hypothetical protein CHLNCDRAFT_133303 [Chlorella variabilis]
Protein Classification
phospholipase D family protein( domain architecture ID 10332436)
phospholipase D family protein may hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group, and may also catalyze the transphosphatidylation of phospholipids to acceptor alcohols
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||
| PLDc_SF super family | cl15239 | Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ... |
26-237 | 3.66e-53 | |||||
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. The actual alignment was detected with superfamily member cd09135: Pssm-ID: 472788 [Multi-domain] Cd Length: 170 Bit Score: 181.59 E-value: 3.66e-53
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| PLDc_PGS1_euk_2 | cd09137 | Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases; Catalytic ... |
447-762 | 1.46e-44 | |||||
Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases; Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate (PGP) synthases, also called CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase (EC 2.7.8.5). Eukaryotic PGP synthases are different and unrelated to prokaryotic PGP synthases and yeast phosphatidylserine synthase. They catalyze the synthesis of PGP from CDP-diacylglycerol and sn-glycerol 3-phosphate, the committed and rate-limiting step in the biosynthesis of cardiolipin (CL), which is an essential component of many mitochondrial functions in eukaryotes. Members in this subfamily all have two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. They may utilize a common two-step ping-pong catalytic mechanism involving a substrate-enzyme intermediate to cleave phosphodiester bonds. The two motifs are suggested to constitute the active site involved in the phosphatidyl group transfer. : Pssm-ID: 197235 Cd Length: 186 Bit Score: 158.51 E-value: 1.46e-44
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| Name | Accession | Description | Interval | E-value | |||||
| PLDc_PGS1_euk_1 | cd09135 | Catalytic domain, repeat 1, of eukaryotic PhosphatidylGlycerophosphate Synthases; Catalytic ... |
26-237 | 3.66e-53 | |||||
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: 181.59 E-value: 3.66e-53
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| PLDc_PGS1_euk_2 | cd09137 | Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases; Catalytic ... |
447-762 | 1.46e-44 | |||||
Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases; Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate (PGP) synthases, also called CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase (EC 2.7.8.5). Eukaryotic PGP synthases are different and unrelated to prokaryotic PGP synthases and yeast phosphatidylserine synthase. They catalyze the synthesis of PGP from CDP-diacylglycerol and sn-glycerol 3-phosphate, the committed and rate-limiting step in the biosynthesis of cardiolipin (CL), which is an essential component of many mitochondrial functions in eukaryotes. Members in this subfamily all have two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. They may utilize a common two-step ping-pong catalytic mechanism involving a substrate-enzyme intermediate to cleave phosphodiester bonds. The two motifs are suggested to constitute the active site involved in the phosphatidyl group transfer. Pssm-ID: 197235 Cd Length: 186 Bit Score: 158.51 E-value: 1.46e-44
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| pssA | PRK09428 | CDP-diacylglycerol--serine O-phosphatidyltransferase; |
20-246 | 7.92e-11 | |||||
CDP-diacylglycerol--serine O-phosphatidyltransferase; Pssm-ID: 236510 [Multi-domain] Cd Length: 451 Bit Score: 65.22 E-value: 7.92e-11
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| Name | Accession | Description | Interval | E-value | |||||
| PLDc_PGS1_euk_1 | cd09135 | Catalytic domain, repeat 1, of eukaryotic PhosphatidylGlycerophosphate Synthases; Catalytic ... |
26-237 | 3.66e-53 | |||||
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: 181.59 E-value: 3.66e-53
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| PLDc_PGS1_euk_2 | cd09137 | Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases; Catalytic ... |
447-762 | 1.46e-44 | |||||
Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases; Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate (PGP) synthases, also called CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase (EC 2.7.8.5). Eukaryotic PGP synthases are different and unrelated to prokaryotic PGP synthases and yeast phosphatidylserine synthase. They catalyze the synthesis of PGP from CDP-diacylglycerol and sn-glycerol 3-phosphate, the committed and rate-limiting step in the biosynthesis of cardiolipin (CL), which is an essential component of many mitochondrial functions in eukaryotes. Members in this subfamily all have two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. They may utilize a common two-step ping-pong catalytic mechanism involving a substrate-enzyme intermediate to cleave phosphodiester bonds. The two motifs are suggested to constitute the active site involved in the phosphatidyl group transfer. Pssm-ID: 197235 Cd Length: 186 Bit Score: 158.51 E-value: 1.46e-44
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| PLDc_CDP-OH_P_transf_II_1 | cd09102 | Catalytic domain, repeat 1, of CDP-alcohol phosphatidyltransferase class-II family members; ... |
27-237 | 1.61e-25 | |||||
Catalytic domain, repeat 1, of CDP-alcohol phosphatidyltransferase class-II family members; Catalytic domain, repeat 1, of CDP-alcohol phosphatidyltransferase class-II family members, which mainly include gram-negative bacterial phosphatidylserine synthases (PSS; CDP-diacylglycerol--serine O-phosphatidyltransferase, EC 2.7.8.8), yeast phosphatidylglycerophosphate synthase (PGP synthase; CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, EC 2.7.8.5), and metazoan PGP synthase 1. All members in this subfamily have two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterize the phospholipase D (PLD) superfamily. They may utilize a common two-step ping-pong catalytic mechanism, involving a substrate-enzyme intermediate, to cleave phosphodiester bonds. The two motifs are suggested to constitute the active site involving phosphatidyl group transfer. Phosphatidylserine synthases from gram-positive bacteria and eukaryotes, and prokaryotic phosphatidylglycerophosphate synthases are not members of this subfamily. Pssm-ID: 197201 [Multi-domain] Cd Length: 168 Bit Score: 103.82 E-value: 1.61e-25
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| PLDc_PSS_G_neg_1 | cd09134 | Catalytic domain, repeat 1, of phosphatidylserine synthases from gram-negative bacteria; ... |
20-235 | 1.57e-13 | |||||
Catalytic domain, repeat 1, of phosphatidylserine synthases from gram-negative bacteria; Catalytic domain, repeat 1, of phosphatidylserine synthases (PSSs) from gram-negative bacteria. There are two subclasses of PSS enzymes in bacteria: subclass I of gram-negative bacteria and subclass II of gram-positive bacteria. It is common that PSSs in gram-positive bacteria and yeast are tight membrane-associated enzymes. By contrast, the gram-negative bacterial PSSs, such as Escherichia coli PSS, are commonly bound to the ribosomes. They are peripheral membrane proteins that can interact with the surface of the inner membrane by binding to the lipid substrate (CDP-diacylglycerol) and the lipid product (phosphatidylserine). The prototypical member of this subfamily is Escherichia coli PSS (also called CDP-diacylglycerol-L-serine O-phosphatidyltransferase, EC 2.7.8.8), which catalyzes the exchange reactions between CMP and CDP-diacylglycerol, and between serine and phosphatidylserine. The phosphatidylserine is then decarboxylated by phosphatidylserine decarboxylase to yield phosphatidylethanolamine, the major phospholipid in Escherichia coli. It also catalyzes the hydrolysis of CDP-diacylglycerol to form phosphatidic acid with the release of CMP. PSS may utilize a ping-pong mechanism involving a phosphatidyl-enzyme intermediate, which is distinct from those of gram-positive bacterial phosphatidylserine synthases. Moreover, all members in this subfamily have two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. The two motifs constitute an active site for the formation of a covalent substrate-enzyme intermediate. Pssm-ID: 197232 [Multi-domain] Cd Length: 173 Bit Score: 69.20 E-value: 1.57e-13
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| pssA | PRK09428 | CDP-diacylglycerol--serine O-phosphatidyltransferase; |
20-246 | 7.92e-11 | |||||
CDP-diacylglycerol--serine O-phosphatidyltransferase; Pssm-ID: 236510 [Multi-domain] Cd Length: 451 Bit Score: 65.22 E-value: 7.92e-11
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| PLDc_CDP-OH_P_transf_II_2 | cd09103 | Catalytic domain, repeat 2, of CDP-alcohol phosphatidyltransferase class-II family members; ... |
515-757 | 3.57e-03 | |||||
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: 39.13 E-value: 3.57e-03
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