RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1966
(59 letters)
>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 = 78.8 bits (195), Expect = 5e-21
Identities = 26/51 (50%), Positives = 33/51 (64%)
Query: 8 IPVRLTGPPYIMHHKFVLIDSSLVLQGSMNWTTQACSGNYENVVITGTPGI 58
IPVR MHHKF +ID +++ GS NWT QA +GN ENV+IT P +
Sbjct: 74 IPVRTDLSSGHMHHKFAVIDGKILITGSFNWTRQAVTGNQENVLITNDPKL 124
>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 = 65.6 bits (161), Expect = 8e-16
Identities = 22/52 (42%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 8 IPVRLTGPPYIMHHKFVLIDSSLVLQGSMNWTTQACSGNYENV-VITGTPGI 58
IPVR+ IMH+K ++ID V+ GS N+T A N EN+ VI P +
Sbjct: 77 IPVRIDDNYAIMHNKVMVIDGKTVITGSFNFTASAEKRNAENLLVIRNPPEL 128
>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 = 64.2 bits (157), Expect = 2e-15
Identities = 22/48 (45%), Positives = 29/48 (60%)
Query: 6 LNIPVRLTGPPYIMHHKFVLIDSSLVLQGSMNWTTQACSGNYENVVIT 53
L IPVR +MHHKF++ID +V+ GS NWT N EN++I
Sbjct: 75 LGIPVRTDSGSKLMHHKFIIIDGKIVITGSANWTKSGFHRNDENLLII 122
>gnl|CDD|221916 pfam13091, PLDc_2, PLD-like domain.
Length = 129
Score = 57.0 bits (138), Expect = 1e-12
Identities = 18/47 (38%), Positives = 24/47 (51%), Gaps = 1/47 (2%)
Query: 7 NIPVRLTGPPYIMHHKFVLIDSSLVLQGSMNWTTQACSGNYENVVIT 53
+ VRL +H KF +ID + GS N T +A S N EN +I
Sbjct: 67 GVEVRLY-YDGSLHAKFYIIDGKTAIIGSSNLTRRALSLNLENNLII 112
>gnl|CDD|197271 cd09174, PLDc_Nuc_like_unchar2, Putative catalytic domain of
uncharacterized hypothetical proteins closely related to
Nuc, , an endonuclease from Salmonella typhimurium.
Putative catalytic domain of uncharacterized
hypothetical proteins, which show high sequence homology
to the endonuclease from Salmonella typhimurium and
vertebrate phospholipase D6. 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
characterizes the PLD superfamily and is essential for
catalysis. Nuc and PLD6 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. However, proteins in this
subfamily have two HKD motifs in a single polypeptide
chain.
Length = 136
Score = 50.8 bits (122), Expect = 4e-10
Identities = 20/46 (43%), Positives = 28/46 (60%), Gaps = 3/46 (6%)
Query: 10 VRLTGPPY--IMHHKFVLIDSSLVLQGSMNWTTQACSGNYENVVIT 53
+ G Y +MH+KF +ID V+ GS NWT A N+EN++IT
Sbjct: 76 LPGNGSRYGNLMHNKFCVIDFKTVITGSYNWTKNA-EYNFENIIIT 120
>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 = 49.1 bits (117), Expect = 1e-09
Identities = 14/53 (26%), Positives = 22/53 (41%)
Query: 1 MPKVQLNIPVRLTGPPYIMHHKFVLIDSSLVLQGSMNWTTQACSGNYENVVIT 53
V + V +H K V+ID + GS N +T + + N E V+
Sbjct: 67 RAGVNVRSYVTPPHFFERLHAKVVVIDGEVAYVGSANLSTASAAQNREAGVLV 119
>gnl|CDD|224419 COG1502, Cls,
Phosphatidylserine/phosphatidylglycerophosphate/cardioli
pin synthases and related enzymes [Lipid metabolism].
Length = 438
Score = 51.0 bits (122), Expect = 1e-09
Identities = 13/52 (25%), Positives = 23/52 (44%)
Query: 7 NIPVRLTGPPYIMHHKFVLIDSSLVLQGSMNWTTQACSGNYENVVITGTPGI 58
+ V +H K ++ID VL GS N ++ N+E ++ P +
Sbjct: 343 GVKVYEYPGGAFLHSKVMIIDDRTVLVGSANLDPRSLRLNFEVGLVIEDPEL 394
Score = 31.7 bits (72), Expect = 0.009
Identities = 9/33 (27%), Positives = 13/33 (39%)
Query: 7 NIPVRLTGPPYIMHHKFVLIDSSLVLQGSMNWT 39
P+R +H K V+ID + G N
Sbjct: 153 PRPLRFRRLNRRLHRKIVVIDGKVAFVGGANIG 185
>gnl|CDD|184389 PRK13912, PRK13912, nuclease NucT; Provisional.
Length = 177
Score = 48.6 bits (116), Expect = 5e-09
Identities = 17/36 (47%), Positives = 23/36 (63%)
Query: 18 IMHHKFVLIDSSLVLQGSMNWTTQACSGNYENVVIT 53
IMH K +ID +V+ GS NW+ A NYE ++IT
Sbjct: 119 IMHQKVAIIDDKIVVLGSANWSKNAFENNYEVLLIT 154
>gnl|CDD|197270 cd09173, PLDc_Nuc_like_unchar1_2, Putative catalytic domain, repeat
2, of uncharacterized hypothetical proteins similar to
Nuc, an endonuclease from Salmonella typhimurium.
