RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy702
(308 letters)
>gnl|CDD|197235 cd09137, PLDc_PGS1_euk_2, Catalytic domain, repeat 2, of eukaryotic
phosphatidylglycerophosphate synthases. Catalytic
domain, repeat 2, of eukaryotic
phosphatidylglycerophosphate (PGP) synthases, also
called CDP-diacylglycerol--glycerol-3-phosphate
3-phosphatidyltransferase (EC 2.7.8.5). Eukaryotic PGP
synthases are different and unrelated to prokaryotic PGP
synthases and yeast phosphatidylserine synthase. They
catalyze the synthesis of PGP from CDP-diacylglycerol
and sn-glycerol 3-phosphate, the committed and
rate-limiting step in the biosynthesis of cardiolipin
(CL), which is an essential component of many
mitochondrial functions in eukaryotes. Members in this
subfamily all have two HKD motifs (H-x-K-x(4)-D, where x
represents any amino acid residue) that characterizes
the phospholipase D (PLD) superfamily. They may utilize
a common two-step ping-pong catalytic mechanism
involving a substrate-enzyme intermediate to cleave
phosphodiester bonds. The two motifs are suggested to
constitute the active site involved in the phosphatidyl
group transfer.
Length = 186
Score = 168 bits (427), Expect = 9e-52
Identities = 67/143 (46%), Positives = 90/143 (62%), Gaps = 5/143 (3%)
Query: 168 TWLAPLIELPPLHIQLDSRVTKLILSLARDGSCVSLGTGYFNLTQEYVRAMLDKPRVNYS 227
TW+ PL+++ PL+I + +VT +L L GS ++L +GYFNLT EY+ +L+ N
Sbjct: 1 TWVYPLLQMGPLNISQEEQVTSRLLQLLPRGSSLTLASGYFNLTPEYLNLLLNSSA-NLD 59
Query: 228 VLMAHPTANGFLGARGAAGGIPYAYTALAARFLSRVSNLK----VAMFEYVRSGWTYHAK 283
VL A P ANGF G++G +G IP AYT +A +FL RV + +FEY R GWT+HAK
Sbjct: 60 VLTASPEANGFYGSKGVSGYIPPAYTYIARQFLKRVRKNGKQPRIKLFEYKRPGWTFHAK 119
Query: 284 GLWYSESPGSKPVLTLIGSPNFG 306
GLW P LTLIGS N+G
Sbjct: 120 GLWIYLPGTDLPSLTLIGSSNYG 142
>gnl|CDD|197233 cd09135, PLDc_PGS1_euk_1, Catalytic domain, repeat 1, of eukaryotic
PhosphatidylGlycerophosphate Synthases. Catalytic
domain, repeat 1, of eukaryotic
phosphatidylglycerophosphate (PGP) synthases, also
called CDP-diacylglycerol--glycerol-3-phosphate
3-phosphatidyltransferase (EC 2.7.8.5). Eukaryotic PGP
synthases are different and unrelated to prokaryotic PGP
synthases and yeast phosphatidylserine synthase. They
catalyze the synthesis of PGP from CDP-diacylglycerol
and sn-glycerol 3-phosphate, the committed and
rate-limiting step in the biosynthesis of cardiolipin
(CL), which is an essential component of many
mitochondrial functions in eukaryotes. Members in this
subfamily all have two HKD motifs (H-x-K-x(4)-D, where x
represents any amino acid residue) that characterizes
the phospholipase D (PLD) superfamily. They may utilize
a common two-step ping-pong catalytic mechanism
involving a substrate-enzyme intermediate to cleave
phosphodiester bonds. The two motifs are suggested to
constitute the active site involved in the phosphatidyl
group transfer.
