phospholipase D/transphosphatidylase [Fictibacillus macauensis ZFHKF-1]
Protein Classification
phospholipase D-like domain-containing protein( domain architecture ID 11445347)
phospholipase D-like domain-containing protein; similar to Bacillus subtilis minor cardiolipin synthase ClsB involved in the biosynthesis of cardiolipin
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||
| Cls | COG1502 | Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ... |
33-400 | 1.24e-123 | ||||||
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and metabolism]; Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase is part of the Pathway/BioSystem: Phospholipid biosynthesis : Pssm-ID: 441111 [Multi-domain] Cd Length: 367 Bit Score: 361.95 E-value: 1.24e-123
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| Name | Accession | Description | Interval | E-value | ||||||
| Cls | COG1502 | Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ... |
33-400 | 1.24e-123 | ||||||
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and metabolism]; Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase is part of the Pathway/BioSystem: Phospholipid biosynthesis Pssm-ID: 441111 [Multi-domain] Cd Length: 367 Bit Score: 361.95 E-value: 1.24e-123
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| cls | PRK01642 | cardiolipin synthetase; Reviewed |
46-397 | 1.26e-112 | ||||||
cardiolipin synthetase; Reviewed Pssm-ID: 234967 [Multi-domain] Cd Length: 483 Bit Score: 337.91 E-value: 1.26e-112
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| bac_cardiolipin | TIGR04265 | cardiolipin synthase; This model is based on experimentally characterized bacterial ... |
44-400 | 3.39e-91 | ||||||
cardiolipin synthase; This model is based on experimentally characterized bacterial cardiolipin synthases (cls) from E. coli, Staphylococcus aureus (two), and Bacillus pseudofirmus OF4. This model describes just one of several homologous but non-orthologous forms of cls. The cutoff score is set arbitrarily high to avoid false-positives. Note that there are two enzymatic activites called cardiolipin synthase. This model represents type 1, which does not rely on a CDP-linked donor, but instead does a reversible transfer of a phosphatidyl group from one phosphatidylglycerol molecule to another. Pssm-ID: 211988 [Multi-domain] Cd Length: 483 Bit Score: 282.84 E-value: 3.39e-91
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| PLDc_CLS_1 | cd09110 | Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Catalytic ... |
51-203 | 6.41e-73 | ||||||
Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Catalytic domain, repeat 1, of bacterial cardiolipin (CL) synthase and a few homologs found in eukaryotes and archaea. Bacterial CL synthases catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. The monomer of bacterial CL synthase 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. 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 belonging to the PLD superfamily. Like other PLD enzymes, bacterial CL synthases 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. Pssm-ID: 197209 [Multi-domain] Cd Length: 154 Bit Score: 224.66 E-value: 6.41e-73
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| PLDc_2 | pfam13091 | PLD-like domain; |
240-356 | 6.49e-31 | ||||||
PLD-like domain; Pssm-ID: 463784 [Multi-domain] Cd Length: 132 Bit Score: 114.70 E-value: 6.49e-31
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| PLDc | smart00155 | Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ... |
144-170 | 5.78e-04 | ||||||
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. Pssm-ID: 197546 [Multi-domain] Cd Length: 28 Bit Score: 36.98 E-value: 5.78e-04
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| Name | Accession | Description | Interval | E-value | ||||||
| Cls | COG1502 | Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ... |
33-400 | 1.24e-123 | ||||||
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and metabolism]; Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase is part of the Pathway/BioSystem: Phospholipid biosynthesis Pssm-ID: 441111 [Multi-domain] Cd Length: 367 Bit Score: 361.95 E-value: 1.24e-123
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| cls | PRK01642 | cardiolipin synthetase; Reviewed |
46-397 | 1.26e-112 | ||||||
cardiolipin synthetase; Reviewed Pssm-ID: 234967 [Multi-domain] Cd Length: 483 Bit Score: 337.91 E-value: 1.26e-112
