NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2217314872|ref|XP_047293059|]
View 

CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X9 [Homo sapiens]

Protein Classification

CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase( domain architecture ID 10173612)

CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase catalyzes the committed step in the biosynthesis of acidic phospholipids

EC:  2.7.8.5
Gene Ontology:  GO:0032049|GO:0008444|GO:0005509|GO:0005524

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PLDc_PGS1_euk_1 cd09135
Catalytic domain, repeat 1, of eukaryotic PhosphatidylGlycerophosphate Synthases; Catalytic ...
 96-269 7.96e-102

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: 302.93  E-value: 7.96e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314872  96 HVRVLSSPAEFFELMKGQIRVAKRRVVMASLYLGTGPLEQELVDCLESTLEKSlqakfpSNLKVSILLDFTRGSRGRKNS 175
Cdd:cd09135     1 QIRILRTPSEFYNTLLDKIRNAKRRIVLSSLYIGTGPLEQELVDALQEALERN------PNLKVSILLDYLRGTRGEPNS 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314872 176 RT--MLLPLLRRFPEQVRVSLFHTPHLRGLLRLLIPERFNETIGLQHIKVYLFDNSVILSGANLSDSYFTNRQDRYVFLQ 253
Cdd:cd09135    75 RTasLLLPLLKLFPDRVRVSLYHTPNLRGLLKKLLPERFNEIIGLQHMKLYIFDDDVILSGANLSDDYFTNRQDRYMLIE 154

                         170
                  ....*....|....*.
gi 2217314872 254 DCAEIADFFTELVDAV 269
Cdd:cd09135   155 NCPELADFYHDLIKAV 170
PLDc_PGS1_euk_2 cd09137
Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases; Catalytic ...
 349-468 4.13e-61

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: 198.57  E-value: 4.13e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314872 349 TWIYPLIQMKPFEIQIDEIVTETLLTEAERGAKVYLTTGYFNLTQAYMDLVLGTRAEYQILLASPEVNGFFGAKGVAGAI 428
Cdd:cd09137     1 TWVYPLLQMGPLNISQEEQVTSRLLQLLPRGSSLTLASGYFNLTPEYLNLLLNSSANLDVLTASPEANGFYGSKGVSGYI 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 2217314872 429 PAAYVHIERQFFSEVCSLGQQERVQLQEYWRRGWTFHAKG 468
Cdd:cd09137    81 PPAYTYIARQFLKRVRKNGKQPRIKLFEYKRPGWTFHAKG 120
 
Name Accession Description Interval E-value
PLDc_PGS1_euk_1 cd09135
Catalytic domain, repeat 1, of eukaryotic PhosphatidylGlycerophosphate Synthases; Catalytic ...
 96-269 7.96e-102

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: 302.93  E-value: 7.96e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314872  96 HVRVLSSPAEFFELMKGQIRVAKRRVVMASLYLGTGPLEQELVDCLESTLEKSlqakfpSNLKVSILLDFTRGSRGRKNS 175
Cdd:cd09135     1 QIRILRTPSEFYNTLLDKIRNAKRRIVLSSLYIGTGPLEQELVDALQEALERN------PNLKVSILLDYLRGTRGEPNS 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314872 176 RT--MLLPLLRRFPEQVRVSLFHTPHLRGLLRLLIPERFNETIGLQHIKVYLFDNSVILSGANLSDSYFTNRQDRYVFLQ 253
Cdd:cd09135    75 RTasLLLPLLKLFPDRVRVSLYHTPNLRGLLKKLLPERFNEIIGLQHMKLYIFDDDVILSGANLSDDYFTNRQDRYMLIE 154

                         170
                  ....*....|....*.
gi 2217314872 254 DCAEIADFFTELVDAV 269
Cdd:cd09135   155 NCPELADFYHDLIKAV 170
PLDc_PGS1_euk_2 cd09137
Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases; Catalytic ...
 349-468 4.13e-61