Length = 170
Score = 163 bits (415), Expect = 4e-50
Identities = 58/99 (58%), Positives = 76/99 (76%), Gaps = 2/99 (2%)
Query: 1 TRGDVNSKT--LLSPIVKQFSHNCHVSFYHTPDLRWPLNRLLPHRYNELIGLQHMKFYLI 58
TRG+ NS+T LL P++K F VS YHTP+LR L +LLP R+NE+IGLQHMK Y+
Sbjct: 68 TRGEPNSRTASLLLPLLKLFPDRVRVSLYHTPNLRGLLKKLLPERFNEIIGLQHMKLYIF 127
Query: 59 DNCVIITGANLSGDYFTSRQDRYMIIQDHKPLSDFFDDL 97
D+ VI++GANLS DYFT+RQDRYM+I++ L+DF+ DL
Sbjct: 128 DDDVILSGANLSDDYFTNRQDRYMLIENCPELADFYHDL 166
>gnl|CDD|197201 cd09102, PLDc_CDP-OH_P_transf_II_1, Catalytic domain, repeat 1, of
CDP-alcohol phosphatidyltransferase class-II family
members. Catalytic domain, repeat 1, of CDP-alcohol
phosphatidyltransferase class-II family members, which
mainly include gram-negative bacterial
phosphatidylserine synthases (PSS;
CDP-diacylglycerol--serine O-phosphatidyltransferase, EC
2.7.8.8), yeast phosphatidylglycerophosphate synthase
(PGP synthase; CDP-diacylglycerol--glycerol-3-phosphate
3-phosphatidyltransferase, EC 2.7.8.5), and metazoan PGP
synthase 1. All members in this subfamily have two HKD
motifs (H-x-K-x(4)-D, where x represents any amino acid
residue) that characterize the phospholipase D (PLD)
superfamily. They may utilize a common two-step
ping-pong catalytic mechanism, involving a
substrate-enzyme intermediate, to cleave phosphodiester
bonds. The two motifs are suggested to constitute the
active site involving phosphatidyl group transfer.
Phosphatidylserine synthases from gram-positive bacteria
and eukaryotes, and prokaryotic
phosphatidylglycerophosphate synthases are not members
of this subfamily.
Length = 168
Score = 94.2 bits (234), Expect = 2e-23
Identities = 29/96 (30%), Positives = 45/96 (46%)
Query: 2 RGDVNSKTLLSPIVKQFSHNCHVSFYHTPDLRWPLNRLLPHRYNELIGLQHMKFYLIDNC 61
R + S+T + + S H +P NE+ G+ H+K Y+ D+
Sbjct: 69 RNLLGSETKSATNADWYCEQRQTSQLHLLPDDGNXFFGVPINTNEVFGVLHVKGYVFDDT 128
Query: 62 VIITGANLSGDYFTSRQDRYMIIQDHKPLSDFFDDL 97
V+++GANLS YF R DRY+ I L+D +L
Sbjct: 129 VLLSGANLSNVYFHYRYDRYVKITHGAELADSXVNL 164
>gnl|CDD|197202 cd09103, PLDc_CDP-OH_P_transf_II_2, Catalytic domain, repeat 2, of
CDP-alcohol phosphatidyltransferase class-II family
members. Catalytic domain, repeat 2, of CDP-alcohol
phosphatidyltransferase class-II family members, which
mainly include gram-negative bacterial
phosphatidylserine synthases (PSS;
CDP-diacylglycerol--serine O-phosphatidyltransferase, EC
2.7.8.8), yeast phosphatidylglycerophosphate synthase
(PGP synthase; CDP-diacylglycerol--glycerol-3-phosphate
3-phosphatidyltransferase, EC 2.7.8.5), and metazoan PGP
synthase 1. All members in this subfamily have two HKD
motifs (H-x-K-x(4)-D, where x represents any amino acid
residue) that characterize the phospholipase D (PLD)
superfamily. They may utilize a common two-step
ping-pong catalytic mechanism, involving a
substrate-enzyme intermediate, to cleave phosphodiester
bonds. The two motifs are suggested to constitute the
active site involving phosphatidyl group transfer.
Phosphatidylserine synthases from gram-positive bacteria
and eukaryotes, and prokaryotic
phosphatidylglycerophosphate synthases are not members
of this subfamily.
Length = 184
Score = 79.6 bits (197), Expect = 6e-18
Identities = 34/150 (22%), Positives = 58/150 (38%), Gaps = 21/150 (14%)
Query: 168 TWLAPLIELPPLHIQLDSRVTKLILSLARDGSCVSLGTGYFNLTQEYVRAM--LDKPRVN 225
+ PL+ L + +R + +++ A + L T YFNL Q +R + L K V
Sbjct: 1 LSITPLVGLGK-RGNILNRTIEQLITSAESK--IILCTPYFNLPQALMRDILRLLKRGVK 57
Query: 226 YSVLMAHPTANGFLGAR----GAAGGIPYAYTALAARFLSRVSNL----KVAMFEYVRSG 277
+++ TAN F G +PY Y RF R+ ++ + +
Sbjct: 58 VEIIVGDKTANDFYIPPEEPFKVIGALPYLYEINLRRFAKRLQKYIDQGQLNVRLWKDGD 117
Query: 278 WTYHAKGLW-YSESPGSKPVLTLIGSPNFG 306
++H KG+W TL+ N
Sbjct: 118 NSFHLKGIWVDDR-------YTLLTGNNLN 140
>gnl|CDD|224419 COG1502, Cls,
Phosphatidylserine/phosphatidylglycerophosphate/cardioli
pin synthases and related enzymes [Lipid metabolism].
