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Conserved domains on  [gi|10383778|ref|NP_009923|]
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CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase [Saccharomyces cerevisiae S288C]

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

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List of domain hits

 Name Accession Description Interval E-value
PLDc_PGS1_euk_1 cd09135
Catalytic domain, repeat 1, of eukaryotic PhosphatidylGlycerophosphate Synthases; Catalytic ...
 64-230 4.35e-88

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: 267.88  E-value: 4.35e-88
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778  64 IDIIESPSQFYDLLKTKILNSQNRIFIASLYLGKS--ETELVDCISQALTKNPKLKVSFLLDGLRGTRELPSACSATLLS 141
Cdd:cd09135   2 IRILRTPSEFYNTLLDKIRNAKRRIVLSSLYIGTGplEQELVDALQEALERNPNLKVSILLDYLRGTRGEPNSRTASLLL 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778 142 SLVAKYgSERVDCRLYKTPAYHGWKKVLVPKRFNEGLGLQHMKIYGFDNEVILSGANLSNDYFTNRQDRYYLFKS-RNFS 220
Cdd:cd09135  82 PLLKLF-PDRVRVSLYHTPNLRGLLKKLLPERFNEIIGLQHMKLYIFDDDVILSGANLSDDYFTNRQDRYMLIENcPELA 160

                       170
                ....*....|
gi 10383778 221 NYYFKLHQLI 230
Cdd:cd09135 161 DFYHDLIKAV 170
PLDc_PGS1_euk_2 cd09137
Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases; Catalytic ...
 295-498 3.41e-78

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: 243.25  E-value: 3.41e-78
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778 295 TLVYPISQFTPLfpkynDKSTEKRTILSLLSTITSNaISWTFTAGYFNILPDIKAKLLATPvAEANVITASPFANGFYQS 374
Cdd:cd09137   1 TWVYPLLQMGPL-----NISQEEQVTSRLLQLLPRG-SSLTLASGYFNLTPEYLNLLLNSS-ANLDVLTASPEANGFYGS 73

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778 375 KGVSSNLPGAYLYLSKKFLQDVCRYRQDHAITLREWQRGvvnkpnGWSYHAKGIWLSardknDANNWKPFITVIGSSNYT 454
Cdd:cd09137  74 KGVSGYIPPAYTYIARQFLKRVRKNGKQPRIKLFEYKRP------GWTFHAKGLWIY-----LPGTDLPSLTLIGSSNYG 142

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....
gi 10383778 455 RRAYSLDLESNALIITRDEELRKKMKAELDNLLQYTKPVTLEDF 498
Cdd:cd09137 143 YRSVHRDLEAQFLIVTNNPKLQQQLKEELENLFEYSKPVTPETF 186
 
Name Accession Description Interval E-value
PLDc_PGS1_euk_1 cd09135
Catalytic domain, repeat 1, of eukaryotic PhosphatidylGlycerophosphate Synthases; Catalytic ...
 64-230 4.35e-88

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: 267.88  E-value: 4.35e-88
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778  64 IDIIESPSQFYDLLKTKILNSQNRIFIASLYLGKS--ETELVDCISQALTKNPKLKVSFLLDGLRGTRELPSACSATLLS 141
Cdd:cd09135   2 IRILRTPSEFYNTLLDKIRNAKRRIVLSSLYIGTGplEQELVDALQEALERNPNLKVSILLDYLRGTRGEPNSRTASLLL 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778 142 SLVAKYgSERVDCRLYKTPAYHGWKKVLVPKRFNEGLGLQHMKIYGFDNEVILSGANLSNDYFTNRQDRYYLFKS-RNFS 220
Cdd:cd09135  82 PLLKLF-PDRVRVSLYHTPNLRGLLKKLLPERFNEIIGLQHMKLYIFDDDVILSGANLSDDYFTNRQDRYMLIENcPELA 160

                       170
                ....*....|
gi 10383778 221 NYYFKLHQLI 230
Cdd:cd09135 161 DFYHDLIKAV 170
PLDc_PGS1_euk_2 cd09137
Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases; Catalytic ...
 295-498 3.41e-78

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: 243.25  E-value: 3.41e-78
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778 295 TLVYPISQFTPLfpkynDKSTEKRTILSLLSTITSNaISWTFTAGYFNILPDIKAKLLATPvAEANVITASPFANGFYQS 374
Cdd:cd09137   1 TWVYPLLQMGPL-----NISQEEQVTSRLLQLLPRG-SSLTLASGYFNLTPEYLNLLLNSS-ANLDVLTASPEANGFYGS 73

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778 375 KGVSSNLPGAYLYLSKKFLQDVCRYRQDHAITLREWQRGvvnkpnGWSYHAKGIWLSardknDANNWKPFITVIGSSNYT 454
Cdd:cd09137  74 KGVSGYIPPAYTYIARQFLKRVRKNGKQPRIKLFEYKRP------GWTFHAKGLWIY-----LPGTDLPSLTLIGSSNYG 142

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....
gi 10383778 455 RRAYSLDLESNALIITRDEELRKKMKAELDNLLQYTKPVTLEDF 498
Cdd:cd09137 143 YRSVHRDLEAQFLIVTNNPKLQQQLKEELENLFEYSKPVTPETF 186
pssA PRK09428
CDP-diacylglycerol--serine O-phosphatidyltransferase;
60-503 1.82e-24

CDP-diacylglycerol--serine O-phosphatidyltransferase;


Pssm-ID: 236510 [Multi-domain]  Cd Length: 451  Bit Score: 106.05  E-value: 1.82e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778   60 QAKEIDIIESPSQFYDLLKTKILNSQNRIFIASLYLGKSET--ELVDCISQALTKNPKLKVSFLLDGLRGTREL----PS 133
Cdd:PRK09428  23 SPDDVETLYSPADFRETLLEKIASAKKRIYIVALYLEDDEAgrEILDALYQAKQQNPELDIKVLVDWHRAQRGLigaaAS 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778  134 ACSATLLSSLVAKYGSERVDcrlyktpaYHGwkkvlVPKRFNEGLGLQHMKIYGFDNEVILSGANLSNDYFTN----RQD 209
Cdd:PRK09428 103 NTNADWYCEMAQEYPGVDIP--------VYG-----VPVNTREALGVLHLKGFIIDDTVLYSGASLNNVYLHQhdkyRYD 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778  210 RYYLFKSRNFSNYYFKL--HQLISSfsyqiikPMVdgsiniiwpdsNPTVEPTKNKRLFLREASQLLDGFLKSSKQSLPI 287
Cdd:PRK09428 170 RYHLIRNAELADSMVNFiqQNLLNS-------PAV-----------NRLDQPNRPKTKEIKNDIRQFRQRLRDAAYQFQG 231

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778  288 TAVGQFSTLvypisqfTPLF--PKyndKSTEKRTILSLLSTITSNAISWTftaGYFNiLP-----DIKaKLLATPVaEAN 360
Cdd:PRK09428 232 QANNDELSV-------TPLVglGK---KNLLNKTIFHLMASAEQKLTICT---PYFN-LPailvrNII-RLLRRGK-KVE 295

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778  361 VITASPFANGFY----QSKGVSSNLPgaYLYLS--KKFLQdvcryRQDHAI-----TLREWqrgvvnKPNGWSYHAKGIW 429
Cdd:PRK09428 296 IIVGDKTANDFYippdEPFKIIGALP--YLYEInlRRFAK-----RLQYYIdngqlNVRLW------KDGDNSYHLKGIW 362

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778  430 LSardkndaNNWkpfiTVIGSSNYTRRAYSLDLEsNALIItRDE--ELRKKMKAELDNLLQYTKPVT----LEDFQSDPE 503
Cdd:PRK09428 363 VD-------DRW----MLLTGNNLNPRAWRLDLE-NALLI-HDPkqELAEQREKELELIRTHTTRVKhysqLESIADYPV 429
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 63-506 1.06e-11

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: 66.50  E-value: 1.06e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778  63 EIDIIESPSQFYDLLKTKILNSQNRIFIASLYLgkSETELVDCISQALTK--NPKLKVSFLLDGLrGTRELPSAcsatLL 140
Cdd:COG1502  16 RVTLLVDGDEAFAALLEAIEAARRSIDLEYYIF--DDDEVGRRLADALIAaaRRGVKVRVLLDGI-GSRALNRD----FL 88

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778 141 SSLVAkygsERVDCRLYKTpayhgwkkvlVPKRFNEGLGLQHMKIYGFDNEV-ILSGANLSNDYFTNRQDRYYlfksrnF 219
Cdd:COG1502  89 RRLRA----AGVEVRLFNP----------VRLLFRRLNGRNHRKIVVIDGRVaFVGGANITDEYLGRDPGFGP------W 148

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778 220 SNYYFklhqlissfsyqiikpMVDGSIniiwpdsnptveptknkrlfLREASQLLDGFLKSSKQSLPITAVGQFSTLVyp 299
Cdd:COG1502 149 RDTHV----------------RIEGPA--------------------VADLQAVFAEDWNFATGEALPFPEPAGDVRV-- 190

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778 300 isQFTPLFPKYNDKSTEkRTILSLLSTITSNAIswtFTAGYFNILPDIKAKLlatpvaeanvITASpfangfyqSKGV-- 377
Cdd:COG1502 191 --QVVPSGPDSPRETIE-RALLAAIASARRRIY---IETPYFVPDRSLLRAL----------IAAA--------RRGVdv 246

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778 378 ------SSNLPGAYlYLSKKFLQDVcryrQDHAITLREWQRGvvnkpngwSYHAKGIWlsARDKndannwkpfITVIGSS 451
Cdd:COG1502 247 rillpaKSDHPLVH-WASRSYYEEL----LEAGVRIYEYEPG--------FLHAKVMV--VDDE---------WALVGSA 302

                       410       420       430       440       450
                ....*....|....*....|....*....|....*....|....*....|....*
gi 10383778 452 NYTRRAYSLDLESNALIitRDEELRKKMKAELDNLLQYTKPVTLEDFQSDPERHV 506
Cdd:COG1502 303 NLDPRSLRLNFEVNLVI--YDPEFAAQLRARFEEDLAHSREVTLEEWRKRPLRRL 355
PLDc_2 pfam13091
PLD-like domain;
421-486 3.97e-05

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 43.43  E-value: 3.97e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 10383778   421 WSYHAKGIWLsarDKNdannwkpfITVIGSSNYTRRAYSLDLESNalIITRDEELRKKMKAELDNL 486
Cdd:pfam13091  79 RSMHAKFYII---DGK--------TVIVGSANLTRRALRLNLENN--VVIKDPELAQELEKEFDRL 131
 
Name Accession Description Interval E-value
PLDc_PGS1_euk_1 cd09135
Catalytic domain, repeat 1, of eukaryotic PhosphatidylGlycerophosphate Synthases; Catalytic ...
 64-230 4.35e-88

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: 267.88  E-value: 4.35e-88
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778  64 IDIIESPSQFYDLLKTKILNSQNRIFIASLYLGKS--ETELVDCISQALTKNPKLKVSFLLDGLRGTRELPSACSATLLS 141
Cdd:cd09135   2 IRILRTPSEFYNTLLDKIRNAKRRIVLSSLYIGTGplEQELVDALQEALERNPNLKVSILLDYLRGTRGEPNSRTASLLL 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778 142 SLVAKYgSERVDCRLYKTPAYHGWKKVLVPKRFNEGLGLQHMKIYGFDNEVILSGANLSNDYFTNRQDRYYLFKS-RNFS 220
Cdd:cd09135  82 PLLKLF-PDRVRVSLYHTPNLRGLLKKLLPERFNEIIGLQHMKLYIFDDDVILSGANLSDDYFTNRQDRYMLIENcPELA 160

                       170
                ....*....|
gi 10383778 221 NYYFKLHQLI 230
Cdd:cd09135 161 DFYHDLIKAV 170
PLDc_PGS1_euk_2 cd09137
Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases; Catalytic ...
 295-498 3.41e-78

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: 243.25  E-value: 3.41e-78
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778 295 TLVYPISQFTPLfpkynDKSTEKRTILSLLSTITSNaISWTFTAGYFNILPDIKAKLLATPvAEANVITASPFANGFYQS 374
Cdd:cd09137   1 TWVYPLLQMGPL-----NISQEEQVTSRLLQLLPRG-SSLTLASGYFNLTPEYLNLLLNSS-ANLDVLTASPEANGFYGS 73

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778 375 KGVSSNLPGAYLYLSKKFLQDVCRYRQDHAITLREWQRGvvnkpnGWSYHAKGIWLSardknDANNWKPFITVIGSSNYT 454
Cdd:cd09137  74 KGVSGYIPPAYTYIARQFLKRVRKNGKQPRIKLFEYKRP------GWTFHAKGLWIY-----LPGTDLPSLTLIGSSNYG 142

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....
gi 10383778 455 RRAYSLDLESNALIITRDEELRKKMKAELDNLLQYTKPVTLEDF 498
Cdd:cd09137 143 YRSVHRDLEAQFLIVTNNPKLQQQLKEELENLFEYSKPVTPETF 186
PLDc_CDP-OH_P_transf_II_1 cd09102
Catalytic domain, repeat 1, of CDP-alcohol phosphatidyltransferase class-II family members; ...
 63-211 1.94e-36

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: 132.71  E-value: 1.94e-36
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778  63 EIDIIESPSQFYDLLKTKILNSQNRIFIASLYLGKSET--ELVDCISQALTKNPKLKVSFLLDGLRGTRELPSacSATLL 140
Cdd:cd09102   1 HIRFLGSPAEFKTQIIELIRNAKRRVYVASLYWGKDEAgqEILDEIYSVKQENPNLDVSVLIDWHRAQRNLLG--SETKS 78

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 10383778 141 SSLVAKYgSERVDCRLYKTPAYHGWKKVLVPKRFNEGLGLQHMKIYGFDNEVILSGANLSNDYFTNRQDRY 211
Cdd:cd09102  79 ATNADWY-CEQRQTSQLHLLPDDGN*FFGVPINTNEVFGVLHVKGYVFDDTVLLSGANLSNVYFHYRYDRY 148
pssA PRK09428
CDP-diacylglycerol--serine O-phosphatidyltransferase;
60-503 1.82e-24

CDP-diacylglycerol--serine O-phosphatidyltransferase;


Pssm-ID: 236510 [Multi-domain]  Cd Length: 451  Bit Score: 106.05  E-value: 1.82e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778   60 QAKEIDIIESPSQFYDLLKTKILNSQNRIFIASLYLGKSET--ELVDCISQALTKNPKLKVSFLLDGLRGTREL----PS 133
Cdd:PRK09428  23 SPDDVETLYSPADFRETLLEKIASAKKRIYIVALYLEDDEAgrEILDALYQAKQQNPELDIKVLVDWHRAQRGLigaaAS 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778  134 ACSATLLSSLVAKYGSERVDcrlyktpaYHGwkkvlVPKRFNEGLGLQHMKIYGFDNEVILSGANLSNDYFTN----RQD 209
Cdd:PRK09428 103 NTNADWYCEMAQEYPGVDIP--------VYG-----VPVNTREALGVLHLKGFIIDDTVLYSGASLNNVYLHQhdkyRYD 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778  210 RYYLFKSRNFSNYYFKL--HQLISSfsyqiikPMVdgsiniiwpdsNPTVEPTKNKRLFLREASQLLDGFLKSSKQSLPI 287
Cdd:PRK09428 170 RYHLIRNAELADSMVNFiqQNLLNS-------PAV-----------NRLDQPNRPKTKEIKNDIRQFRQRLRDAAYQFQG 231

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778  288 TAVGQFSTLvypisqfTPLF--PKyndKSTEKRTILSLLSTITSNAISWTftaGYFNiLP-----DIKaKLLATPVaEAN 360
Cdd:PRK09428 232 QANNDELSV-------TPLVglGK---KNLLNKTIFHLMASAEQKLTICT---PYFN-LPailvrNII-RLLRRGK-KVE 295

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778  361 VITASPFANGFY----QSKGVSSNLPgaYLYLS--KKFLQdvcryRQDHAI-----TLREWqrgvvnKPNGWSYHAKGIW 429
Cdd:PRK09428 296 IIVGDKTANDFYippdEPFKIIGALP--YLYEInlRRFAK-----RLQYYIdngqlNVRLW------KDGDNSYHLKGIW 362

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778  430 LSardkndaNNWkpfiTVIGSSNYTRRAYSLDLEsNALIItRDE--ELRKKMKAELDNLLQYTKPVT----LEDFQSDPE 503
Cdd:PRK09428 363 VD-------DRW----MLLTGNNLNPRAWRLDLE-NALLI-HDPkqELAEQREKELELIRTHTTRVKhysqLESIADYPV 429
PLDc_CDP-OH_P_transf_II_2 cd09103
Catalytic domain, repeat 2, of CDP-alcohol phosphatidyltransferase class-II family members; ...
 295-494 4.93e-24

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: 99.22  E-value: 4.93e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778 295 TLVYPISQFTPLFPKYNdkstekRTILSLLSTITSNAISWTftaGYFNiLPDIKAKLLATPV---AEANVITASPFANGF 371
Cdd:cd09103   1 LSITPLVGLGKRGNILN------RTIEQLITSAESKIILCT---PYFN-LPQALMRDILRLLkrgVKVEIIVGDKTANDF 70

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778 372 Y----QSKGVSSNLPGAYLYLSKKFLQDVCRYRQDHAITLREWQRGvvnkpnGWSYHAKGIWLSARdkndannWkpfiTV 447
Cdd:cd09103  71 YippeEPFKVIGALPYLYEINLRRFAKRLQKYIDQGQLNVRLWKDG------DNSFHLKGIWVDDR-------Y----TL 133

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*..
gi 10383778 448 IGSSNYTRRAYSLDLESNALIITRDEELRKKMKAELDNLLQYTKPVT 494
Cdd:cd09103 134 LTGNNLNPRAWRLDLENGLLIHDPQKQLQQQLEKELEQILLHTTRIS 180
PLDc_PSS_G_neg_1 cd09134
Catalytic domain, repeat 1, of phosphatidylserine synthases from gram-negative bacteria; ...
 60-221 1.63e-18

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: 83.07  E-value: 1.63e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778  60 QAKEIDIIESPSQFYDLLKTKILNSQNRIFIASLYLGKSET--ELVDCISQALTKNPKLKVSFLLDGLRGTREL----PS 133
Cdd:cd09134   7 QPEDIDVLYSPKDFRARLLELISNAKKRIYIVALYLEDDEAgrEILDALYEAKANNPGLDIKVLVDWHRAQRGLigakKS 86

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778 134 ACSATLLSSLVAKYGServdcrlyKTPAYHgwkkvlVPKRFNEGLGLQHMKIYGFDNEVILSGANLSNDYFTN----RQD 209
Cdd:cd09134  87 LGNADWYRKIAQRYGH--------DVPIYG------VPVKTRELFGVLHLKGFIIDDTVLYSGASLNNVYLHQfdkyRYD 152

                       170
                ....*....|..
gi 10383778 210 RYYLFKSRNFSN 221
Cdd:cd09134 153 RYHLIYNPELAD 164
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 63-506 1.06e-11

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: 66.50  E-value: 1.06e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778  63 EIDIIESPSQFYDLLKTKILNSQNRIFIASLYLgkSETELVDCISQALTK--NPKLKVSFLLDGLrGTRELPSAcsatLL 140
Cdd:COG1502  16 RVTLLVDGDEAFAALLEAIEAARRSIDLEYYIF--DDDEVGRRLADALIAaaRRGVKVRVLLDGI-GSRALNRD----FL 88

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778 141 SSLVAkygsERVDCRLYKTpayhgwkkvlVPKRFNEGLGLQHMKIYGFDNEV-ILSGANLSNDYFTNRQDRYYlfksrnF 219
Cdd:COG1502  89 RRLRA----AGVEVRLFNP----------VRLLFRRLNGRNHRKIVVIDGRVaFVGGANITDEYLGRDPGFGP------W 148

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778 220 SNYYFklhqlissfsyqiikpMVDGSIniiwpdsnptveptknkrlfLREASQLLDGFLKSSKQSLPITAVGQFSTLVyp 299
Cdd:COG1502 149 RDTHV----------------RIEGPA--------------------VADLQAVFAEDWNFATGEALPFPEPAGDVRV-- 190

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778 300 isQFTPLFPKYNDKSTEkRTILSLLSTITSNAIswtFTAGYFNILPDIKAKLlatpvaeanvITASpfangfyqSKGV-- 377
Cdd:COG1502 191 --QVVPSGPDSPRETIE-RALLAAIASARRRIY---IETPYFVPDRSLLRAL----------IAAA--------RRGVdv 246

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778 378 ------SSNLPGAYlYLSKKFLQDVcryrQDHAITLREWQRGvvnkpngwSYHAKGIWlsARDKndannwkpfITVIGSS 451
Cdd:COG1502 247 rillpaKSDHPLVH-WASRSYYEEL----LEAGVRIYEYEPG--------FLHAKVMV--VDDE---------WALVGSA 302

                       410       420       430       440       450
                ....*....|....*....|....*....|....*....|....*....|....*
gi 10383778 452 NYTRRAYSLDLESNALIitRDEELRKKMKAELDNLLQYTKPVTLEDFQSDPERHV 506
Cdd:COG1502 303 NLDPRSLRLNFEVNLVI--YDPEFAAQLRARFEEDLAHSREVTLEEWRKRPLRRL 355
PLDc_PSS_G_neg_2 cd09136
Catalytic domain, repeat 2, of phosphatidylserine synthases from gram-negative bacteria; ...
 318-503 6.84e-11

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: 61.85  E-value: 6.84e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778 318 RTILSLLSTITSNAISWTftaGYFN----ILPDIkAKLLATPVaEANVITASPFANGFY----QSKGVSSNLPgaYLYLS 389
Cdd:cd09136  18 RTIRQLIQSAESELIICT---PYFNlprsLVRDI-ARLLKRGV-KVEIIVGDKTANDFYippeEPFKTIGALP--YLYEI 90

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778 390 --KKFLQDVCRYRQDHAITLREWqrgvvnKPNGWSYHAKGIWLSARdkndannWkpfiTVIGSSNYTRRAYSLDLEsNAL 467
Cdd:cd09136  91 nlRRFAKRLQKYIDNGQLNVRLW------KDGNNSFHLKGIWVDDR-------Y----HLLTGNNLNPRAWRLDLE-NGL 152

                       170       180       190       200
                ....*....|....*....|....*....|....*....|..
gi 10383778 468 IItRDE--ELRKKMKAELDNLLQYTKPVT----LEDFQSDPE 503
Cdd:cd09136 153 LI-HDPqgQLKAQFEKELEQILAHTTRIKhysqLESIADYPE 193
PLDc_2 pfam13091
PLD-like domain;
421-486 3.97e-05

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 43.43  E-value: 3.97e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 10383778   421 WSYHAKGIWLsarDKNdannwkpfITVIGSSNYTRRAYSLDLESNalIITRDEELRKKMKAELDNL 486
Cdd:pfam13091  79 RSMHAKFYII---DGK--------TVIVGSANLTRRALRLNLENN--VVIKDPELAQELEKEFDRL 131
PLDc_CLS_2 cd09112
catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; This CD ...
 445-499 8.18e-04

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: 40.54  E-value: 8.18e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 10383778 445 ITVIGSSNYTRRAYSLDLESNALIitRDEELRKKMKAELDNLLQYTKPVTLEDFQ 499
Cdd:cd09112 104 IASVGTANLDIRSFELNFEVNAVI--YDKEVAKKLEEIFEEDLKDSELLTLEEWR 156
PLDc_ybhO_like_2 cd09159
Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; ...
 409-499 2.94e-03

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: 38.67  E-value: 2.94e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 10383778 409 EWQRGVvnkpngwsYHAK-----GIWlsardkndannwkpfiTVIGSSNYTRRAYSLDLESNALIitRDEELRKKMKAEL 483
Cdd:cd09159  87 EYQPSM--------LHAKtavidGDW----------------ATVGSSNLDPRSLRLNLEANLVV--EDPAFAAQLEELF 140

                        90
                ....*....|....*.
gi 10383778 484 DNLLQYTKPVTLEDFQ 499
Cdd:cd09159 141 EEDLARSREITLEEWR 156
 
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.
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