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: 198.57  E-value: 4.13e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314872 349 TWIYPLIQMKPFEIQIDEIVTETLLTEAERGAKVYLTTGYFNLTQAYMDLVLGTRAEYQILLASPEVNGFFGAKGVAGAI 428
Cdd:cd09137     1 TWVYPLLQMGPLNISQEEQVTSRLLQLLPRGSSLTLASGYFNLTPEYLNLLLNSSANLDVLTASPEANGFYGSKGVSGYI 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 2217314872 429 PAAYVHIERQFFSEVCSLGQQERVQLQEYWRRGWTFHAKG 468
Cdd:cd09137    81 PPAYTYIARQFLKRVRKNGKQPRIKLFEYKRPGWTFHAKG 120
pssA PRK09428
CDP-diacylglycerol--serine O-phosphatidyltransferase;
88-267 3.39e-15

CDP-diacylglycerol--serine O-phosphatidyltransferase;


Pssm-ID: 236510 [Multi-domain]  Cd Length: 451  Bit Score: 77.54  E-value: 3.39e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314872  88 PEFGVSSSHVRVLSSPAEFFELMKGQIRVAKRRVVMASLYLGTGPLEQELVDCLestleksLQAK--FPsNLKVSILLDF 165
Cdd:PRK09428   18 PKIPQSPDDVETLYSPADFRETLLEKIASAKKRIYIVALYLEDDEAGREILDAL-------YQAKqqNP-ELDIKVLVDW 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314872 166 TRGSRGR---KNSRT---MLLPLLRRFPEqVRVSLFhtphlrGllrllIPERFNETIGLQHIKVYLFDNSVILSGANLSD 239
Cdd:PRK09428   90 HRAQRGLigaAASNTnadWYCEMAQEYPG-VDIPVY------G-----VPVNTREALGVLHLKGFIIDDTVLYSGASLNN 157

                         170       180       190
                  ....*....|....*....|....*....|..
gi 2217314872 240 SYFtNRQDRYVF----LQDCAEIADFFTELVD 267
Cdd:PRK09428  158 VYL-HQHDKYRYdryhLIRNAELADSMVNFIQ 188
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 91-317 2.92e-12

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: 68.05  E-value: 2.92e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314872  91 GVSSSHVRVLSSPAEFFELMKGQIRVAKRRVVMASLYLGTGPLEQELVDCLEstlekslqAKFPSNLKVSILLDFTrGSR 170
Cdd:COG1502    11 LVGGNRVTLLVDGDEAFAALLEAIEAARRSIDLEYYIFDDDEVGRRLADALI--------AAARRGVKVRVLLDGI-GSR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314872 171 GRKNSrtmLLPLLRRfpEQVRVSLFHTPHLRgllrlliPERFNetiGLQHIKVYLFDNSV-ILSGANLSDSYF------T 243
Cdd:COG1502    82 ALNRD---FLRRLRA--AGVEVRLFNPVRLL-------FRRLN---GRNHRKIVVIDGRVaFVGGANITDEYLgrdpgfG 146

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2217314872 244 NRQDRYVFLQD--CAEIADFFTELVDAVGDVSL---QLQGDDTVQVVdgMVHPYKGDRaeyckAANKRVMDVINSARTR 317
Cdd:COG1502   147 PWRDTHVRIEGpaVADLQAVFAEDWNFATGEALpfpEPAGDVRVQVV--PSGPDSPRE-----TIERALLAAIASARRR 218
 
Name Accession Description Interval E-value
PLDc_PGS1_euk_1 cd09135
Catalytic domain, repeat 1, of eukaryotic PhosphatidylGlycerophosphate Synthases; Catalytic ...
 96-269 7.96e-102

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: 302.93  E-value: 7.96e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314872  96 HVRVLSSPAEFFELMKGQIRVAKRRVVMASLYLGTGPLEQELVDCLESTLEKSlqakfpSNLKVSILLDFTRGSRGRKNS 175
Cdd:cd09135     1 QIRILRTPSEFYNTLLDKIRNAKRRIVLSSLYIGTGPLEQELVDALQEALERN------PNLKVSILLDYLRGTRGEPNS 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314872 176 RT--MLLPLLRRFPEQVRVSLFHTPHLRGLLRLLIPERFNETIGLQHIKVYLFDNSVILSGANLSDSYFTNRQDRYVFLQ 253
Cdd:cd09135    75 RTasLLLPLLKLFPDRVRVSLYHTPNLRGLLKKLLPERFNEIIGLQHMKLYIFDDDVILSGANLSDDYFTNRQDRYMLIE 154

