
ethyl 4-chloro-3-oxobutanoate to ethyl
(R)-4-chloro-3-hydroxybutanoate. The related flavonoid
reductases act in the NADP-dependent reduction of
flavonoids, ketone-containing plant secondary
metabolites. 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 = 318
Score = 28.4 bits (64), Expect = 1.5
Identities = 27/104 (25%), Positives = 35/104 (33%), Gaps = 29/104 (27%)
Query: 69 VRAMLE-------LAREIRQLKLFLRLKTEVPHFLEKISAVAGDVSLPGLGLSETDRELL 121
VRA+L L R L L EV V GD+ TD L
Sbjct: 15 VRALLAQGYRVRALVRSGSDAVLLDGLPVEV---------VEGDL---------TDAASL 56
Query: 122 R---TNVNVIFHGAATVRF-DEKIQLAVAINVLGVRAMLELARE 161
+ +FH AA + + NV G R +L+ A E
Sbjct: 57 AAAMKGCDRVFHLAAFTSLWAKDRKELYRTNVEGTRNVLDAALE 100
Score = 26.5 bits (59), Expect = 8.4
Identities = 14/50 (28%), Positives = 20/50 (40%), Gaps = 4/50 (8%)
Query: 33 TDRELLR---TNVNVIFHGAATVRF-DEKIQLAVAINVLGVRAMLELARE 78
TD L + +FH AA + + NV G R +L+ A E
Sbjct: 51 TDAASLAAAMKGCDRVFHLAAFTSLWAKDRKELYRTNVEGTRNVLDAALE 100
>gnl|CDD|193493 cd02690, M28, M28 Zn-peptidases include aminopeptidases and
carboxypeptidases. Peptidase M28 family (also called
aminopeptidase Y family) contains aminopeptidases as
well as carboxypeptidases. They have co-catalytic zinc
ions; each zinc ion is tetrahedrally co-ordinated, with
three amino acid ligands plus activated water; one
aspartate residue binds both metal ions. The
aminopeptidases in this family are also called bacterial
leucyl aminopeptidases, but are able to release a
variety of N-terminal amino acids. IAP aminopeptidase
and aminopeptidase Y preferentially release basic amino
acids while glutamate carboxypeptidase II preferentially
releases C-terminal glutamates. Plasma glutamate
carboxypeptidase (PGCP) and glutamate carboxypeptidase
II (NAALADase) hydrolyze dipeptides. Several members of
the M28 peptidase family have PA domain inserts which
may participate in substrate binding and/or in promoting
conformational changes, which influence the stability
and accessibility of the site to substrate. These
include prostate-specific membrane antigen (PSMA), yeast
aminopeptidase S (SGAP), human transferrin receptors
(TfR1 and TfR2), plasma glutamate carboxypeptidase
(PGCP) and several predicted aminopeptidases where
relatively little is known about them. Also included in
the M28 family are the glutaminyl cyclases (QC) which
are involved in N-terminal glutamine cyclization of many
endocrine peptides. Nicastrin and nicalin belong to this
family but lack the amino-acid conservation required for
catalytically active aminopeptidases.
Length = 252
Score = 28.2 bits (63), Expect = 2.3
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 65 NVLGVRAMLELAREIRQLKL 84
N GV +LELAR + +L L
Sbjct: 91 NASGVAVLLELARVLSKLPL 110
Score = 27.0 bits (60), Expect = 4.5
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 148 NVLGVRAMLELAREIRQLK 166
N GV +LELAR + +L
Sbjct: 91 NASGVAVLLELARVLSKLP 109
>gnl|CDD|224016 COG1091, RfbD, dTDP-4-dehydrorhamnose reductase [Cell envelope
biogenesis, outer membrane].
Length = 281
Score = 27.6 bits (62), Expect = 3.2
Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 4/49 (8%)
Query: 35 RELLR-TNVNVIFHGAATVRFDEKIQ---LAVAINVLGVRAMLELAREI 79
E++R T +V+ + AA D+ LA A+N G + A E+
Sbjct: 43 LEVIRETRPDVVINAAAYTAVDKAESEPELAFAVNATGAENLARAAAEV 91
Score = 27.6 bits (62), Expect = 3.2
Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 4/49 (8%)
Query: 118 RELLR-TNVNVIFHGAATVRFDEKIQ---LAVAINVLGVRAMLELAREI 162
E++R T +V+ + AA D+ LA A+N G + A E+
Sbjct: 43 LEVIRETRPDVVINAAAYTAVDKAESEPELAFAVNATGAENLARAAAEV 91
>gnl|CDD|130249 TIGR01181, dTDP_gluc_dehyt, dTDP-glucose 4,6-dehydratase. This
protein is related to UDP-glucose 4-epimerase (GalE) and
likewise has an NAD cofactor [Cell envelope,
Biosynthesis and degradation of surface polysaccharides
and lipopolysaccharides].
Length = 317
Score = 27.3 bits (61), Expect = 3.8
Identities = 27/113 (23%), Positives = 39/113 (34%), Gaps = 27/113 (23%)
Query: 14 EKISAVAGDVSLPGLGLSETDRELLR-----TNVNVIFHGAATVRFDEKIQLAVAI---N 65
+ V GD+ DREL+ + + H AA D I A N
Sbjct: 50 PRYRFVKGDI---------GDRELVSRLFTEHQPDAVVHFAAESHVDRSISGPAAFIETN 100
Query: 66 VLGVRAMLELAREIRQLKLFLRLKTEVPHFLEKISAVAGDVSLPGLGLSETDR 118
V+G +LE R+ F + T+ V GD+ G +ET
Sbjct: 101 VVGTYTLLEAVRKYWHEFRFHHISTD---------EVYGDLE-KGDAFTETTP 143
Score = 26.6 bits (59), Expect = 6.3
Identities = 19/73 (26%), Positives = 27/73 (36%), Gaps = 17/73 (23%)
Query: 97 EKISAVAGDVSLPGLGLSETDRELLR-----TNVNVIFHGAATVRFDEKIQLAVAI---N 148
+ V GD+ DREL+ + + H AA D I A N
Sbjct: 50 PRYRFVKGDI---------GDRELVSRLFTEHQPDAVVHFAAESHVDRSISGPAAFIETN 100
Query: 149 VLGVRAMLELARE 161
V+G +LE R+
Sbjct: 101 VVGTYTLLEAVRK 113
>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 = 26.8 bits (60), Expect = 5.7
Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 3/53 (5%)
Query: 30 LSETDRELLRTNVNVIFHGAATVRFD--EK-IQLAVAINVLGVRAMLELAREI 79
+ + +VI + AA R D E +LA +NVL + A+E+
Sbjct: 44 PDAVEEAIRDYKPDVIINCAAYTRVDKCESDPELAYRVNVLAPENLARAAKEV 96
Score = 26.8 bits (60), Expect = 5.7
Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 3/53 (5%)
Query: 113 LSETDRELLRTNVNVIFHGAATVRFD--EK-IQLAVAINVLGVRAMLELAREI 162
+ + +VI + AA R D E +LA +NVL + A+E+
Sbjct: 44 PDAVEEAIRDYKPDVIINCAAYTRVDKCESDPELAYRVNVLAPENLARAAKEV 96
>gnl|CDD|185309 PRK15411, rcsA, colanic acid capsular biosynthesis activation
protein A; Provisional.
Length = 207
Score = 26.2 bits (58), Expect = 8.1
Identities = 10/29 (34%), Positives = 17/29 (58%)
Query: 11 HFLEKISAVAGDVSLPGLGLSETDRELLR 39
L+K + + ++LP L LS T+ +LR
Sbjct: 119 DILKKETTITSFLNLPTLSLSRTESSMLR 147
Score = 26.2 bits (58), Expect = 8.1
Identities = 10/29 (34%), Positives = 17/29 (58%)
Query: 94 HFLEKISAVAGDVSLPGLGLSETDRELLR 122
L+K + + ++LP L LS T+ +LR
Sbjct: 119 DILKKETTITSFLNLPTLSLSRTESSMLR 147
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
0.324 0.140 0.377
Gapped
Lambda K H
0.267 0.0728 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,707,497
Number of extensions: 845318
Number of successful extensions: 1161
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1149
Number of HSP's successfully gapped: 67
Length of query: 166
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 76
Effective length of database: 6,945,742
Effective search space: 527876392
Effective search space used: 527876392
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 55 (25.0 bits)