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Conserved domains on  [gi|28572961|ref|NP_650751|]
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phosphatidylglycerophosphate synthase 1 [Drosophila melanogaster]

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 ...
 61-227 1.24e-94

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: 284.06  E-value: 1.24e-94
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961  61 QIQVIHEPKHFYETLVQRIGQAKRRIVLASLYLGTGQLENAMVQTLRHSLEQQSALRLNVLLDFTRGTRGTLNSKT--ML 138
Cdd:cd09135   1 QIRILRTPSEFYNTLLDKIRNAKRRIVLSSLYIGTGPLEQELVDALQEALERNPNLKVSILLDYLRGTRGEPNSRTasLL 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961 139 LPLVRDFASQVQLSLYHTPDLRGMTKRLAPPRWNELLGLQHMKVYLFDDAVIISGANLSNDYFTNRQDRYILIED-KPLA 217
Cdd:cd09135  81 LPLLKLFPDRVRVSLYHTPNLRGLLKKLLPERFNEIIGLQHMKLYIFDDDVILSGANLSDDYFTNRQDRYMLIENcPELA 160

                       170
                ....*....|
gi 28572961 218 DFYAQFIERV 227
Cdd:cd09135 161 DFYHDLIKAV 170
PLDc_PGS1_euk_2 cd09137
Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases; Catalytic ...
 289-474 6.07e-94

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: 282.93  E-value: 6.07e-94
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961 289 TWIFPLLEMGQIGIHHDSVVTKRLLSNCLSGSRLKLATGYFNLTQEYMDTLTHkCLAQCSILMAHPNANGFQGAKGPAGG 368
Cdd:cd09137   1 TWVYPLLQMGPLNISQEEQVTSRLLQLLPRGSSLTLASGYFNLTPEYLNLLLN-SSANLDVLTASPEANGFYGSKGVSGY 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961 369 IPAAYTLIAKSFYESLVRRKQNHRVNFFEYEKPGWTYHAKGLWYYLPEAILPNLTLIGSSNFGERSVNRDLETQVCLVTA 448
Cdd:cd09137  80 IPPAYTYIARQFLKRVRKNGKQPRIKLFEYKRPGWTFHAKGLWIYLPGTDLPSLTLIGSSNYGYRSVHRDLEAQFLIVTN 159

                       170       180
                ....*....|....*....|....*.
gi 28572961 449 NKDLSQRLQAEADRLYDLSQTAEREI 474
Cdd:cd09137 160 NPKLQQQLKEELENLFEYSKPVTPET 185
 
Name Accession Description Interval E-value
PLDc_PGS1_euk_1 cd09135
Catalytic domain, repeat 1, of eukaryotic PhosphatidylGlycerophosphate Synthases; Catalytic ...
 61-227 1.24e-94

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: 284.06  E-value: 1.24e-94
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961  61 QIQVIHEPKHFYETLVQRIGQAKRRIVLASLYLGTGQLENAMVQTLRHSLEQQSALRLNVLLDFTRGTRGTLNSKT--ML 138
Cdd:cd09135   1 QIRILRTPSEFYNTLLDKIRNAKRRIVLSSLYIGTGPLEQELVDALQEALERNPNLKVSILLDYLRGTRGEPNSRTasLL 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961 139 LPLVRDFASQVQLSLYHTPDLRGMTKRLAPPRWNELLGLQHMKVYLFDDAVIISGANLSNDYFTNRQDRYILIED-KPLA 217
Cdd:cd09135  81 LPLLKLFPDRVRVSLYHTPNLRGLLKKLLPERFNEIIGLQHMKLYIFDDDVILSGANLSDDYFTNRQDRYMLIENcPELA 160

                       170
                ....*....|
gi 28572961 218 DFYAQFIERV 227
Cdd:cd09135 161 DFYHDLIKAV 170
PLDc_PGS1_euk_2 cd09137
Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases; Catalytic ...
 289-474 6.07e-94

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: 282.93  E-value: 6.07e-94
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961 289 TWIFPLLEMGQIGIHHDSVVTKRLLSNCLSGSRLKLATGYFNLTQEYMDTLTHkCLAQCSILMAHPNANGFQGAKGPAGG 368
Cdd:cd09137   1 TWVYPLLQMGPLNISQEEQVTSRLLQLLPRGSSLTLASGYFNLTPEYLNLLLN-SSANLDVLTASPEANGFYGSKGVSGY 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961 369 IPAAYTLIAKSFYESLVRRKQNHRVNFFEYEKPGWTYHAKGLWYYLPEAILPNLTLIGSSNFGERSVNRDLETQVCLVTA 448
Cdd:cd09137  80 IPPAYTYIARQFLKRVRKNGKQPRIKLFEYKRPGWTFHAKGLWIYLPGTDLPSLTLIGSSNYGYRSVHRDLEAQFLIVTN 159

                       170       180
                ....*....|....*....|....*.
gi 28572961 449 NKDLSQRLQAEADRLYDLSQTAEREI 474
Cdd:cd09137 160 NPKLQQQLKEELENLFEYSKPVTPET 185
pssA PRK09428
CDP-diacylglycerol--serine O-phosphatidyltransferase;
48-226 1.28e-23

CDP-diacylglycerol--serine O-phosphatidyltransferase;


Pssm-ID: 236510 [Multi-domain]  Cd Length: 451  Bit Score: 103.35  E-value: 1.28e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961   48 LHNLaPCFPLRGDQIQVIHEPKHFYETLVQRIGQAKRRIVLASLYLGTGQLENAMVQTLRHSLEQQSALRLNVLLDFTRG 127
Cdd:PRK09428  14 LAQL-PKIPQSPDDVETLYSPADFRETLLEKIASAKKRIYIVALYLEDDEAGREILDALYQAKQQNPELDIKVLVDWHRA 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961  128 TRGTLNSKTML--LPLVRDFASQVQlslYHTPDLRGMtkrlaPPRWNELLGLQHMKVYLFDDAVIISGANLSNDYFTN-- 203
Cdd:PRK09428  93 QRGLIGAAASNtnADWYCEMAQEYP---GVDIPVYGV-----PVNTREALGVLHLKGFIIDDTVLYSGASLNNVYLHQhd 164

                        170       180
                 ....*....|....*....|....*
gi 28572961  204 --RQDRYILIEDKPLADFYAQFIER 226
Cdd:PRK09428 165 kyRYDRYHLIRNAELADSMVNFIQQ 189
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 47-491 1.32e-19

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: 90.39  E-value: 1.32e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961  47 WLHNLAPCFPL-RGDQIQVIHEPKHFYETLVQRIGQAKRRIVLASLYLGTGQLENAMVQTLRHSleQQSALRLNVLLDFT 125
Cdd:COG1502   1 KAAPLAAGLPLvGGNRVTLLVDGDEAFAALLEAIEAARRSIDLEYYIFDDDEVGRRLADALIAA--ARRGVKVRVLLDGI 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961 126 rGTRGTlnSKTMLLPLVrdfASQVQLSLYHTPdlrgmtkRLAPPRWNellGLQHMKVYLFDDAV-IISGANLSNDYF--- 201
Cdd:COG1502  79 -GSRAL--NRDFLRRLR---AAGVEVRLFNPV-------RLLFRRLN---GRNHRKIVVIDGRVaFVGGANITDEYLgrd 142

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961 202 ---TNRQDRYILIEDKPLADFYAQFIERVQEfslavapdaseglHRNWRILPYEGTKEQFIQLAR---KRISDLVQETFQ 275
Cdd:COG1502 143 pgfGPWRDTHVRIEGPAVADLQAVFAEDWNF-------------ATGEALPFPEPAGDVRVQVVPsgpDSPRETIERALL 209

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961 276 ---RQARTkeqnpqadtwifpllemgqigihhdsvvtkrllsnclsgsRLKLATGYFNLTQEYMDTLTHKCLAQCS---I 349
Cdd:COG1502 210 aaiASARR----------------------------------------RIYIETPYFVPDRSLLRALIAAARRGVDvriL 249

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961 350 LMAHPNANGFQGAkgpaggipaaytliAKSFYESLVRrkqnHRVNFFEYEKPgwTYHAKGLWyylpeaILPNLTLIGSSN 429
Cdd:COG1502 250 LPAKSDHPLVHWA--------------SRSYYEELLE----AGVRIYEYEPG--FLHAKVMV------VDDEWALVGSAN 303

                       410       420       430       440       450       460
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 28572961 430 FGERSVNRDLEtqVCLVTANKDLSQRLQAEADRLYDLSQTAEREIVQ-RPVPRWVQAVVRIFR 491
Cdd:COG1502 304 LDPRSLRLNFE--VNLVIYDPEFAAQLRARFEEDLAHSREVTLEEWRkRPLRRLRERLARLLS 364
PLDc_2 pfam13091
PLD-like domain;
386-463 2.32e-07

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 49.60  E-value: 2.32e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 28572961   386 RRKQNHRVNFFEYEKPGWTYHAKGLWyylpeaILPNLTLIGSSNFGERSVNRDLETqvCLVTANKDLSQRLQAEADRL 463
Cdd:pfam13091  62 RSLLRAGVEIREYQSFLRSMHAKFYI------IDGKTVIVGSANLTRRALRLNLEN--NVVIKDPELAQELEKEFDRL 131
PLDc_2 pfam13091
PLD-like domain;
75-226 9.88e-06

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 44.98  E-value: 9.88e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961    75 LVQRIGQAKRRIVLASLYLGTGQ-LENAMVQTLRhsleqqSALRLNVLLDFTRGTRGtlnsktmllplvrdFASQVQLSL 153
Cdd:pfam13091   1 LIDLINSAKKSIDIATYYFVPDReIIDALIAAAK------RGVDVRIILDSNKDDAG--------------GPKKASLKE 60

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 28572961   154 YHTPDLRGMTKRLAPPRWNELlglqHMKVYLFDDA-VIISGANLSNDYFTNRQDRYILIEDKPLADFYAQFIER 226
Cdd:pfam13091  61 LRSLLRAGVEIREYQSFLRSM----HAKFYIIDGKtVIVGSANLTRRALRLNLENNVVIKDPELAQELEKEFDR 130
 
Name Accession Description Interval E-value
PLDc_PGS1_euk_1 cd09135
Catalytic domain, repeat 1, of eukaryotic PhosphatidylGlycerophosphate Synthases; Catalytic ...
 61-227 1.24e-94

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: 284.06  E-value: 1.24e-94
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961  61 QIQVIHEPKHFYETLVQRIGQAKRRIVLASLYLGTGQLENAMVQTLRHSLEQQSALRLNVLLDFTRGTRGTLNSKT--ML 138
Cdd:cd09135   1 QIRILRTPSEFYNTLLDKIRNAKRRIVLSSLYIGTGPLEQELVDALQEALERNPNLKVSILLDYLRGTRGEPNSRTasLL 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961 139 LPLVRDFASQVQLSLYHTPDLRGMTKRLAPPRWNELLGLQHMKVYLFDDAVIISGANLSNDYFTNRQDRYILIED-KPLA 217
Cdd:cd09135  81 LPLLKLFPDRVRVSLYHTPNLRGLLKKLLPERFNEIIGLQHMKLYIFDDDVILSGANLSDDYFTNRQDRYMLIENcPELA 160

                       170
                ....*....|
gi 28572961 218 DFYAQFIERV 227
Cdd:cd09135 161 DFYHDLIKAV 170
PLDc_PGS1_euk_2 cd09137
Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases; Catalytic ...
 289-474 6.07e-94

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: 282.93  E-value: 6.07e-94
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961 289 TWIFPLLEMGQIGIHHDSVVTKRLLSNCLSGSRLKLATGYFNLTQEYMDTLTHkCLAQCSILMAHPNANGFQGAKGPAGG 368
Cdd:cd09137   1 TWVYPLLQMGPLNISQEEQVTSRLLQLLPRGSSLTLASGYFNLTPEYLNLLLN-SSANLDVLTASPEANGFYGSKGVSGY 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961 369 IPAAYTLIAKSFYESLVRRKQNHRVNFFEYEKPGWTYHAKGLWYYLPEAILPNLTLIGSSNFGERSVNRDLETQVCLVTA 448
Cdd:cd09137  80 IPPAYTYIARQFLKRVRKNGKQPRIKLFEYKRPGWTFHAKGLWIYLPGTDLPSLTLIGSSNYGYRSVHRDLEAQFLIVTN 159