                         170
                  ....*....|....*.
gi 2217314872 254 DCAEIADFFTELVDAV 269
Cdd:cd09135   155 NCPELADFYHDLIKAV 170
PLDc_CDP-OH_P_transf_II_1 cd09102
Catalytic domain, repeat 1, of CDP-alcohol phosphatidyltransferase class-II family members; ...
 96-269 5.35e-91

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: 275.24  E-value: 5.35e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314872  96 HVRVLSSPAEFFELMKGQIRVAKRRVVMASLYLGTGPLEQELVDCLESTLEKSlqakfpSNLKVSILLDFTRGSRGRKNS 175
Cdd:cd09102     1 HIRFLGSPAEFKTQIIELIRNAKRRVYVASLYWGKDEAGQEILDEIYSVKQEN------PNLDVSVLIDWHRAQRNLLGS 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314872 176 RTMLLPLLRRFPEQVRVSLFHTPHLRGLLRLLIPERFNETIGLQHIKVYLFDNSVILSGANLSDSYFTNRQDRYVFLQDC 255
Cdd:cd09102    75 ETKSATNADWYCEQRQTSQLHLLPDDGN*FFGVPINTNEVFGVLHVKGYVFDDTVLLSGANLSNVYFHYRYDRYVKITHG 154

                         170
                  ....*....|....
gi 2217314872 256 AEIADFFTELVDAV 269
Cdd:cd09102   155 AELADS*VNLINAY 168
PLDc_PGS1_euk_2 cd09137
Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases; Catalytic ...
 349-468 4.13e-61

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: 198.57  E-value: 4.13e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314872 349 TWIYPLIQMKPFEIQIDEIVTETLLTEAERGAKVYLTTGYFNLTQAYMDLVLGTRAEYQILLASPEVNGFFGAKGVAGAI 428
Cdd:cd09137     1 TWVYPLLQMGPLNISQEEQVTSRLLQLLPRGSSLTLASGYFNLTPEYLNLLLNSSANLDVLTASPEANGFYGSKGVSGYI 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 2217314872 429 PAAYVHIERQFFSEVCSLGQQERVQLQEYWRRGWTFHAKG 468
Cdd:cd09137    81 PPAYTYIARQFLKRVRKNGKQPRIKLFEYKRPGWTFHAKG 120
PLDc_CDP-OH_P_transf_II_2 cd09103
Catalytic domain, repeat 2, of CDP-alcohol phosphatidyltransferase class-II family members; ...
 349-468 4.49e-36

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: 132.35  E-value: 4.49e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314872 349 TWIYPLIQMKPFeIQIDEIVTETLLTEAERgaKVYLTTGYFNLTQAYMDLVLG---TRAEYQILLASPEVNGFFGAK--- 422
Cdd:cd09103     1 LSITPLVGLGKR-GNILNRTIEQLITSAES--KIILCTPYFNLPQALMRDILRllkRGVKVEIIVGDKTANDFYIPPeep 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2217314872 423 -GVAGAIPAAYVHIERQFFSEVCSLGQQERVQLQEYWRRGWTFHAKG 468
Cdd:cd09103    78 fKVIGALPYLYEINLRRFAKRLQKYIDQGQLNVRLWKDGDNSFHLKG 124
PLDc_PSS_G_neg_1 cd09134
Catalytic domain, repeat 1, of phosphatidylserine synthases from gram-negative bacteria; ...
 88-267 1.30e-21

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: 91.93  E-value: 1.30e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314872  88 PEFGVSSSHVRVLSSPAEFFELMKGQIRVAKRRVVMASLYLGTGPLEQELVDCLestleksLQAK--FPsNLKVSILLDF 165
Cdd:cd09134     2 PKIPQQPEDIDVLYSPKDFRARLLELISNAKKRIYIVALYLEDDEAGREILDAL-------YEAKanNP-GLDIKVLVDW 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314872 166 TRGSRGR---KNSRT---MLLPLLRRFPEQVRVslfhtphlrgllrLLIPERFNETIGLQHIKVYLFDNSVILSGANLSD 239
Cdd:cd09134    74 HRAQRGLigaKKSLGnadWYRKIAQRYGHDVPI-------------YGVPVKTRELFGVLHLKGFIIDDTVLYSGASLNN 140