Length = 438
Score = 47.5 bits (113), Expect = 4e-06
Identities = 55/277 (19%), Positives = 84/277 (30%), Gaps = 61/277 (22%)
Query: 37 NRLLPHRYNELIGLQHMKFYLIDN-CVIITGANLSGDYFTS------RQDRYMIIQDHKP 89
P R+ L H K +ID + GAN+ +YF +D ++ I
Sbjct: 151 ASPRPLRFRRLNRRLHRKIVVIDGKVAFVGGANIGDEYFHKDKGLGYWRDLHVRIT---- 206
Query: 90 LSDFFDDLSRVLCKISFQLTPDGKFILDKEFPLSPVSVTQRGEYLKRSRSLVLDMYDGYR 149
DL+R+ FI D + R
Sbjct: 207 -GPAVADLARL-------------FIQDWNL----------------ESGSSKPLLALVR 236
Query: 150 TRNTTAVSPALSSTQPPDT-WLAPLIELPPLHIQLDSRVTKLILSLARDGSCVSLGTGYF 208
+ + P L I+L+ + K I S AR+ + + T YF
Sbjct: 237 PPLQSLSLLPVGRGSTVQVLSSGPDKGLGSELIELNRLLLKAINS-ARES--ILIATPYF 293
Query: 209 NLTQEYVRAMLDKPRVNYSVLMAHPTANGFLGARGAAGGIPYAYTALAARFLSRVSNLKV 268
+E + A+ R V LGA +A + AY A L V
Sbjct: 294 VPDRELLAALKAAARRGVDV----RIIIPSLGANDSA-IVHAAYRAYLKELL----EAGV 344
Query: 269 AMFEYVRSGWTYHAKGLWYSESPGSKPVLTLIGSPNF 305
++EY G H+K + L+GS N
Sbjct: 345 KVYEY-PGGAFLHSKVMIID------DRTVLVGSANL 374
>gnl|CDD|197232 cd09134, PLDc_PSS_G_neg_1, Catalytic domain, repeat 1, of
phosphatidylserine synthases from gram-negative
bacteria. Catalytic domain, repeat 1, of
phosphatidylserine synthases (PSSs) from gram-negative
bacteria. There are two subclasses of PSS enzymes in
bacteria: subclass I of gram-negative bacteria and
subclass II of gram-positive bacteria. It is common that
PSSs in gram-positive bacteria and yeast are tight
membrane-associated enzymes. By contrast, the
gram-negative bacterial PSSs, such as Escherichia coli
PSS, are commonly bound to the ribosomes. They are
peripheral membrane proteins that can interact with the
surface of the inner membrane by binding to the lipid
substrate (CDP-diacylglycerol) and the lipid product
(phosphatidylserine). The prototypical member of this
subfamily is Escherichia coli PSS (also called
CDP-diacylglycerol-L-serine O-phosphatidyltransferase,
EC 2.7.8.8), which catalyzes the exchange reactions
between CMP and CDP-diacylglycerol, and between serine
and phosphatidylserine. The phosphatidylserine is then
decarboxylated by phosphatidylserine decarboxylase to
yield phosphatidylethanolamine, the major phospholipid
in Escherichia coli. It also catalyzes the hydrolysis of
CDP-diacylglycerol to form phosphatidic acid with the
release of CMP. PSS may utilize a ping-pong mechanism
involving a phosphatidyl-enzyme intermediate, which is
distinct from those of gram-positive bacterial
phosphatidylserine synthases. Moreover, all members in
this subfamily have two HKD motifs (H-x-K-x(4)-D, where
x represents any amino acid residue) that characterizes
the phospholipase D (PLD) superfamily. The two motifs
constitute an active site for the formation of a
covalent substrate-enzyme intermediate.
Length = 173
Score = 44.9 bits (107), Expect = 1e-05
Identities = 20/57 (35%), Positives = 34/57 (59%), Gaps = 5/57 (8%)
Query: 40 LPHRYNELIGLQHMKFYLIDNCVIITGANLSGDYFTS----RQDRYMIIQDHKPLSD 92
+P + EL G+ H+K ++ID+ V+ +GA+L+ Y R DRY +I + L+D
Sbjct: 109 VPVKTRELFGVLHLKGFIIDDTVLYSGASLNNVYLHQFDKYRYDRYHLIY-NPELAD 164
>gnl|CDD|236510 PRK09428, pssA, phosphatidylserine synthase; Provisional.