Putative catalytic domain, repeat 2, of uncharacterized
hypothetical proteins, which show high sequence homology
to the endonuclease from Salmonella typhimurium and
vertebrate phospholipase D6. 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
characterizes the PLD superfamily and is essential for
catalysis. Nuc and PLD6 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. However, proteins in this
subfamily have two HKD motifs in a single polypeptide
chain.
Length = 159
Score = 43.9 bits (104), Expect = 3e-07
Identities = 16/45 (35%), Positives = 26/45 (57%), Gaps = 4/45 (8%)
Query: 18 IMHHKFVLID----SSLVLQGSMNWTTQACSGNYENVVITGTPGI 58
+HHKF++ID +V+ GS N++ A N EN+++ P I
Sbjct: 100 KLHHKFMVIDPFGDDPVVITGSHNFSGAANDNNDENLLVIRDPAI 144
>gnl|CDD|197229 cd09131, PLDc_unchar3, Putative catalytic domain of uncharacterized
phospholipase D-like proteins. Putative catalytic
domain of uncharacterized phospholipase D (PLD, EC
3.1.4.4)-like proteins. Members of this subfamily
contain one copy of HKD motif (H-x-K-x(4)-D, where x
represents any amino acid residue) that characterizes
the PLD superfamily.
Length = 143
Score = 43.1 bits (102), Expect = 4e-07
Identities = 19/52 (36%), Positives = 25/52 (48%)
Query: 7 NIPVRLTGPPYIMHHKFVLIDSSLVLQGSMNWTTQACSGNYENVVITGTPGI 58
+ VR P H K V+ID V GS NWT A N+E V+ +P +
Sbjct: 81 GVEVRFDSPSVTTHTKLVVIDGRTVYVGSHNWTYSALDYNHEASVLIESPEV 132
>gnl|CDD|197226 cd09128, PLDc_unchar1_2, Putative catalytic domain, repeat 2, of
uncharacterized phospholipase D-like proteins. Putative
catalytic domain, repeat 2, of uncharacterized
phospholipase D (PLD, EC 3.1.4.4)-like proteins. PLD
enzymes hydrolyze phospholipid phosphodiester bonds to
yield phosphatidic acid and a free polar head group.
They can also catalyze transphosphatidylation of
phospholipids to acceptor alcohols. Members of this
subfamily contain two HKD motifs (H-x-K-x(4)-D, where x
represents any amino acid residue) that characterizes
the PLD superfamily. The two motifs may be part of the
active site and may be involved in phosphatidyl group
transfer.
Length = 142
Score = 43.0 bits (102), Expect = 4e-07
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 8 IPVRLTGPPYI-MHHKFVLIDSSLVLQGSMNWTTQACSGNYENVVITGTPGIK 59
+PVRL ++ +H K +++D L GS NW+ + N E +I P +
Sbjct: 79 VPVRLLKDKFLKIHAKGIVVDGKTALVGSENWSANSLDRNREVGLIFDDPEVA 131
>gnl|CDD|197269 cd09172, PLDc_Nuc_like_unchar1_1, Putative catalytic domain, repeat
1, of uncharacterized hypothetical proteins similar to
Nuc, an endonuclease from Salmonella typhimurium.
Putative catalytic domain, repeat 1, of uncharacterized
hypothetical proteins, which show high sequence homology
to the endonuclease from Salmonella typhimurium and
vertebrate phospholipase D6. 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
characterizes the PLD superfamily and is essential for
catalysis. Nuc and PLD6 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. However, proteins in this
subfamily have two HKD motifs in a single polypeptide
chain.
Length = 144
Score = 38.1 bits (89), Expect = 3e-05
Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 4/39 (10%)
Query: 18 IMHHKFVLIDSSL----VLQGSMNWTTQACSGNYENVVI 52
+MH+KF+++D VL GS N+TT G NV+I
Sbjct: 89 LMHNKFLVVDRKDGPNRVLTGSTNFTTSGLYGQSNNVLI 127
>gnl|CDD|197225 cd09127, PLDc_unchar1_1, Putative catalytic domain, repeat 1, of
uncharacterized phospholipase D-like proteins. Putative
catalytic domain, repeat 1, of uncharacterized
phospholipase D (PLD, EC 3.1.4.4)-like proteins. PLD
enzymes hydrolyze phospholipid phosphodiester bonds to
yield phosphatidic acid and a free polar head group.
They can also catalyze transphosphatidylation of
phospholipids to acceptor alcohols. Members of this
subfamily contain two HKD motifs (H-x-K-x(4)-D, where x
represents any amino acid residue) that characterizes
the PLD superfamily. The two motifs may be part of the
active site and may be involved in phosphatidyl group
transfer.
Length = 141
Score = 35.3 bits (82), Expect = 3e-04
Identities = 12/50 (24%), Positives = 21/50 (42%), Gaps = 3/50 (6%)
Query: 7 NIPVRLTGP--PYIMHH-KFVLIDSSLVLQGSMNWTTQACSGNYENVVIT 53
+ VR T Y H K++++D L + N+ +G V+T
Sbjct: 76 GVEVRWTNGTARYRYTHAKYIVVDDERALVLTENFKPSGFTGTRGFGVVT 125
>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 = 31.6 bits (73), Expect = 0.002
Identities = 6/24 (25%), Positives = 12/24 (50%)
Query: 16 PYIMHHKFVLIDSSLVLQGSMNWT 39
++H K +++D + GS N
Sbjct: 2 DGVLHTKLMIVDDEIAYIGSANLD 25
>gnl|CDD|197259 cd09162, PLDc_CLS_unchar1_2, Putative catalytic domain, repeat 2,
of uncharacterized proteins similar to bacterial
cardiolipin synthase. Putative catalytic domain, repeat
2, 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 = 172
Score = 31.8 bits (73), Expect = 0.008
Identities = 15/43 (34%), Positives = 22/43 (51%)
Query: 15 PPYIMHHKFVLIDSSLVLQGSMNWTTQACSGNYENVVITGTPG 57
P ++H K V++D L L GS N ++ NYE V +P
Sbjct: 89 QPGMLHAKAVVVDDKLALVGSANLDMRSLFLNYEVAVFFYSPA 131
>gnl|CDD|197260 cd09163, PLDc_CLS_unchar2_2, Putative catalytic domain, repeat 2,
of uncharacterized proteins similar to bacterial
cardiolipin synthase. Putative catalytic domain, repeat
2, 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 = 176
Score = 31.8 bits (73), Expect = 0.008
Identities = 11/35 (31%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 4 VQLNIPVRLTGPPYIMHHKFVLIDSSLVLQGSMNW 38
++ + + L PP+ H K +++D + L GS NW
Sbjct: 79 LEHGVRIYLQPPPF-DHSKLMVVDGAWALIGSANW 112
>gnl|CDD|197275 cd09178, PLDc_N_Snf2_like, N-terminal putative catalytic domain of
uncharacterized HKD family nucleases fused to putative
helicases from the Snf2-like family. N-terminal
putative catalytic domain of uncharacterized archaeal
and prokaryotic HKD family nucleases fused to putative
helicases from the Snf2-like family, which belong to the
DNA/RNA helicase superfamily II (SF2). Although
Snf2-like family enzymes do not possess helicase
activity, they contain a helicase-like region, where
seven helicase-related sequence motifs are found,
similar to those in DEAD/DEAH box helicases, which
represent the biggest family within the SF2 superfamily.
In addition to the helicase-like region, members of this
family also contain an N-terminal putative catalytic
domain with one copy of the conserved HKD motif
(H-x-K-x(4)-D, where x represents any amino acid
residue), and have been classified as members of the
phospholipase D (PLD, EC 3.1.4.4) superfamily.
Length = 134
Score = 31.0 bits (71), Expect = 0.015
Identities = 10/44 (22%), Positives = 17/44 (38%), Gaps = 1/44 (2%)
Query: 17 YIMHHKFVLIDSSLVLQGSMNWTTQACSGNYE-NVVITGTPGIK 59
Y+ + GS N+T +GN E NV + ++
Sbjct: 78 YLFDGPDNDNGPGTAIVGSSNFTKAGLTGNLELNVEVKDRDDVE 121
>gnl|CDD|197256 cd09159, PLDc_ybhO_like_2, Catalytic domain, repeat 2, of
Escherichia coli cardiolipin synthase ybhO and similar
proteins. Catalytic domain, repeat 2, of Escherichia
coli cardiolipin (CL) synthase ybhO and similar
proteins. In Escherichia coli, there are two genes, f413
(ybhO) and o493 (ymdC), which are homologous to gene cls
that encodes the Escherichia coli CL synthase. The
prototype of this subfamily is Escherichia coli CL
synthase ybhO specified by the f413 (ybhO) gene. ybhO is
a membrane-bound protein that catalyzes the formation of
cardiolipin (CL) by transferring phosphatidyl group
between two phosphatidylglycerol molecules. It can also
catalyze phosphatidyl group transfer to water to form
phosphatidate. In contrast to the Escherichia coli CL
synthase encoded by the cls gene (EcCLS), ybhO does not
hydrolyze CL. Moreover, ybhO lacks an N-terminal segment
encoded by Escherichia coli cls, which makes ybhO easy
to denature. The monomer of ybhO consists of two
catalytic domains. Each catalytic domain contains one
copy of the conserved HKD motif (H-x-K-x(4)-D, where x
represents any amino acid residue) that characterizes
the phospholipase D (PLD) superfamily. Two HKD motifs
from two domains form a single active site involved in
phosphatidyl group transfer. ybhO can be stimulated by
phosphate and inhibited by CL, the product of the
reaction, and by phosphatidate. Phosphate stimulation
may be unique to enzymes with CL synthase activity
belonging to the PLD superfamily.
Length = 170
Score = 30.6 bits (70), Expect = 0.019
Identities = 12/38 (31%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 16 PYIMHHKFVLIDSSLVLQGSMNWTTQACSGNYE-NVVI 52
P ++H K +ID GS N ++ N E N+V+
Sbjct: 90 PSMLHAKTAVIDGDWATVGSSNLDPRSLRLNLEANLVV 127
>gnl|CDD|197230 cd09132, PLDc_unchar4, Putative catalytic domain of uncharacterized
phospholipase D-like proteins. Putative catalytic
domain of uncharacterized phospholipase D (PLD, EC
3.1.4.4)-like proteins. Members of this subfamily
contain one copy of HKD motif (H-x-K-x(4)-D, where x
represents any amino acid residue) that characterizes
the PLD superfamily.
Length = 122
Score = 29.9 bits (68), Expect = 0.033
Identities = 10/35 (28%), Positives = 14/35 (40%)
Query: 14 GPPYIMHHKFVLIDSSLVLQGSMNWTTQACSGNYE 48
G +H K ++ D +L S N T N E
Sbjct: 83 GKRASLHAKVIVADRRRLLVTSANLTGAGMERNIE 117
>gnl|CDD|197231 cd09133, PLDc_unchar5, Putative catalytic domain of uncharacterized
hypothetical proteins with one or two copies of the HKD
motif. Putative catalytic domain of uncharacterized
hypothetical proteins with similarity to phospholipase D
(PLD, EC 3.1.4.4). PLD enzymes hydrolyze phospholipid
phosphodiester bonds to yield phosphatidic acid and a
free polar head group. They can also catalyze
transphosphatidylation of phospholipids to acceptor
alcohols. Members of this subfamily contain one or two
copies of the HKD motif (H-x-K-x(4)-D, where x
represents any amino acid residue) that characterizes
the PLD superfamily.
Length = 127
Score = 29.2 bits (66), Expect = 0.052
Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 4/34 (11%)
Query: 5 QLNIPVRLTGPPYIMHHKFVLIDSSLVLQGSMNW 38
+N+ +R TG H KF++ D L GS NW
Sbjct: 79 GVNVHLRTTG----SHAKFLVCDDWFALVGSCNW 108
>gnl|CDD|197276 cd09179, PLDc_N_DEXD_a, N-terminal putative catalytic domain of
uncharacterized prokaryotic and archeal HKD family
nucleases fused to a DEAD/DEAH box helicase domain.
N-terminal putative catalytic domain of uncharacterized
prokaryotic and archeal HKD family nucleases fused to a
DEAD/DEAH box helicase domain. All members of this
subfamily are uncharacterized. Other characterized
members of the superfamily that have a related domain
architecture ( containing a DEAD/DEAH box helicase
domain), include the DNA/RNA helicase superfamily II
(SF2) and Res-subunit of type III restriction
endonucleases. In addition to the helicase-like region,
members of this subfamily also contain one copy of the
conserved HKD motif (H-x-K-x(4)-D, where x represents
any amino acid residue) in the N-terminal putative
catalytic domain. The HKD motif characterizes the
phospholipase D (PLD, EC 3.1.4.4) superfamily.
Length = 190
Score = 29.5 bits (67), Expect = 0.052
Identities = 12/37 (32%), Positives = 17/37 (45%), Gaps = 4/37 (10%)
Query: 18 IMHHKF-VLIDS---SLVLQGSMNWTTQACSGNYENV 50
I H K + D+ + GS N T A NYE++
Sbjct: 127 IFHEKAGIFTDADGNKVAFSGSANETASAWKRNYESI 163
>gnl|CDD|197216 cd09117, PLDc_Bfil_DEXD_like, Catalytic domain of type II
restriction endonucleases BfiI and NgoFVII, and
uncharacterized proteins with a DEAD domain. Catalytic
domain of type II restriction endonucleases BfiI and
NgoFVII, uncharacterized type III restriction
endonuclease Res subunit, and uncharacterized DNA/RNA
helicase superfamily II members. Proteins in this family
are found mainly in prokaryotes. They contain one copy
of the conserved HKD motif (H-x-K-x(4)-D, where x
represents any amino acid residue) in a single
polypeptide chain, and have been classified as members
of the phospholipase D (PLD, EC 3.1.4.4) superfamily.
BfiI consists of two discrete domains with distinct
functions: an N-terminal catalytic domain with
non-specific nuclease activity and dimerization function
that is more closely related to Nuc, an EDTA-resistant
nuclease from the phospholipase D (PLD) superfamily; and
a C-terminal domain that specifically recognizes its
target sequences, 5'-ACTGGG-3'. BfiI forms a
functionally active homodimer which has two DNA-binding
surfaces located at the C-terminal domains but only one
active site, located at the dimer interface between the
two N-terminal catalytic domains that contain the two
HKD motifs from both subunits. BfiI utilizes a single
active site to cut both DNA strands, which represents a
novel mechanism for the scission of double-stranded DNA.
It uses a histidine residue from the HKD motif in one
subunit as the nucleophile for the cleavage of the
target phosphodiester bond in both of the anti-parallel
DNA strands, while the symmetrically-related histidine
residue from the HKD motif of the opposite subunit acts
as the proton donor/acceptor during both strand-scission
events.