                         170       180       190
                  ....*....|....*....|....*....|..
gi 2217314872 240 SYFTN----RQDRYVFLQDcAEIADFFTELVD 267
Cdd:cd09134   141 VYLHQfdkyRYDRYHLIYN-PELADSMVNFIQ 171
pssA PRK09428
CDP-diacylglycerol--serine O-phosphatidyltransferase;
88-267 3.39e-15

CDP-diacylglycerol--serine O-phosphatidyltransferase;


Pssm-ID: 236510 [Multi-domain]  Cd Length: 451  Bit Score: 77.54  E-value: 3.39e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314872  88 PEFGVSSSHVRVLSSPAEFFELMKGQIRVAKRRVVMASLYLGTGPLEQELVDCLestleksLQAK--FPsNLKVSILLDF 165
Cdd:PRK09428   18 PKIPQSPDDVETLYSPADFRETLLEKIASAKKRIYIVALYLEDDEAGREILDAL-------YQAKqqNP-ELDIKVLVDW 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314872 166 TRGSRGR---KNSRT---MLLPLLRRFPEqVRVSLFhtphlrGllrllIPERFNETIGLQHIKVYLFDNSVILSGANLSD 239
Cdd:PRK09428   90 HRAQRGLigaAASNTnadWYCEMAQEYPG-VDIPVY------G-----VPVNTREALGVLHLKGFIIDDTVLYSGASLNN 157

                         170       180       190
                  ....*....|....*....|....*....|..
gi 2217314872 240 SYFtNRQDRYVF----LQDCAEIADFFTELVD 267
Cdd:PRK09428  158 VYL-HQHDKYRYdryhLIRNAELADSMVNFIQ 188
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 91-317 2.92e-12

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: 68.05  E-value: 2.92e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314872  91 GVSSSHVRVLSSPAEFFELMKGQIRVAKRRVVMASLYLGTGPLEQELVDCLEstlekslqAKFPSNLKVSILLDFTrGSR 170
Cdd:COG1502    11 LVGGNRVTLLVDGDEAFAALLEAIEAARRSIDLEYYIFDDDEVGRRLADALI--------AAARRGVKVRVLLDGI-GSR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314872 171 GRKNSrtmLLPLLRRfpEQVRVSLFHTPHLRgllrlliPERFNetiGLQHIKVYLFDNSV-ILSGANLSDSYF------T 243
Cdd:COG1502    82 ALNRD---FLRRLRA--AGVEVRLFNPVRLL-------FRRLN---GRNHRKIVVIDGRVaFVGGANITDEYLgrdpgfG 146

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2217314872 244 NRQDRYVFLQD--CAEIADFFTELVDAVGDVSL---QLQGDDTVQVVdgMVHPYKGDRaeyckAANKRVMDVINSARTR 317
Cdd:COG1502   147 PWRDTHVRIEGpaVADLQAVFAEDWNFATGEALpfpEPAGDVRVQVV--PSGPDSPRE-----TIERALLAAIASARRR 218
PLDc_SF cd00138
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ...
 114-250 4.29e-06

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: 45.97  E-value: 4.29e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314872 114 IRVAKRRVVMASLYLGTGpleqelvdcLESTLEKSLQAKFPSNLKVSILLDftRGSRGRKNSRTMLLPLLRRFPEQVRVS 193
Cdd:cd00138     7 LKNAKESIFIATPNFSFN---------SADRLLKALLAAAERGVDVRLIID--KPPNAAGSLSAALLEALLRAGVNVRSY 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2217314872 194 LFHTPHLRGLlrlliperfnetiglqHIKVYLFDNS-VILSGANLSDSYFTNRQDRYV 250
Cdd:cd00138    76 VTPPHFFERL----------------HAKVVVIDGEvAYVGSANLSTASAAQNREAGV 117
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH