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Conserved domains on  [gi|1040489334|ref|WP_065112066|]
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CDP-diacylglycerol--serine O-phosphatidyltransferase [Vibrio lentus]

Protein Classification

CDP-diacylglycerol--serine O-phosphatidyltransferase( domain architecture ID 11484158)

CDP-diacylglycerol--serine O-phosphatidyltransferase catalyzes de novo synthesis of phosphatidylserine from CDP-diacylglycerol and L-serine which leads eventually to the production of phosphatidylethanolamine; binds to the ribosome

EC:  2.7.8.8
Gene Symbol:  pssA
Gene Ontology:  GO:0003882|GO:0008654
PubMed:  1323044

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
pssA PRK09428
CDP-diacylglycerol--serine O-phosphatidyltransferase;
4-446 0e+00

CDP-diacylglycerol--serine O-phosphatidyltransferase;


:

Pssm-ID: 236510 [Multi-domain]  Cd Length: 451  Bit Score: 792.47  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334   4 SRNPFIQLPTIAQNPDKFEVLLSAHEFRTRLLDEISRATTRISLVALYLEDDDAGREILTALYEAKQKNPELDVSVCVDW 83
Cdd:PRK09428   10 HQQHLAQLPKIPQSPDDVETLYSPADFRETLLEKIASAKKRIYIVALYLEDDEAGREILDALYQAKQQNPELDIKVLVDW 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334  84 HRAQRGLIGAESSEGNAAMYKEFADKYQ-HTVPVYGIPVRGKEVFGVLHLKGFIVDDSVIYSGASLNNIYLSYHDRYRFD 162
Cdd:PRK09428   90 HRAQRGLIGAAASNTNADWYCEMAQEYPgVDIPVYGVPVNTREALGVLHLKGFIIDDTVLYSGASLNNVYLHQHDKYRYD 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 163 RYHVLNNATLADSMFSYIQEQMISDIAVYDLADKNKPLTKELKPAIRQFRASLARSQYKFDSQeVSADQVAVTPLVGIGK 242
Cdd:PRK09428  170 RYHLIRNAELADSMVNFIQQNLLNSPAVNRLDQPNRPKTKEIKNDIRQFRQRLRDAAYQFQGQ-ANNDELSVTPLVGLGK 248

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 243 RrNRLNQGINQLVAQAKDEIFICTPYFNFPPSLAKEVKKALKRGVKVTIVVGDKTANDFFISPEEEFKTIGGLPYLYELN 322
Cdd:PRK09428  249 K-NLLNKTIFHLMASAEQKLTICTPYFNLPAILVRNIIRLLRRGKKVEIIVGDKTANDFYIPPDEPFKIIGALPYLYEIN 327

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 323 LRRFAKANEANIASRNLSIRLWQHDSNSFHLKGIWVDKRYMLLTGNNLNPRAWKLDLENGIFIQDNYHHLTDKFQAEVDN 402
Cdd:PRK09428  328 LRRFAKRLQYYIDNGQLNVRLWKDGDNSYHLKGIWVDDRWMLLTGNNLNPRAWRLDLENALLIHDPKQELAEQREKELEL 407

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|....
gi 1040489334 403 IVQHTQLICTYKQLDKVDSYPMEVQKLIRKITRVKADRVLKQIL 446
Cdd:PRK09428  408 IRTHTTRVKHYSQLESIADYPVKVRKLIRRLRRIRIDRLIKRIL 451
 
Name Accession Description Interval E-value
pssA PRK09428
CDP-diacylglycerol--serine O-phosphatidyltransferase;
4-446 0e+00

CDP-diacylglycerol--serine O-phosphatidyltransferase;


Pssm-ID: 236510 [Multi-domain]  Cd Length: 451  Bit Score: 792.47  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334   4 SRNPFIQLPTIAQNPDKFEVLLSAHEFRTRLLDEISRATTRISLVALYLEDDDAGREILTALYEAKQKNPELDVSVCVDW 83
Cdd:PRK09428   10 HQQHLAQLPKIPQSPDDVETLYSPADFRETLLEKIASAKKRIYIVALYLEDDEAGREILDALYQAKQQNPELDIKVLVDW 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334  84 HRAQRGLIGAESSEGNAAMYKEFADKYQ-HTVPVYGIPVRGKEVFGVLHLKGFIVDDSVIYSGASLNNIYLSYHDRYRFD 162
Cdd:PRK09428   90 HRAQRGLIGAAASNTNADWYCEMAQEYPgVDIPVYGVPVNTREALGVLHLKGFIIDDTVLYSGASLNNVYLHQHDKYRYD 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 163 RYHVLNNATLADSMFSYIQEQMISDIAVYDLADKNKPLTKELKPAIRQFRASLARSQYKFDSQeVSADQVAVTPLVGIGK 242
Cdd:PRK09428  170 RYHLIRNAELADSMVNFIQQNLLNSPAVNRLDQPNRPKTKEIKNDIRQFRQRLRDAAYQFQGQ-ANNDELSVTPLVGLGK 248