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| bac_cardiolipin | TIGR04265 | cardiolipin synthase; This model is based on experimentally characterized bacterial ... |
44-400 | 3.39e-91 | ||||||
cardiolipin synthase; This model is based on experimentally characterized bacterial cardiolipin synthases (cls) from E. coli, Staphylococcus aureus (two), and Bacillus pseudofirmus OF4. This model describes just one of several homologous but non-orthologous forms of cls. The cutoff score is set arbitrarily high to avoid false-positives. Note that there are two enzymatic activites called cardiolipin synthase. This model represents type 1, which does not rely on a CDP-linked donor, but instead does a reversible transfer of a phosphatidyl group from one phosphatidylglycerol molecule to another. Pssm-ID: 211988 [Multi-domain] Cd Length: 483 Bit Score: 282.84 E-value: 3.39e-91
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| PRK12452 | PRK12452 | cardiolipin synthase; |
40-400 | 1.82e-81 | ||||||
cardiolipin synthase; Pssm-ID: 171510 [Multi-domain] Cd Length: 509 Bit Score: 258.70 E-value: 1.82e-81
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| PLDc_CLS_1 | cd09110 | Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Catalytic ... |
51-203 | 6.41e-73 | ||||||
Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Catalytic domain, repeat 1, of bacterial cardiolipin (CL) synthase and a few homologs found in eukaryotes and archaea. Bacterial CL synthases catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. The monomer of bacterial CL synthase 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. 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 belonging to the PLD superfamily. Like other PLD enzymes, bacterial CL synthases 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. Pssm-ID: 197209 [Multi-domain] Cd Length: 154 Bit Score: 224.66 E-value: 6.41e-73
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| PLDc_CLS_2 | cd09112 | catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; This CD ... |
236-397 | 2.59e-54 | ||||||
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. Pssm-ID: 197211 [Multi-domain] Cd Length: 174 Bit Score: 177.67 E-value: 2.59e-54
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| PLDc_PaCLS_like_1 | cd09155 | Putative catalytic domain, repeat 1, of Pseudomonas aeruginosa cardiolipin synthase and ... |
53-203 | 6.88e-54 | ||||||
Putative catalytic domain, repeat 1, of Pseudomonas aeruginosa cardiolipin synthase and similar proteins; Putative catalytic domain, repeat 1, 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. Pssm-ID: 197252 [Multi-domain] Cd Length: 156 Bit Score: 175.89 E-value: 6.88e-54
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| PLDc_PaCLS_like_2 | cd09161 | Putative catalytic domain, repeat 2, of Pseudomonas aeruginosa cardiolipin synthase and ... |
239-400 | 1.58e-49 | ||||||
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. Pssm-ID: 197258 [Multi-domain] Cd Length: 176 Bit Score: 165.15 E-value: 1.58e-49
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| PLDc_CLS_unchar1_1 | cd09156 | Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial ... |
51-204 | 9.07e-48 | ||||||
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. Pssm-ID: 197253 [Multi-domain] Cd Length: 154 Bit Score: 159.73 E-value: 9.07e-48
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| PLDc_EcCLS_like_2 | cd09158 | Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase and similar proteins; ... |
239-398 | 7.68e-44 | ||||||
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. Pssm-ID: 197255 [Multi-domain] Cd Length: 174 Bit Score: 150.42 E-value: 7.68e-44
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| PRK11263 | PRK11263 | cardiolipin synthase ClsB; |
49-385 | 2.29e-42 | ||||||
cardiolipin synthase ClsB; Pssm-ID: 236888 [Multi-domain] Cd Length: 411 Bit Score: 153.18 E-value: 2.29e-42
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| PLDc_ybhO_like_2 | cd09159 | Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; ... |
233-389 | 9.86e-41 | ||||||
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. Pssm-ID: 197256 [Multi-domain] Cd Length: 170 Bit Score: 141.91 E-value: 9.86e-41
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| PLDc_EcCLS_like_1 | cd09152 | Catalytic domain, repeat 1, of Escherichia coli cardiolipin synthase and similar proteins; ... |
46-204 | 2.48e-37 | ||||||
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. Pssm-ID: 197250 [Multi-domain] Cd Length: 163 Bit Score: 132.72 E-value: 2.48e-37
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| PLDc_CLS_unchar1_2 | cd09162 | Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial ... |
238-372 | 5.69e-35 | ||||||
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. Pssm-ID: 197259 [Multi-domain] Cd Length: 172 Bit Score: 126.99 E-value: 5.69e-35
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| PLDc_CLS_unchar2_1 | cd09157 | Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial ... |
53-204 | 6.26e-34 | ||||||
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. Pssm-ID: 197254 [Multi-domain] Cd Length: 155 Bit Score: 123.44 E-value: 6.26e-34
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| PLDc_SMU_988_like_2 | cd09160 | Putative catalytic domain, repeat 2, of Streptococcus mutans uncharacterized protein SMU_988 ... |
241-400 | 3.62e-33 | ||||||
Putative catalytic domain, repeat 2, of Streptococcus mutans uncharacterized protein SMU_988 and similar proteins; Putative catalytic domain, repeat 2, of Streptococcus mutans uncharacterized protein SMU_988 and similar proteins. Although SMU_988 and similar proteins have not been functionally characterized, members in this subfamily show high sequence homology 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. Pssm-ID: 197257 [Multi-domain] Cd Length: 176 Bit Score: 122.22 E-value: 3.62e-33
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| PLDc_2 | pfam13091 | PLD-like domain; |
240-356 | 6.49e-31 | ||||||
PLD-like domain; Pssm-ID: 463784 [Multi-domain] Cd Length: 132 Bit Score: 114.70 E-value: 6.49e-31
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| PLDc_SMU_988_like_1 | cd09154 | Putative catalytic domain, repeat 1, of Streptococcus mutans uncharacterized protein SMU_988 ... |
53-204 | 3.05e-29 | ||||||
Putative catalytic domain, repeat 1, of Streptococcus mutans uncharacterized protein SMU_988 and similar proteins; Putative catalytic domain, repeat 1, of Streptococcus mutans uncharacterized protein SMU_988 and similar proteins. Although SMU_988 and similar proteins have not been functionally characterized, members in this subfamily show high sequence homology 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. Pssm-ID: 197251 [Multi-domain] Cd Length: 155 Bit Score: 111.08 E-value: 3.05e-29
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| PLDc_CLS_unchar2_2 | cd09163 | Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial ... |
240-400 | 5.01e-26 | ||||||
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. Pssm-ID: 197260 [Multi-domain] Cd Length: 176 Bit Score: 103.02 E-value: 5.01e-26
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| PLDc_ymdC_like_2 | cd09113 | Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and ... |
240-386 | 6.27e-23 | ||||||
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. Pssm-ID: 197212 [Multi-domain] Cd Length: 218 Bit Score: 95.75 E-value: 6.27e-23
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| PLDc_ymdC_like_1 | cd09111 | Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and ... |
64-204 | 4.43e-22 | ||||||
Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins; Putative catalytic domain, repeat 1, 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. Pssm-ID: 197210 [Multi-domain] Cd Length: 162 Bit Score: 91.83 E-value: 4.43e-22
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| PLDc_SF | cd00138 | Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ... |
238-348 | 7.06e-17 | ||||||
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. Pssm-ID: 197200 [Multi-domain] Cd Length: 119 Bit Score: 76.02 E-value: 7.06e-17
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| PLDc_2 | pfam13091 | PLD-like domain; |
60-203 | 9.83e-14 | ||||||
PLD-like domain; Pssm-ID: 463784 [Multi-domain] Cd Length: 132 Bit Score: 67.70 E-value: 9.83e-14
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| PLDc_unchar1_2 | cd09128 | Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; ... |
240-367 | 1.56e-13 | ||||||
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. Pssm-ID: 197226 [Multi-domain] Cd Length: 142 Bit Score: 67.30 E-value: 1.56e-13
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| PLDc_vPLD3_4_5_like_1 | cd09106 | Putative catalytic domain, repeat 1, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral ... |
244-341 | 2.67e-09 | ||||||
Putative catalytic domain, repeat 1, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral envelope proteins K4 and p37, and similar proteins; Putative catalytic domain, repeat 1, 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). Pssm-ID: 197205 [Multi-domain] Cd Length: 153 Bit Score: 55.72 E-value: 2.67e-09
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| PLDc_vPLD1_2_like_2 | cd09105 | Catalytic domain, repeat 2, of vertebrate phospholipases, PLD1 and PLD2, and similar proteins; ... |
246-352 | 1.51e-08 | ||||||
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. Pssm-ID: 197204 [Multi-domain] Cd Length: 146 Bit Score: 53.07 E-value: 1.51e-08
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| PLDc_vPLD1_2_like_1 | cd09104 | Catalytic domain, repeat 1, of vertebrate phospholipases, PLD1 and PLD2, and similar proteins; ... |
47-166 | 2.23e-08 | ||||||
Catalytic domain, repeat 1, of vertebrate phospholipases, PLD1 and PLD2, and similar proteins; Catalytic domain, repeat 1, 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. Pssm-ID: 197203 [Multi-domain] Cd Length: 147 Bit Score: 52.79 E-value: 2.23e-08
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| PLDc_unchar1_2 | cd09128 | Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; ... |
64-203 | 9.45e-08 | ||||||
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. Pssm-ID: 197226 [Multi-domain] Cd Length: 142 Bit Score: 50.74 E-value: 9.45e-08
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| PLDc_unchar3 | cd09131 | Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic ... |
55-174 | 1.02e-07 | ||||||
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. Pssm-ID: 197229 [Multi-domain] Cd Length: 143 Bit Score: 50.80 E-value: 1.02e-07
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| PLDc_unchar1_1 | cd09127 | Putative catalytic domain, repeat 1, of uncharacterized phospholipase D-like proteins; ... |
245-341 | 2.29e-07 | ||||||
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. Pssm-ID: 197225 [Multi-domain] Cd Length: 141 Bit Score: 49.57 E-value: 2.29e-07
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| PLDc_unchar4 | cd09132 | Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic ... |
240-346 | 2.66e-07 | ||||||
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. Pssm-ID: 197230 [Multi-domain] Cd Length: 122 Bit Score: 49.20 E-value: 2.66e-07
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| PLDc_unchar3 | cd09131 | Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic ... |
240-356 | 3.40e-07 | ||||||
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. Pssm-ID: 197229 [Multi-domain] Cd Length: 143 Bit Score: 49.26 E-value: 3.40e-07
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| PLDc_Nuc_like | cd09116 | Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar ... |
232-347 | 3.41e-07 | ||||||
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. Pssm-ID: 197215 [Multi-domain] Cd Length: 138 Bit Score: 49.22 E-value: 3.41e-07
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| PLDc_SF | cd00138 | Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ... |
62-165 | 3.66e-07 | ||||||
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. Pssm-ID: 197200 [Multi-domain] Cd Length: 119 Bit Score: 48.67 E-value: 3.66e-07
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| PLDc_CLS_1 | cd09110 | Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Catalytic ... |
240-346 | 1.51e-06 | ||||||
Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Catalytic domain, repeat 1, of bacterial cardiolipin (CL) synthase and a few homologs found in eukaryotes and archaea. Bacterial CL synthases catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. The monomer of bacterial CL synthase 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. 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 belonging to the PLD superfamily. Like other PLD enzymes, bacterial CL synthases 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. Pssm-ID: 197209 [Multi-domain] Cd Length: 154 Bit Score: 47.47 E-value: 1.51e-06
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| PRK13912 | PRK13912 | nuclease NucT; Provisional |
232-347 | 5.27e-06 | ||||||
nuclease NucT; Provisional Pssm-ID: 184389 [Multi-domain] Cd Length: 177 Bit Score: 46.31 E-value: 5.27e-06
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| PLDc_CDP-OH_P_transf_II_2 | cd09103 | Catalytic domain, repeat 2, of CDP-alcohol phosphatidyltransferase class-II family members; ... |
246-369 | 1.61e-05 | ||||||
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. Pssm-ID: 197202 [Multi-domain] Cd Length: 184 Bit Score: 45.29 E-value: 1.61e-05
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| PLDc_Nuc | cd09170 | Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar ... |
240-336 | 1.88e-05 | ||||||
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. Pssm-ID: 197267 [Multi-domain] Cd Length: 142 Bit Score: 44.05 E-value: 1.88e-05
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| PLDc_vPLD3_1 | cd09144 | Putative catalytic domain, repeat 1, of vertebrate phospholipase PLD3; Putative catalytic ... |
235-364 | 5.33e-05 | ||||||
Putative catalytic domain, repeat 1, of vertebrate phospholipase PLD3; Putative catalytic domain, repeat 1, of phospholipase D3 (PLD3, EC 3.1.4.4). The human protein is also known as Hu-K4 or HUK4 and it was identified as a human homolog of the vaccinia virus protein K4, which is encoded by the HindIII K4L gene. PLD3 is found in many human organs with highest expression levels found in the central nervous system. 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), PLD3 has been assigned to the PLD superfamily although no catalytic activity has been detected experimentally. PLD3 is a membrane-bound protein that colocalizes with protein disulfide isomerase, an endoplasmic reticulum (ER) protein. Like other homologs of protein K4, PLD3 might alter the lipid content of associated membranes by selectively hydrolyzing phosphatidylcholine (PC) into the corresponding phosphatidic acid, which is thought to be involved in the regulation of lipid movement. Pssm-ID: 197242 [Multi-domain] Cd Length: 172 Bit Score: 43.40 E-value: 5.33e-05
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| PLDc_CLS_2 | cd09112 | catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; This CD ... |
58-165 | 6.44e-05 | ||||||
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. Pssm-ID: 197211 [Multi-domain] Cd Length: 174 Bit Score: 43.24 E-value: 6.44e-05
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| PLDc_unchar1_1 | cd09127 | Putative catalytic domain, repeat 1, of uncharacterized phospholipase D-like proteins; ... |
64-202 | 9.13e-05 | ||||||
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. Pssm-ID: 197225 [Multi-domain] Cd Length: 141 Bit Score: 42.25 E-value: 9.13e-05
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| PLDc_vPLD6_like | cd09171 | Catalytic domain of vertebrate phospholipase D6 and similar proteins; Catalytic domain of ... |
59-165 | 1.79e-04 | ||||||
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. Pssm-ID: 197268 [Multi-domain] Cd Length: 136 Bit Score: 41.06 E-value: 1.79e-04
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| PLDc_yjhR_C_like | cd09118 | C-terminal domain of Escherichia coli uncharacterized protein yjhR and similar proteins; ... |
239-280 | 3.37e-04 | ||||||
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. Pssm-ID: 197217 [Multi-domain] Cd Length: 144 Bit Score: 40.76 E-value: 3.37e-04
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| PLDc_Nuc | cd09170 | Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar ... |
62-165 | 3.88e-04 | ||||||
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. Pssm-ID: 197267 [Multi-domain] Cd Length: 142 Bit Score: 40.19 E-value: 3.88e-04
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| PLDc_Nuc_like_unchar1_1 | cd09172 | Putative catalytic domain, repeat 1, of uncharacterized hypothetical proteins similar to Nuc, ... |
240-342 | 4.52e-04 | ||||||
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. Pssm-ID: 197269 [Multi-domain] Cd Length: 144 Bit Score: 40.03 E-value: 4.52e-04
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| PLDc_PMFPLD_like_1 | cd09108 | Catalytic domain, repeat 1, of phospholipase D from Streptomyces Sp. Strain PMF and similar ... |
93-203 | 5.50e-04 | ||||||
Catalytic domain, repeat 1, of phospholipase D from Streptomyces Sp. Strain PMF and similar proteins; Catalytic domain, repeat 1, 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. Pssm-ID: 197207 [Multi-domain] Cd Length: 210 Bit Score: 40.88 E-value: 5.50e-04
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| PLDc | smart00155 | Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ... |
144-170 | 5.78e-04 | ||||||
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. Pssm-ID: 197546 [Multi-domain] Cd Length: 28 Bit Score: 36.98 E-value: 5.78e-04
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| PLDc_Nuc_like | cd09116 | Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar ... |
58-165 | 6.47e-04 | ||||||
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. Pssm-ID: 197215 [Multi-domain] Cd Length: 138 Bit Score: 39.59 E-value: 6.47e-04
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| PLDc_unchar6 | cd09176 | Putative catalytic domain of uncharacterized hypothetical proteins with one or two copies of ... |
239-347 | 1.40e-03 | ||||||
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. Pssm-ID: 197273 [Multi-domain] Cd Length: 114 Bit Score: 38.09 E-value: 1.40e-03
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| PLDc | pfam00614 | Phospholipase D Active site motif; Phosphatidylcholine-hydrolysing phospholipase D (PLD) ... |
143-170 | 1.65e-03 | ||||||
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 homolog 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 homologs 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. Pssm-ID: 395489 [Multi-domain] Cd Length: 28 Bit Score: 35.47 E-value: 1.65e-03
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| PLDc_C_DEXD_like | cd09126 | C-terminal putative phospholipase D-like domain of uncharacterized prokaryotic HKD family ... |
229-336 | 2.44e-03 | ||||||
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. Pssm-ID: 197224 [Multi-domain] Cd Length: 126 Bit Score: 37.62 E-value: 2.44e-03
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| PLDc_vPLD1_2_yPLD_like_1 | cd09138 | Catalytic domain, repeat 1, of vertebrate phospholipases, PLD1 and PLD2, yeast PLDs, and ... |
53-163 | 3.47e-03 | ||||||
Catalytic domain, repeat 1, of vertebrate phospholipases, PLD1 and PLD2, yeast PLDs, and similar proteins; Catalytic domain, repeat 1, of vertebrate phospholipases D (PLD1 and PLD2), yeast phospholipase D (PLD SPO14/PLD1), and other similar eukaryotic proteins. These PLD enzymes play a pivotal role in transmembrane signaling and cellular regulation. 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. The vertebrate PLD1 and PLD2 are membrane associated phosphatidylinositol 4,5-bisphosphate (PIP2)-dependent enzymes that selectively hydrolyze phosphatidylcholine (PC). Protein cofactors and calcium may be required for their activation. Yeast SPO14/PLD1 is a calcium-independent PLD, which needs PIP2 for its activity. Instead of the regulatory calcium-dependent phospholipid-binding C2 domain in plants, most mammalian and yeast PLDs have adjacent Phox (PX) and the Pleckstrin homology (PH) domains at the N-terminus, which have been shown to mediate membrane targeting of the protein and are closely linked to polyphosphoinositide signaling. The PX and PH domains are also present in zeta-type PLD from Arabidopsis, which is more closely related to vertebrate PLDs than to other plant PLD types. In addition, this subfamily also includes some related proteins which have either PX-like or PH domains in their N-termini. Like other members of the PLD superfamily, the monomer of mammalian and yeast PLDs consists of two catalytic domains, each containing one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue). Two HKD motifs from the two domains form a single active site. These 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. Pssm-ID: 197236 [Multi-domain] Cd Length: 146 Bit Score: 37.54 E-value: 3.47e-03
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| PHA02820 | PHA02820 | phospholipase-D-like protein; Provisional |
239-365 | 4.54e-03 | ||||||
phospholipase-D-like protein; Provisional Pssm-ID: 222934 [Multi-domain] Cd Length: 424 Bit Score: 38.82 E-value: 4.54e-03
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| PLDc_PSS_G_neg_2 | cd09136 | Catalytic domain, repeat 2, of phosphatidylserine synthases from gram-negative bacteria; ... |
240-369 | 6.49e-03 | ||||||
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. Pssm-ID: 197234 Cd Length: 215 Bit Score: 37.58 E-value: 6.49e-03
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| PLDc_PGS1_euk_1 | cd09135 | Catalytic domain, repeat 1, of eukaryotic PhosphatidylGlycerophosphate Synthases; Catalytic ... |
48-170 | 9.75e-03 | ||||||
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. Pssm-ID: 197233 [Multi-domain] Cd Length: 170 Bit Score: 36.76 E-value: 9.75e-03
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