                       170       180
                ....*....|....*....|....*.
gi 28572961 449 NKDLSQRLQAEADRLYDLSQTAEREI 474
Cdd:cd09137 160 NPKLQQQLKEELENLFEYSKPVTPET 185
PLDc_CDP-OH_P_transf_II_1 cd09102
Catalytic domain, repeat 1, of CDP-alcohol phosphatidyltransferase class-II family members; ...
 61-227 1.34e-51

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: 172.77  E-value: 1.34e-51
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961  61 QIQVIHEPKHFYETLVQRIGQAKRRIVLASLYLGTGQLENAMVQTLRHSLEQQSALRLNVLLDFTRGTRGTLNSKTMLLP 140
Cdd:cd09102   1 HIRFLGSPAEFKTQIIELIRNAKRRVYVASLYWGKDEAGQEILDEIYSVKQENPNLDVSVLIDWHRAQRNLLGSETKSAT 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961 141 LVRDFASQVQLSLYHTPDLRGMTKRLAPPRWNELLGLQHMKVYLFDDAVIISGANLSNDYFTNRQDRYILIED-KPLADF 219
Cdd:cd09102  81 NADWYCEQRQTSQLHLLPDDGN*FFGVPINTNEVFGVLHVKGYVFDDTVLLSGANLSNVYFHYRYDRYVKITHgAELADS 160


                ....*...
gi 28572961 220 YAQFIERV 227
Cdd:cd09102 161 *VNLINAY 168
PLDc_CDP-OH_P_transf_II_2 cd09103
Catalytic domain, repeat 2, of CDP-alcohol phosphatidyltransferase class-II family members; ...
 289-464 1.46e-27

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: 108.85  E-value: 1.46e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961 289 TWIFPLLEMGQiGIHHDSVVTKRLLsnCLSGSRLKLATGYFNLTQEYMDTLTH--KCLAQCSILMAHPNANGFQGAK--- 363
Cdd:cd09103   1 LSITPLVGLGK-RGNILNRTIEQLI--TSAESKIILCTPYFNLPQALMRDILRllKRGVKVEIIVGDKTANDFYIPPeep 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961 364 -GPAGGIPAAYTLIAKSFYESLVRRKQNHRVNFFEYEKPGWTYHAKGLWYYLpeailpNLTLIGSSNFGERSVNRDLETQ 442
Cdd:cd09103  78 fKVIGALPYLYEINLRRFAKRLQKYIDQGQLNVRLWKDGDNSFHLKGIWVDD------RYTLLTGNNLNPRAWRLDLENG 151

                       170       180
                ....*....|....*....|..
gi 28572961 443 VCLVTANKDLSQRLQAEADRLY 464
Cdd:cd09103 152 LLIHDPQKQLQQQLEKELEQIL 173
PLDc_PSS_G_neg_1 cd09134
Catalytic domain, repeat 1, of phosphatidylserine synthases from gram-negative bacteria; ...
 53-226 6.88e-26

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: 103.87  E-value: 6.88e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961  53 PCFPLRGDQIQVIHEPKHFYETLVQRIGQAKRRIVLASLYLGTGQLENAMVQTLRHSLEQQSALRLNVLLDFTRGTRGTL 132
Cdd:cd09134   2 PKIPQQPEDIDVLYSPKDFRARLLELISNAKKRIYIVALYLEDDEAGREILDALYEAKANNPGLDIKVLVDWHRAQRGLI 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961 133 NSKtmllplvrdfASQVQLSLYhtpdlRGMTKRLA--------PPRWNELLGLQHMKVYLFDDAVIISGANLSNDYFTN- 203
Cdd:cd09134  82 GAK----------KSLGNADWY-----RKIAQRYGhdvpiygvPVKTRELFGVLHLKGFIIDDTVLYSGASLNNVYLHQf 146

                       170       180
                ....*....|....*....|....*.
gi 28572961 204 ---RQDRYILIEDKPLADFYAQFIER 226
Cdd:cd09134 147 dkyRYDRYHLIYNPELADSMVNFIQD 172
pssA PRK09428
CDP-diacylglycerol--serine O-phosphatidyltransferase;
48-226 1.28e-23

CDP-diacylglycerol--serine O-phosphatidyltransferase;


Pssm-ID: 236510 [Multi-domain]  Cd Length: 451  Bit Score: 103.35  E-value: 1.28e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961   48 LHNLaPCFPLRGDQIQVIHEPKHFYETLVQRIGQAKRRIVLASLYLGTGQLENAMVQTLRHSLEQQSALRLNVLLDFTRG 127
Cdd:PRK09428  14 LAQL-PKIPQSPDDVETLYSPADFRETLLEKIASAKKRIYIVALYLEDDEAGREILDALYQAKQQNPELDIKVLVDWHRA 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961  128 TRGTLNSKTML--LPLVRDFASQVQlslYHTPDLRGMtkrlaPPRWNELLGLQHMKVYLFDDAVIISGANLSNDYFTN-- 203
Cdd:PRK09428  93 QRGLIGAAASNtnADWYCEMAQEYP---GVDIPVYGV-----PVNTREALGVLHLKGFIIDDTVLYSGASLNNVYLHQhd 164

                        170       180
                 ....*....|....*....|....*
gi 28572961  204 --RQDRYILIEDKPLADFYAQFIER 226
Cdd:PRK09428 165 kyRYDRYHLIRNAELADSMVNFIQQ 189
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 47-491 1.32e-19

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: 90.39  E-value: 1.32e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961  47 WLHNLAPCFPL-RGDQIQVIHEPKHFYETLVQRIGQAKRRIVLASLYLGTGQLENAMVQTLRHSleQQSALRLNVLLDFT 125
Cdd:COG1502   1 KAAPLAAGLPLvGGNRVTLLVDGDEAFAALLEAIEAARRSIDLEYYIFDDDEVGRRLADALIAA--ARRGVKVRVLLDGI 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961 126 rGTRGTlnSKTMLLPLVrdfASQVQLSLYHTPdlrgmtkRLAPPRWNellGLQHMKVYLFDDAV-IISGANLSNDYF--- 201
Cdd:COG1502  79 -GSRAL--NRDFLRRLR---AAGVEVRLFNPV-------RLLFRRLN---GRNHRKIVVIDGRVaFVGGANITDEYLgrd 142

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961 202 ---TNRQDRYILIEDKPLADFYAQFIERVQEfslavapdaseglHRNWRILPYEGTKEQFIQLAR---KRISDLVQETFQ 275
Cdd:COG1502 143 pgfGPWRDTHVRIEGPAVADLQAVFAEDWNF-------------ATGEALPFPEPAGDVRVQVVPsgpDSPRETIERALL 209

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961 276 ---RQARTkeqnpqadtwifpllemgqigihhdsvvtkrllsnclsgsRLKLATGYFNLTQEYMDTLTHKCLAQCS---I 349
Cdd:COG1502 210 aaiASARR----------------------------------------RIYIETPYFVPDRSLLRALIAAARRGVDvriL 249

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961 350 LMAHPNANGFQGAkgpaggipaaytliAKSFYESLVRrkqnHRVNFFEYEKPgwTYHAKGLWyylpeaILPNLTLIGSSN 429
Cdd:COG1502 250 LPAKSDHPLVHWA--------------SRSYYEELLE----AGVRIYEYEPG--FLHAKVMV------VDDEWALVGSAN 303

                       410       420       430       440       450       460
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 28572961 430 FGERSVNRDLEtqVCLVTANKDLSQRLQAEADRLYDLSQTAEREIVQ-RPVPRWVQAVVRIFR 491
Cdd:COG1502 304 LDPRSLRLNFE--VNLVIYDPEFAAQLRARFEEDLAHSREVTLEEWRkRPLRRLRERLARLLS 364
PLDc_2 pfam13091
PLD-like domain;
386-463 2.32e-07