Length = 451
Score = 41.3 bits (98), Expect = 4e-04
Identities = 19/56 (33%), Positives = 33/56 (58%), Gaps = 5/56 (8%)
Query: 41 PHRYNELIGLQHMKFYLIDNCVIITGANLSGDYFTS----RQDRYMIIQDHKPLSD 92
P E +G+ H+K ++ID+ V+ +GA+L+ Y R DRY +I+ + L+D
Sbjct: 127 PVNTREALGVLHLKGFIIDDTVLYSGASLNNVYLHQHDKYRYDRYHLIR-NAELAD 181
Score = 29.8 bits (68), Expect = 2.0
Identities = 27/99 (27%), Positives = 38/99 (38%), Gaps = 24/99 (24%)
Query: 205 TGYFNLTQEYVRAM--LDKPRVNYSVLMAHPTANGFLGARG----AAGGIPYAYTALAAR 258
T YFNL VR + L + +++ TAN F G +PY Y R
Sbjct: 271 TPYFNLPAILVRNIIRLLRRGKKVEIIVGDKTANDFYIPPDEPFKIIGALPYLYEINLRR 330
Query: 259 FLSRVSNLKVAMFEYVRSG------W-----TYHAKGLW 286
F R+ Y+ +G W +YH KG+W
Sbjct: 331 FAKRLQY-------YIDNGQLNVRLWKDGDNSYHLKGIW 362
>gnl|CDD|197215 cd09116, PLDc_Nuc_like, Catalytic domain of EDTA-resistant nuclease
Nuc, vertebrate phospholipase D6, and similar proteins.
Catalytic domain of EDTA-resistant nuclease Nuc,
vertebrate phospholipase D6 (PLD6, EC 3.1.4.4), and
similar proteins. Nuc is an endonuclease from Salmonella
typhimurium and the smallest known member of the PLD
superfamily. It cleaves both single- and double-stranded
DNA. PLD6 selectively hydrolyzes the terminal
phosphodiester bond of phosphatidylcholine (PC), with
the formation of phosphatidic acid and alcohols.
Phosphatidic acid is an essential compound involved in
signal transduction. PLD6 also catalyzes the
transphosphatidylation of phospholipids to acceptor
alcohols, by which various phospholipids can be
synthesized. Both Nuc and PLD6 belong to the
phospholipase D (PLD) superfamily. They contain a short
conserved sequence motif, the HKD motif (H-x-K-x(4)-D,
where x represents any amino acid residue), which is
essential for catalysis. PLDs utilize a two-step
mechanism to cleave phosphodiester bonds: Upon substrate
binding, the bond is first attacked by a histidine
residue from one HKD motif to form a covalent
phosphohistidine intermediate, which is then hydrolyzed
by water with the aid of a second histidine residue from
the other HKD motif in the opposite subunit. This
subfamily also includes some uncharacterized
hypothetical proteins, which have two HKD motifs in a
single polypeptide chain.
Length = 138
Score = 36.5 bits (85), Expect = 0.004
Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 2/47 (4%)
Query: 49 GLQHMKFYLIDNCVIITG-ANLSGDYFTSRQDRYMIIQDHKPLSDFF 94
L H KF +ID ++ITG AN + F R D ++I D L+ F
Sbjct: 86 KLMHHKFIIIDGKIVITGSANWTKSGF-HRNDENLLIIDDPKLAASF 131
>gnl|CDD|197546 smart00155, PLDc, Phospholipase D. Active site motifs.
Phosphatidylcholine-hydrolyzing phospholipase D (PLD)
isoforms are activated by ADP-ribosylation factors
(ARFs). PLD produces phosphatidic acid from
phosphatidylcholine, which may be essential for the
formation of certain types of transport vesicles or may
be constitutive vesicular transport to signal
transduction pathways. PC-hydrolysing PLD is a
homologue of cardiolipin synthase, phosphatidylserine
synthase, bacterial PLDs, and viral proteins. Each of
these appears to possess a domain duplication which is
apparent by the presence of two motifs containing
well-conserved histidine, lysine, aspartic acid, and/or
asparagine residues which may contribute to the active
site. An E. coli endonuclease (nuc) and similar
proteins appear to be PLD homologues but possess only
one of these motifs. The profile contained here
represents only the putative active site regions, since
an accurate multiple alignment of the repeat units has
not been achieved.
Length = 28
Score = 33.1 bits (77), Expect = 0.008
Identities = 9/26 (34%), Positives = 13/26 (50%), Gaps = 1/26 (3%)
Query: 49 GLQHMKFYLIDN-CVIITGANLSGDY 73
G+ H K ++D+ I ANL G
Sbjct: 3 GVLHTKLMIVDDEIAYIGSANLDGRS 28
>gnl|CDD|197234 cd09136, PLDc_PSS_G_neg_2, Catalytic domain, repeat 2, of
phosphatidylserine synthases from gram-negative
bacteria. Catalytic domain, repeat 2, of
phosphatidylserine synthases (PSSs) from gram-negative
bacteria. There are two subclasses of PSS enzymes in
bacteria: subclass I of gram-negative bacteria and
subclass II of gram-positive bacteria. It is common that
PSSs in gram-positive bacteria and yeast are tight
membrane-associated enzymes. By contrast, the
gram-negative bacterial PSSs, such as Escherichia coli
PSS, are commonly bound to the ribosomes. They are
peripheral membrane proteins that can interact with the
surface of the inner membrane by binding to the lipid
substrate (CDP-diacylglycerol) and the lipid product
(phosphatidylserine). The prototypical member of this
subfamily is Escherichia coli PSS (also called
CDP-diacylglycerol-L-serine O-phosphatidyltransferase,
EC 2.7.8.8), which catalyzes the exchange reactions
between CMP and CDP-diacylglycerol, and between serine
and phosphatidylserine. The phosphatidylserine is then
decarboxylated by phosphatidylserine decarboxylase to
yield phosphatidylethanolamine, the major phospholipid
in Escherichia coli. It also catalyzes the hydrolysis of
CDP-diacylglycerol to form phosphatidic acid with the
release of CMP. PSS may utilize a ping-pong mechanism
involving a phosphatidyl-enzyme intermediate, which is
distinct from those of gram-positive bacterial
phosphatidylserine synthases. Moreover, all members in
this subfamily have two HKD motifs (H-x-K-x(4)-D, where
x represents any amino acid residue) that characterizes
the phospholipase D (PLD) superfamily. The two motifs
constitute an active site for the formation of a
covalent substrate-enzyme intermediate.
Length = 215
Score = 35.3 bits (82), Expect = 0.021
Identities = 35/127 (27%), Positives = 55/127 (43%), Gaps = 17/127 (13%)
Query: 172 PLIELPPLHIQLDSRVTKLILSLARDGSCVSLGTGYFNLTQEYVRAM--LDKPRVNYSVL 229
PL+ L QL+ + +LI S + + + T YFNL + VR + L K V ++
Sbjct: 5 PLVGLGKRGNQLNRTIRQLIQSAESE---LIICTPYFNLPRSLVRDIARLLKRGVKVEII 61
Query: 230 MAHPTANGFLGAR----GAAGGIPYAYTALAARFLSRVSN------LKVAMFEYVRSGWT 279
+ TAN F G +PY Y RF R+ L V +++ +
Sbjct: 62 VGDKTANDFYIPPEEPFKTIGALPYLYEINLRRFAKRLQKYIDNGQLNVRLWKD--GNNS 119
Query: 280 YHAKGLW 286
+H KG+W
Sbjct: 120 FHLKGIW 126
>gnl|CDD|216022 pfam00614, PLDc, Phospholipase D Active site motif.
Phosphatidylcholine-hydrolysing phospholipase D (PLD)
isoforms are activated by ADP-ribosylation factors
(ARFs). PLD produces phosphatidic acid from
phosphatidylcholine, which may be essential for the
formation of certain types of transport vesicles or may
be constitutive vesicular transport to signal
transduction pathways. PC-hydrolysing PLD is a
homologue of cardiolipin synthase, phosphatidylserine
synthase, bacterial PLDs, and viral proteins. Each of
these appears to possess a domain duplication which is
apparent by the presence of two motifs containing
well-conserved histidine, lysine, and/or asparagine
residues which may contribute to the active site.
aspartic acid. An E. coli endonuclease (nuc) and
similar proteins appear to be PLD homologues but
possess only one of these motifs. The profile contained
here represents only the putative active site regions,
since an accurate multiple alignment of the repeat
units has not been achieved.
Length = 28
Score = 31.2 bits (72), Expect = 0.040
Identities = 10/28 (35%), Positives = 13/28 (46%), Gaps = 1/28 (3%)
Query: 47 LIGLQHMKFYLIDN-CVIITGANLSGDY 73
G H K ++D+ I GANL G
Sbjct: 1 NDGRLHTKIVVVDDEVAYIGGANLDGGS 28
>gnl|CDD|221916 pfam13091, PLDc_2, PLD-like domain.
Length = 129
Score = 33.5 bits (77), Expect = 0.043
Identities = 13/38 (34%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 52 HMKFYLIDNCVIITG-ANLSGDYFTSRQDRYMIIQDHK 88
H KFY+ID I G +NL+ + + +II D +
Sbjct: 79 HAKFYIIDGKTAIIGSSNLTRRALSLNLENNLIIDDPE 116
>gnl|CDD|197267 cd09170, PLDc_Nuc, Catalytic domain of EDTA-resistant nuclease Nuc
from Salmonella typhimurium and similar proteins.
Catalytic domain of an EDTA-resistant nuclease Nuc from
Salmonella typhimurium and similar proteins. Nuc is an
endonuclease cleaving both single- and double-stranded
DNA. It is the smallest known member of the
phospholipase D (PLD, EC 3.1.4.4) superfamily that
includes a diverse group of proteins with various
catalytic functions. Most members of this superfamily
have two copies of the conserved HKD motif
(H-x-K-x(4)-D, where x represents any amino acid
residue) in a single polypeptide chain and both are
required for catalytic activity. However, Nuc only has
one copy of the HKD motif per subunit but form a
functionally active homodimer (it is most likely also
active in solution as a multimeric protein), which has a
single active site at the dimer interface containing the
HKD motifs from both subunits. Due to the lack of a
distinct domain for DNA binding, Nuc cuts DNA
non-specifically. It utilizes a two-step mechanism to
cleave phosphodiester bonds: Upon substrate binding, the
bond is first attacked by a histidine residue from one
HKD motif to form a covalent phosphohistidine
intermediate, which is then hydrolyzed by water with the
aid of a second histidine residue from the other HKD
motif in the opposite subunit.
Length = 142
Score = 32.9 bits (76), Expect = 0.081
Identities = 12/50 (24%), Positives = 24/50 (48%), Gaps = 11/50 (22%)
Query: 49 GLQHMKFYLIDNCVIITGA-NLSGDYFTSRQDRY-----MIIQDHKPLSD 92
+ H K +ID +ITG+ N FT+ ++ ++I++ L+
Sbjct: 86 AIMHNKVMVIDGKTVITGSFN-----FTASAEKRNAENLLVIRNPPELAQ 130
>gnl|CDD|197200 cd00138, PLDc_SF, Catalytic domain of phospholipase D superfamily
proteins. Catalytic domain of phospholipase D (PLD)
superfamily proteins. The PLD superfamily is composed of
a large and diverse group of proteins including plant,
mammalian and bacterial PLDs, bacterial cardiolipin (CL)
synthases, bacterial phosphatidylserine synthases (PSS),
eukaryotic phosphatidylglycerophosphate (PGP) synthase,
eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and
some bacterial endonucleases (Nuc and BfiI), among
others. PLD enzymes hydrolyze phospholipid
phosphodiester bonds to yield phosphatidic acid and a
free polar head group. They can also catalyze the
transphosphatidylation of phospholipids to acceptor
alcohols. The majority of members in this superfamily
contain a short conserved sequence motif (H-x-K-x(4)-D,
where x represents any amino acid residue), called the
HKD signature motif. There are varying expanded forms of
this motif in different family members. Some members
contain variant HKD motifs. Most PLD enzymes are
monomeric proteins with two HKD motif-containing
domains. Two HKD motifs from two domains form a single
active site. Some PLD enzymes have only one copy of the
HKD motif per subunit but form a functionally active
dimer, which has a single active site at the dimer
interface containing the two HKD motifs from both
subunits. Different PLD enzymes may have evolved through
domain fusion of a common catalytic core with separate
substrate recognition domains. Despite their various
catalytic functions and a very broad range of substrate
specificities, the diverse group of PLD enzymes can bind
to a phosphodiester moiety. Most of them are active as
bi-lobed monomers or dimers, and may possess similar
core structures for catalytic activity. They are
generally thought to utilize a common two-step ping-pong
catalytic mechanism, involving an enzyme-substrate
intermediate, to cleave phosphodiester bonds. The two
histidine residues from the two HKD motifs play key
roles in the catalysis. Upon substrate binding, a
histidine from one HKD motif could function as the
nucleophile, attacking the phosphodiester bond to create
a covalent phosphohistidine intermediate, while the
other histidine residue from the second HKD motif could
serve as a general acid, stabilizing the leaving group.
Length = 119
Score = 30.6 bits (69), Expect = 0.40
Identities = 8/35 (22%), Positives = 15/35 (42%), Gaps = 1/35 (2%)
Query: 51 QHMKFYLIDNC-VIITGANLSGDYFTSRQDRYMII 84
H K +ID + ANLS ++ +++
Sbjct: 85 LHAKVVVIDGEVAYVGSANLSTASAAQNREAGVLV 119
>gnl|CDD|100071 cd02642, R3H_encore_like, R3H domain of encore-like and DIP1-like
proteins. Drosophila encore is involved in the germline
exit after four mitotic divisions, by facilitating
SCF-ubiquitin-proteasome-dependent proteolysis. Maize
DBF1-interactor protein 1 (DIP1) containing an R3H
domain is a potential regulator of DBF1 activity in
stress responses. The name of the R3H domain comes from
the characteristic spacing of the most conserved
arginine and histidine residues. The function of the
domain is predicted to bind ssDNA or ssRNA in a
sequence-specific manner.
Length = 63
Score = 28.3 bits (64), Expect = 0.87
Identities = 11/29 (37%), Positives = 13/29 (44%)
Query: 37 NRLLPHRYNELIGLQHMKFYLIDNCVIIT 65
RLL HR + GL H CVI+
Sbjct: 33 YRLLAHRVAQYYGLDHNVDNSGGKCVIVN 61
>gnl|CDD|197206 cd09107, PLDc_vPLD3_4_5_like_2, Putative catalytic domain, repeat
2, of vertebrate phospholipases, PLD3, PLD4 and PLD5,
viral envelope proteins K4 and p37, and similar
proteins. Putative catalytic domain, repeat 2, of
vertebrate phospholipases D, PLD3, PLD4, and PLD5 (EC
3.1.4.4), viral envelope proteins (vaccinia virus
proteins K4 and p37), and similar proteins. Most family
members contain two copies of the HKD motifs
(H-x-K-x(4)-D, where x represents any amino acid
residue), and have been classified into the
phospholipase D (PLD) superfamily. Proteins in this
subfamily are associated with Golgi membranes, altering
their lipid content by the conversion of phospholipids
into phosphatidic acid, which is thought to be involved
in the regulation of lipid movement. ADP ribosylation
factor (ARF), a small guanosine triphosphate binding
protein, might be required activity. The vaccinia virus
p37 protein, encoded by the F13L gene, is also
associated with Golgi membranes and is required for the
envelopment and spread of the extracellular enveloped
virus (EEV). The vaccinia virus protein K4, encoded by
the HindIII K4L gene, remains to be characterized.
Sequence analysis indicates that the vaccinia virus
proteins K4 and p37 might have evolved from one or more
captured eukaryotic genes involved in cellular lipid
metabolism. Up to date, no catalytic activity of PLD3
has been shown. Furthermore, due to the lack of
functional important histidine and lysine residues in
the HKD motif, mammalian PLD5 has been characterized as
an inactive PLD. The poxvirus p37 proteins may also lack
PLD enzymatic activity, since they contain only one
partially conserved HKD motif (N-x-K-x(4)-D).
Length = 175
Score = 29.9 bits (68), Expect = 1.1
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 52 HMKFYLIDNCVIITGANLSGDYFTS 76
H K+ + D I +N SGDYF +
Sbjct: 125 HAKYMVTDERAYIGTSNWSGDYFYN 149
>gnl|CDD|197268 cd09171, PLDc_vPLD6_like, Catalytic domain of vertebrate
phospholipase D6 and similar proteins. Catalytic domain
of vertebrate phospholipase D6 (PLD6, EC 3.1.4.4), a
homolog of the EDTA-resistant nuclease Nuc from
Salmonella typhimurium, and similar proteins. PLD6 can
selectively hydrolyze the terminal phosphodiester bond
of phosphatidylcholine (PC) with the formation of
phosphatidic acid and alcohols. Phosphatidic acid is an
essential compound involved in signal transduction. It
also catalyzes the transphosphatidylation of
phospholipids to acceptor alcohols, by which various
phospholipids can be synthesized. PLD6 belongs to the
phospholipase D (PLD) superfamily. Its monomer contains
a short conserved sequence motif, H-x-K-x(4)-D (where x
represents any amino acid residue), termed the HKD
motif, which is essential in catalysis. PLD6 is more
closely related to the nuclease Nuc than to other
vertebrate phospholipases, which have two copies of the
HKD motif in a single polypeptide chain. Like Nuc, PLD6
may utilize a two-step mechanism to cleave
phosphodiester bonds: Upon substrate binding, the bond
is first attacked by a histidine residue from the HKD
motif of one subunit to form a covalent phosphohistidine
intermediate, which is then hydrolyzed by water with the
aid of a second histidine residue from the other HKD
motif in the opposite subunit.
Length = 136
Score = 29.1 bits (66), Expect = 1.2
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 43 RYNELIGLQHMKFYLIDNCVIITG 66
R + G H KF +ID ++ITG
Sbjct: 77 RTDLSSGHMHHKFAVIDGKILITG 100
>gnl|CDD|197253 cd09156, PLDc_CLS_unchar1_1, Putative catalytic domain, repeat 1,
of uncharacterized proteins similar to bacterial
cardiolipin synthase. Putative catalytic domain, repeat
1, of uncharacterized proteins similar to bacterial
cardiolipin (CL) synthases, which catalyze the
reversible phosphatidyl group transfer between two
phosphatidylglycerol molecules to form CL and glycerol.
Members of this subfamily contain two HKD motifs
(H-x-K-x(4)-D, where x represents any amino acid
residue) that characterizes the phospholipase D (PLD)
superfamily. The two motifs may be part of the active
site and may be involved in phosphatidyl group transfer.
Length = 154
Score = 29.2 bits (66), Expect = 1.4
Identities = 8/26 (30%), Positives = 12/26 (46%), Gaps = 1/26 (3%)
Query: 52 HMKFYLIDNCVIIT-GANLSGDYFTS 76
H K + D I+ G NL+ +Y
Sbjct: 98 HRKIAIADGSTAISGGMNLANEYMGP 123
>gnl|CDD|184076 PRK13479, PRK13479, 2-aminoethylphosphonate--pyruvate transaminase;
Provisional.
Length = 368
Score = 28.0 bits (63), Expect = 7.3
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 136 RSRSLVLDMYDGYRTRNTT 154
SRSL LD+YD + T
Sbjct: 217 NSRSLSLDLYDQWAYMEKT 235
>gnl|CDD|118101 pfam09565, RE_NgoFVII, NgoFVII restriction endonuclease. This
family includes the NgoFVII (recognises GCSGC but
cleavage site unknown) restriction endonuclease.
Length = 296
Score = 27.8 bits (62), Expect = 8.4
Identities = 13/44 (29%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 63 IITGANLS-GDYFTSRQDRYMIIQDHKPLSDFFDDLSRVLCKIS 105
+I ANLS + FT+RQ ++ D P D ++ L + +
Sbjct: 98 LIGSANLSQINAFTTRQYEAVVTLDPAPAYDLYEFLLSNIVCLH 141
>gnl|CDD|239173 cd02772, MopB_NDH-1_NuoG2, MopB_NDH-1_NuoG2: The second domain of
the NuoG subunit of the NADH-quinone oxidoreductase/NADH
dehydrogenase-1 (NDH-1), found in beta- and
gammaproteobacteria. The NDH-1 is the first
energy-transducting complex in the respiratory chain and
functions as a redox pump that uses the redox energy to
translocate H+ ions across the membrane, resulting in a
significant contribution to energy production. In
Escherichia coli NDH-1, the largest subunit is encoded
by the nuoG gene, and is part of the 14 distinct
subunits constituting the functional enzyme. The NuoG
subunit is made of two domains: the first contains three
binding sites for FeS clusters (the fer2 domain), the
second domain (this CD), is of unknown function or, as
postulated, has lost an ancestral formate dehydrogenase
activity that became redundant during the evolution of
the complex I enzyme. Although only vestigial sequence
evidence remains of a molybdopterin binding site, this
protein domain belongs to the molybdopterin_binding
(MopB) superfamily of proteins.
Length = 414
Score = 27.7 bits (62), Expect = 9.1
Identities = 25/87 (28%), Positives = 35/87 (40%), Gaps = 9/87 (10%)
Query: 216 RAMLDKPRVNYSVLMAHP---TANGFLGARGA--AGGIPYAYTALAARFLSRVSN--LKV 268
AML++PR Y +L P AN A A A +A A+ L ++ L +
Sbjct: 312 AAMLEQPRKAYLLLNVEPELDCANPA-QALAALNQAEFVVALSAFASAALLDYADVLLPI 370
Query: 269 AMFEYVRSGWTYHAKGLWYSESPGSKP 295
A F SG + +G S KP
Sbjct: 371 APF-TETSGTFVNLEGRVQSFKGVVKP 396
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
0.322 0.138 0.426
Gapped
Lambda K H
0.267 0.0901 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,011,786
Number of extensions: 1545533
Number of successful extensions: 1283
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1272
Number of HSP's successfully gapped: 30
Length of query: 308
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 211
Effective length of database: 6,635,264
Effective search space: 1400040704
Effective search space used: 1400040704
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 (21.9 bits)
S2: 59 (26.2 bits)