Length = 117
Score = 29.3 bits (66), Expect = 0.058
Identities = 15/54 (27%), Positives = 23/54 (42%), Gaps = 3/54 (5%)
Query: 3 KVQLNIPVRLTGPPYIMHHKFVLIDSSL---VLQGSMNWTTQACSGNYENVVIT 53
N+ VR+ ++H K L ++ + GS N T SGN E V+
Sbjct: 64 LALGNLNVRIFDAGPLLHAKLYLFENDDPTRAIVGSANLTQGGLSGNIEAAVVI 117
>gnl|CDD|197217 cd09118, PLDc_yjhR_C_like, C-terminal domain of Escherichia coli
uncharacterized protein yjhR and similar proteins.
C-terminal domain of Escherichia coli uncharacterized
protein yjhR, encoded by the o338 gene, and similar
proteins. Although the biological function of yjhR
remains unknown, it shows sequence similarity to the
C-terminal portions of superfamily I DNA and RNA
helicases, which are ubiquitous enzymes mediating
ATP-dependent unwinding of DNA and RNA duplexes, and
play essential roles in gene replication and expression.
Moreover, The C-termini of yjhR and similar proteins
contain one HKD motif (H-x-K-x(4)-D, where x represents
any amino acid residue) that characterizes the
phospholipase D (PLD) superfamily. The PLDc-like domain
of yjhR is similar to bacterial endonucleases, Nuc and
BfiI, both of which have only one copy of the HKD motif
per chain. They function as homodimers, with a single
active site at the dimer interface containing the HKD
motifs from both subunits. They 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.
Length = 144
Score = 28.8 bits (65), Expect = 0.091
Identities = 13/39 (33%), Positives = 19/39 (48%), Gaps = 4/39 (10%)
Query: 20 HHKFVLIDSSLVLQGSMNWTTQACSGNYEN----VVITG 54
H K V++D+ L+ GS NW + G Y +V G
Sbjct: 89 HSKIVIVDNHLLAVGSFNWLSAVRDGKYARHETSLVYRG 127
>gnl|CDD|219624 pfam07894, DUF1669, Protein of unknown function (DUF1669). This
family is composed of sequences derived from
hypothetical eukaryotic proteins of unknown function.
Some members of this family are annotated as being
potential phospholipases but no literature was found to
support this.
Length = 284
Score = 28.4 bits (64), Expect = 0.13
Identities = 15/48 (31%), Positives = 21/48 (43%), Gaps = 13/48 (27%)
Query: 7 NIPVR-LTGPPYIM----------HHKFVLIDSSLVLQG--SMNWTTQ 41
N+ VR +TG Y KF+L+D VL G S W++
Sbjct: 205 NLRVRTVTGSTYYTRSGTKFKGQLREKFLLVDGDKVLSGSYSFTWSSG 252
>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 = 26.6 bits (60), Expect = 0.16
Identities = 6/24 (25%), Positives = 10/24 (41%)
Query: 16 PYIMHHKFVLIDSSLVLQGSMNWT 39
+H K V++D + G N
Sbjct: 2 DGRLHTKIVVVDDEVAYIGGANLD 25
>gnl|CDD|197212 cd09113, PLDc_ymdC_like_2, Putative catalytic domain, repeat 2, of
Escherichia coli uncharacterized protein ymdC and
similar proteins. Putative catalytic domain, repeat 2,
of Escherichia coli uncharacterized protein ymdC and
similar proteins. In Escherichia coli, there are two
genes, f413 (ybhO) and o493 (ymdC), which are homologous
to gene cls that encodes the Escherichia coli
cardiolipin (CL) synthase. The prototype of this
subfamily is an uncharacterized protein ymdC specified
by the o493 (ymdC) gene. Although the functional
characterization of ymdC and similar proteins remains
unknown, members of this subfamily show high sequence
homology to bacterial CL synthases, which catalyze the
reversible phosphatidyl group transfer between two
phosphatidylglycerol molecules to form CL and glycerol.
Moreover, ymdC and its similar proteins contain two HKD
motifs (H-x-K-x(4)-D, where x represents any amino acid
residue) that characteriszes the phospholipase D (PLD)
superfamily. The two motifs may be part of the active
site and may be involved in phosphatidyl group transfer.
Length = 218
Score = 28.0 bits (63), Expect = 0.21
Identities = 9/20 (45%), Positives = 11/20 (55%)
Query: 19 MHHKFVLIDSSLVLQGSMNW 38
+H K +ID LV GS N
Sbjct: 117 LHAKSFVIDDRLVFVGSFNL 136
>gnl|CDD|197218 cd09119, PLDc_FAM83_N, N-terminal phospholipase D-like domain of
proteins from the Family with sequence similarity 83.
N-terminal phospholipase D (PLD)-like domain of
vetebrate proteins from the Family with sequence
similarity 83 (FAM83), which is comprised of 8 members,
designated FAM83A through FAM83H. Since the N-terminal
PLD-like domain of FAM83 proteins shows only trace
similarity to the PLD catalytic domain and lacks the
functionally important histidine residue, the FAM83
proteins may share a similar three-dimensional fold with
PLD enzymes, but are unlikely to carry PLD activity.
Members of the FAM83 are mostly uncharacterized
proteins. FAM83A, also known as tumor antigen BJ-TSA-9,
is a novel tumor-specific gene highly expressed in human
lung adenocarcinoma. FAM83D, also known as spindle
protein CHICA, is a cell-cycle-regulated spindle
component which localizes to the mitotic spindle and is
both upregulated and phosphorylated during mitosis. The
gene encoding protein FAM83H is the first gene involved
in the etiology of amelogenesis imperfecta (AI), that
encodes a non-secreted protein due to the absence of a
signal peptide. Defects in gene FAM83H cause autosomal
dominant hypocalcified amelogenesis imperfecta (ADHCAI).
FAM83B, FAM83C, FAM83F, and FAM83G are uncharacterized
proteins present across vertebrates while FAM83E is an
uncharacterized protein found only in mammals.
Length = 269
Score = 27.7 bits (62), Expect = 0.27
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 11/44 (25%)
Query: 7 NIPVR-LTGPPYI----------MHHKFVLIDSSLVLQGSMNWT 39
N+ VR + G Y M KF+L+D V+ GS ++T
Sbjct: 193 NMRVRSVGGKTYCSRSGKKFKGQMKEKFLLVDGDRVVSGSYSFT 236
>gnl|CDD|197208 cd09109, PLDc_PMFPLD_like_2, Catalytic domain, repeat 2, of
phospholipase D from Streptomyces Sp. Strain PMF and
similar proteins. Catalytic domain, repeat 2, of
phospholipases D (PLD, EC 3.1.4.4) from Streptomyces Sp.
Strain PMF (PMFPLD) and similar proteins, which are
generally extracellular and bear N-terminal signal
sequences. PMFPLD hydrolyzes the terminal phosphodiester
bond of phospholipids with the formation of phosphatidic
acid and alcohols. Phosphatidic acid is an essential
compound involved in signal transduction. It also
catalyzes a transphosphatidylation of phospholipids to
acceptor alcohols, by which various phospholipids can be
synthesized. In contrast to eukaryotic PLDs, PMFPLD has
a compact structure, which consists of two catalytic
domains, but lacks the regulatory domains. Each
catalytic domain contains one copy of the HKD motif
(H-x-K-x(4)-D, where x represents any amino acid
residue) that characterizes the PLD superfamily. Two HKD
motifs from two domains form a single active site. Like
other PLD enzymes, PMFPLD may 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 residue 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. A
calcium-dependent PLD from Streptomyce chromofuscus is
excluded from this family, since it displays very little
sequence homology with other Streptomyces PLDs.
Moreover, it does not contain the conserved HKD motif
and hydrolyzes the phospholipids via a different
mechanism.
Length = 212
Score = 27.6 bits (61), Expect = 0.27
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 14 GPPYIMHHKFVLIDSSLVLQGSMN 37
G PY +H K V++D L GS N
Sbjct: 155 GAPYALHAKLVIVDGKLFYIGSDN 178
>gnl|CDD|197211 cd09112, PLDc_CLS_2, catalytic domain repeat 2 of bacterial
cardiolipin synthase and similar proteins. This CD
corresponds to the catalytic domain repeat 2 of
bacterial cardiolipin synthase (CL synthase, EC 2.7.8.-)
and a few homologs found in eukaryotes and archea.
Bacterial CL synthases catalyze reversible phosphatidyl
group transfer between two phosphatidylglycerol
molecules to form cardiolipin (CL) and glycerol. The
monomer of bacterial CL synthase consists of two
catalytic domains. Each catalytic domain contains one
copy of conserved HKD motifs (H-X-K-X(4)-D, X represents
any amino acid residue) that are the characteristic of
the phospholipase D (PLD) superfamily. Two HKD motifs
from two domains together form a single active site
involving in phosphatidyl group transfer. Bacterial CL
synthases can be stimulated by phosphate and inhibited
by CL, the product of the reaction, and by
phosphatidate. Phosphate stimulation may be unique to
enzymes with CL synthase activity in PLD superfamily.
Like other PLD enzymes, bacterial CL synthase 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 residue 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 = 174
Score = 27.4 bits (62), Expect = 0.29
Identities = 10/35 (28%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 19 MHHKFVLIDSSLVLQGSMNWTTQACSGNYE-NVVI 52
+H K +++D + G+ N ++ N+E N VI
Sbjct: 93 LHSKTLIVDDEIASVGTANLDIRSFELNFEVNAVI 127
>gnl|CDD|197204 cd09105, PLDc_vPLD1_2_like_2, Catalytic domain, repeat 2, of
vertebrate phospholipases, PLD1 and PLD2, and similar
proteins. Catalytic domain, repeat 2, of phospholipase
D (PLD, EC 3.1.4.4) found in yeast, plants, and
vertebrates, and their bacterial homologs. PLDs are
involved in signal transduction, vesicle formation,
protein transport, and mitosis by participating in
phospholipid metabolism. They hydrolyze the terminal
phosphodiester bond of phospholipids resulting in the
formation of phosphatidic acid and alcohols.
Phosphatidic acid is an essential compound involved in
signal transduction. PLDs also catalyze the
transphosphatidylation of phospholipids to acceptor
alcohols, by which various phospholipids can be
synthesized. Both prokaryotic and eukaryotic PLDs have
two HKD motifs (H-x-K-x(4)-D, where x represents any
amino acid residue) that characterizes the phospholipase
D (PLD) superfamily. PLDs are active as bi-lobed
monomers. Each monomer contains two domains, each of
which carries one copy of the HKD motif. Two HKD motifs
from two domains form a single active site. PLDs 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 residue 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 = 146
Score = 27.3 bits (61), Expect = 0.33
Identities = 11/32 (34%), Positives = 15/32 (46%)
Query: 7 NIPVRLTGPPYIMHHKFVLIDSSLVLQGSMNW 38
+ L GPP +H K V++D GS N
Sbjct: 98 HRRGLLGGPPIYVHSKVVIVDDEWATVGSANL 129
>gnl|CDD|197224 cd09126, PLDc_C_DEXD_like, C-terminal putative phospholipase D-like
domain of uncharacterized prokaryotic HKD family
nucleases fused to DEAD/DEAH box helicases. C-terminal
putative phospholipase D (PLD)-like domain of
uncharacterized prokaryotic HKD family nucleases fused
to a DEAD/DEAH box helicase domain. All members of this
subfamily are uncharacterized. In addition to the
helicase-like region, members of this family also
contain a PLD-like domain in the C-terminal region,
which is characterized by a variant HKD (H-x-K-x(4)-D
motif, where x represents any amino acid residue) motif.
Due to the lack of key residues related to PLD activity
in the variant HKD motif, members of this subfamily are
most unlikely to carry PLD activity.
Length = 126
Score = 27.2 bits (61), Expect = 0.35
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 19 MHHKFVLIDSSLVLQGSMN 37
+H KF +ID +V GS+N
Sbjct: 83 IHEKFAIIDKKIVWYGSIN 101
>gnl|CDD|234967 PRK01642, cls, cardiolipin synthetase; Reviewed.
Length = 483
Score = 26.7 bits (60), Expect = 0.54
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 19 MHHKFVLIDSSLVLQGSMNW 38
+H K VL+D L L G++N
Sbjct: 400 LHTKSVLVDDELALVGTVNL 419
Score = 24.4 bits (54), Expect = 4.4
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 19 MHHKFVLIDSSLVLQGSMN 37
H K V+ID + GSMN
Sbjct: 220 NHRKIVVIDGYIAYTGSMN 238
>gnl|CDD|236646 PRK10064, PRK10064, catecholate siderophore receptor CirA;
Provisional.
Length = 663
Score = 26.4 bits (58), Expect = 0.70
Identities = 11/29 (37%), Positives = 18/29 (62%), Gaps = 3/29 (10%)
Query: 31 VLQGSMNWTTQACSGNYENVVITGTPGIK 59
+LQ S +WT+ +C G + I G+P +K
Sbjct: 423 LLQLSPDWTSNSCRGACK---IVGSPDLK 448
>gnl|CDD|197258 cd09161, PLDc_PaCLS_like_2, Putative catalytic domain, repeat 2, of
Pseudomonas aeruginosa cardiolipin synthase and similar
proteins. Putative catalytic domain, repeat 2, of
Pseudomonas aeruginosa cardiolipin (CL) synthase (PaCLS)
and similar proteins. Although PaCLS and similar
proteins have not been functionally characterized,
members in this subfamily show high sequence homology to
bacterial CL synthases, which catalyze the reversible
phosphatidyl group transfer between two
phosphatidylglycerol molecules to form CL and glycerol.
Moreover, PaCLS and other 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 = 176
Score = 26.1 bits (58), Expect = 0.83
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 19 MHHKFVLIDSSLVLQGSMN 37
+H K VL+D L G+ N
Sbjct: 93 LHQKVVLVDDELAAVGTAN 111
>gnl|CDD|219648 pfam07929, PRiA4_ORF3, Plasmid pRiA4b ORF-3-like protein.
Members of this family are similar to the protein
product of ORF-3 found on plasmid pRiA4 in the
bacterium Agrobacterium rhizogenes. This plasmid is
responsible for tumourigenesis at wound sites of plants
infected by this bacterium, but the ORF-3 product does
not seem to be involved in the pathogenetic process.
Other proteins found in this family are annotated as
being putative TnpR resolvases, but no further evidence
was found to back this. Moreover, another member of
this family is described as a probable lexA repressor
and in fact carries a LexA DNA binding domain
(pfam01726), but no references were found to expand on
this.
Length = 175
Score = 25.8 bits (57), Expect = 1.1
Identities = 12/44 (27%), Positives = 17/44 (38%), Gaps = 6/44 (13%)
Query: 1 MPKVQLNIPVRLTGPPYIMHHKFVLIDSSL-----VLQGSMNWT 39
+L + +R PP I V D +L V+Q M W
Sbjct: 1 AKVYRLKVTLRGIEPP-IWRRLEVPADLTLADLHDVIQAVMGWE 43
>gnl|CDD|197250 cd09152, PLDc_EcCLS_like_1, Catalytic domain, repeat 1, of
Escherichia coli cardiolipin synthase and similar
proteins. Catalytic domain, repeat 1, of Escherichia
coli cardiolipin (CL) synthase and similar proteins.
Escherichia coli CL synthase (EcCLS), specified by the
cls gene, is the prototype of this family. EcCLS is a
multi-pass membrane protein that catalyzes reversible
phosphatidyl group transfer between two
phosphatidylglycerol molecules to form cardiolipin (CL)
and glycerol. The monomer of EcCLS consists of two
catalytic domains. Each catalytic domain contains one
copy of the conserved HKD motif (H-x-K-x(4)-D, where x
represents any amino acid residue) that characterizes
the phospholipase D (PLD) superfamily. Two HKD motifs
from two domains form a single active site involved in
phosphatidyl group transfer. EcCLS can be stimulated by
phosphate and inhibited by CL, the product of the
reaction, and by phosphatidate. Phosphate stimulation
may be unique to enzymes with CL synthase activity
belonging to the PLD superfamily. Like other PLD
enzymes, EcCLS utilizes 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 residue 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 = 163
Score = 25.6 bits (57), Expect = 1.1
Identities = 7/18 (38%), Positives = 9/18 (50%)
Query: 20 HHKFVLIDSSLVLQGSMN 37
H K +ID + GS N
Sbjct: 107 HRKIAVIDGRIAYTGSQN 124
>gnl|CDD|171510 PRK12452, PRK12452, cardiolipin synthetase; Reviewed.
Length = 509
Score = 24.9 bits (54), Expect = 2.6
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 19 MHHKFVLIDSSLVLQGSMNWTTQACSGNYE 48
MH K VL+D + G+ N ++ NYE
Sbjct: 426 MHAKIVLVDDKIATIGTANMDVRSFELNYE 455
>gnl|CDD|197243 cd09145, PLDc_vPLD4_1, Putative catalytic domain, repeat 1, of
vertebrate phospholipase PLD4. Putative catalytic
domain, repeat 1, of vertebrate phospholipases D4 (PLD4,
EC 3.1.4.4), homologs of the vaccinia virus protein K4
which is encoded by the HindIII K4L gene. Due to the
presence of two copies of the conserved HKD motif
(H-x-K-x(4)-D, where x represents any amino acid
residue), PLD4 has been assigned to PLD superfamily
although no catalytic activity has been detected to
date. Unlike PLD1 and PLD2, PLD4 does not contain Phox
(PX) and Pleckstrin homology (PH) domains but has a
putative transmembrane domain. Like other vertebrate
homologs of protein K4, PLD4 might be associated with
Golgi membranes and alter their lipid content by
selectively hydrolyze phosphatidylcholine (PC) into
corresponding phosphatidic acid, which is thought to be
involved in the regulation of lipid movement.
Length = 170
Score = 24.9 bits (54), Expect = 2.6
Identities = 13/30 (43%), Positives = 18/30 (60%), Gaps = 4/30 (13%)
Query: 11 RLTGPPYIMHHKFVLIDSSLVLQGS--MNW 38
RLTG ++H KF +ID + GS M+W
Sbjct: 110 RLTGG--VLHSKFWIIDKKHIYVGSANMDW 137
>gnl|CDD|197255 cd09158, PLDc_EcCLS_like_2, Catalytic domain, repeat 2, of
Escherichia coli cardiolipin synthase and similar
proteins. Catalytic domain, repeat 2, of Escherichia
coli cardiolipin (CL) synthase and similar proteins.
Escherichia coli CL synthase (EcCLS), specified by the
cls gene, is the prototype of this family. EcCLS is a
multi-pass membrane protein that catalyzes reversible
phosphatidyl group transfer between two
phosphatidylglycerol molecules to form cardiolipin (CL)
and glycerol. The monomer of EcCLS consists of two
catalytic domains. Each catalytic domain contains one
copy of the conserved HKD motif (H-x-K-x(4)-D, where x
represents any amino acid residue) that characterizes
the phospholipase D (PLD) superfamily. Two HKD motifs
from two domains form a single active site involved in
phosphatidyl group transfer. EcCLS can be stimulated by
phosphate and inhibited by CL, the product of the
reaction, and by phosphatidate. Phosphate stimulation
may be unique to enzymes with CL synthase activity
belonging to the PLD superfamily. Like other PLD
enzymes, EcCLS utilizes 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 residue 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 = 174
Score = 24.5 bits (54), Expect = 3.5
Identities = 11/37 (29%), Positives = 21/37 (56%)
Query: 16 PYIMHHKFVLIDSSLVLQGSMNWTTQACSGNYENVVI 52
++H K V +D + L GS N+ ++ + N+E +I
Sbjct: 90 GGLLHAKTVTVDDEVALVGSSNFDIRSFALNFEISLI 126
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 0.136 0.425
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: 2,881,653
Number of extensions: 182522
Number of successful extensions: 179
Number of sequences better than 10.0: 1
Number of HSP's gapped: 177
Number of HSP's successfully gapped: 41
Length of query: 59
Length of database: 10,937,602
Length adjustment: 31
Effective length of query: 28
Effective length of database: 9,562,628
Effective search space: 267753584
Effective search space used: 267753584
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: 53 (23.9 bits)