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 49.60  E-value: 2.32e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 28572961   386 RRKQNHRVNFFEYEKPGWTYHAKGLWyylpeaILPNLTLIGSSNFGERSVNRDLETqvCLVTANKDLSQRLQAEADRL 463
Cdd:pfam13091  62 RSLLRAGVEIREYQSFLRSMHAKFYI------IDGKTVIVGSANLTRRALRLNLEN--NVVIKDPELAQELEKEFDRL 131
PLDc_2 pfam13091
PLD-like domain;
75-226 9.88e-06

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 44.98  E-value: 9.88e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961    75 LVQRIGQAKRRIVLASLYLGTGQ-LENAMVQTLRhsleqqSALRLNVLLDFTRGTRGtlnsktmllplvrdFASQVQLSL 153
Cdd:pfam13091   1 LIDLINSAKKSIDIATYYFVPDReIIDALIAAAK------RGVDVRIILDSNKDDAG--------------GPKKASLKE 60

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 28572961   154 YHTPDLRGMTKRLAPPRWNELlglqHMKVYLFDDA-VIISGANLSNDYFTNRQDRYILIEDKPLADFYAQFIER 226
Cdd:pfam13091  61 LRSLLRAGVEIREYQSFLRSM----HAKFYIIDGKtVIVGSANLTRRALRLNLENNVVIKDPELAQELEKEFDR 130
PLDc_ybhO_like_2 cd09159
Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; ...
 377-483 5.06e-05

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: 43.68  E-value: 5.06e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961 377 AKSFYESLVRrkqnHRVNFFEYEKPgwTYHAK-----GLWyylpeailpnlTLIGSSNFGERSVNRDLEtqVCLVTANKD 451
Cdd:cd09159  71 SRALYGKLLR----AGVRIFEYQPS--MLHAKtavidGDW-----------ATVGSSNLDPRSLRLNLE--ANLVVEDPA 131

                        90       100       110
                ....*....|....*....|....*....|....*
gi 28572961 452 LSQRLQAEADRlyDLSQTAE---REIVQRPVPRWV 483
Cdd:cd09159 132 FAAQLEELFEE--DLARSREitlEEWRRRPLWQRL 164
PLDc_Nuc_like cd09116
Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar ...
 73-225 1.34e-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: 41.90  E-value: 1.34e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961  73 ETLVQRIGQAKRRIVLASLYLGTGQLENAMVQTLRHSLeqqsalRLNVLLDfTRGTRGTLNSKTMLLplvrdfasqvqLS 152
Cdd:cd09116  12 RLIVALIANAKSSIDVAMYALTDPEIAEALKRAAKRGV------RVRIILD-KDSLADNLSITLLAL-----------LS 73

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 28572961 153 LYHTPDlrgmtkrlappRWNELLGLQHMKVYLFDDAVIISG-ANLS-NDYFTNRQDRYILIEDKPLADFYAQFIE 225
Cdd:cd09116  74 NLGIPV-----------RTDSGSKLMHHKFIIIDGKIVITGsANWTkSGFHRNDENLLIIDDPKLAASFEEEFNR 137
PLDc_SF cd00138
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ...
 73-211 4.43e-03

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: 37.11  E-value: 4.43e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961  73 ETLVQRIGQAKRRIVLASLYLgTGQLENAMVQTLRHSLEQqsALRLNVLLDFTRGTRGTLNSKTMLLPLVRDFasqvqls 152
Cdd:cd00138   1 EALLELLKNAKESIFIATPNF-SFNSADRLLKALLAAAER--GVDVRLIIDKPPNAAGSLSAALLEALLRAGV------- 70

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 28572961 153 lyhtpDLRGMTKRLAPPRWNellglqHMKVYLFDDA-VIISGANLSNDYFTNRQDRYILI 211
Cdd:cd00138  71 -----NVRSYVTPPHFFERL------HAKVVVIDGEvAYVGSANLSTASAAQNREAGVLV 119
 
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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