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 243 RrNRLNQGINQLVAQAKDEIFICTPYFNFPPSLAKEVKKALKRGVKVTIVVGDKTANDFFISPEEEFKTIGGLPYLYELN 322
Cdd:PRK09428  249 K-NLLNKTIFHLMASAEQKLTICTPYFNLPAILVRNIIRLLRRGKKVEIIVGDKTANDFYIPPDEPFKIIGALPYLYEIN 327

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 323 LRRFAKANEANIASRNLSIRLWQHDSNSFHLKGIWVDKRYMLLTGNNLNPRAWKLDLENGIFIQDNYHHLTDKFQAEVDN 402
Cdd:PRK09428  328 LRRFAKRLQYYIDNGQLNVRLWKDGDNSYHLKGIWVDDRWMLLTGNNLNPRAWRLDLENALLIHDPKQELAEQREKELEL 407

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|....
gi 1040489334 403 IVQHTQLICTYKQLDKVDSYPMEVQKLIRKITRVKADRVLKQIL 446
Cdd:PRK09428  408 IRTHTTRVKHYSQLESIADYPVKVRKLIRRLRRIRIDRLIKRIL 451
PLDc_PSS_G_neg_2 cd09136
Catalytic domain, repeat 2, of phosphatidylserine synthases from gram-negative bacteria; ...
 232-446 4.30e-127

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: 366.54  E-value: 4.30e-127
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 232 VAVTPLVGIGKRRNRLNQGINQLVAQAKDEIFICTPYFNFPPSLAKEVKKALKRGVKVTIVVGDKTANDFFISPEEEFKT 311
Cdd:cd09136     1 LSITPLVGLGKRGNQLNRTIRQLIQSAESELIICTPYFNLPRSLVRDIARLLKRGVKVEIIVGDKTANDFYIPPEEPFKT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 312 IGGLPYLYELNLRRFAKANEANIASRNLSIRLWQHDSNSFHLKGIWVDKRYMLLTGNNLNPRAWKLDLENGIFIQDNYHH 391
Cdd:cd09136    81 IGALPYLYEINLRRFAKRLQKYIDNGQLNVRLWKDGNNSFHLKGIWVDDRYHLLTGNNLNPRAWRLDLENGLLIHDPQGQ 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1040489334 392 LTDKFQAEVDNIVQHTQLICTYKQLDKVDSYPMEVQKLIRKITRVKADRVLKQIL 446
Cdd:cd09136   161 LKAQFEKELEQILAHTTRIKHYSQLESIADYPEKVQKLLRRIRRVRADRLLKRIL 215
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 15-436 8.28e-50

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: 173.20  E-value: 8.28e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334  15 AQNPDKFEVLLSAHEFRTRLLDEISRATTRISLVALYLEDDDAGREILTALYEAKQknPELDVSVCVDWhraqrglIGae 94
Cdd:COG1502    11 LVGGNRVTLLVDGDEAFAALLEAIEAARRSIDLEYYIFDDDEVGRRLADALIAAAR--RGVKVRVLLDG-------IG-- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334  95 SSEGNAAMYKEFAD---KYQHTVPVYGIPVRgkeVFGVLHLKGFIVDDSVIY-SGASLNNIYLSYHDR--YRFDRYHVLN 168
Cdd:COG1502    80 SRALNRDFLRRLRAagvEVRLFNPVRLLFRR---LNGRNHRKIVVIDGRVAFvGGANITDEYLGRDPGfgPWRDTHVRIE 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 169 NATLADsmfsyIQEQMISDIavYDLADKNKPLTKELKPAIRQFraslarsqykfdsqevsadqVAVTPlvgiGKRRNRLN 248
Cdd:COG1502   157 GPAVAD-----LQAVFAEDW--NFATGEALPFPEPAGDVRVQV--------------------VPSGP----DSPRETIE 205

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 249 QGINQLVAQAKDEIFICTPYFNFPPSLAKEVKKALKRGVKVTIVVGDKtaNDFFispeeeFKTIGGLPYLYELnlrrfak 328
Cdd:COG1502   206 RALLAAIASARRRIYIETPYFVPDRSLLRALIAAARRGVDVRILLPAK--SDHP------LVHWASRSYYEEL------- 270

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 329 aneaniasRNLSIRLWQHDSNSFHLKGIWVDKRYMLLTGNNLNPRAWKLDLENGIFIQDnyHHLTDKFQAEVDNIVQHTQ 408
Cdd:COG1502   271 --------LEAGVRIYEYEPGFLHAKVMVVDDEWALVGSANLDPRSLRLNFEVNLVIYD--PEFAAQLRARFEEDLAHSR 340

                         410       420
                  ....*....|....*....|....*...
gi 1040489334 409 LIctykQLDKVDSYPMevQKLIRKITRV 436
Cdd:COG1502   341 EV----TLEEWRKRPL--RRLRERLARL 362
PLDc_2 pfam13091
PLD-like domain;
251-403 1.05e-24

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 98.52  E-value: 1.05e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 251 INQLVAQAKDEIFICTPYFNFPPSLAKEVKKALKRGVKVTIVVGDKTAnDFFISPEEEFKtigglpylyelNLRRFAKAn 330
Cdd:pfam13091   1 LIDLINSAKKSIDIATYYFVPDREIIDALIAAAKRGVDVRIILDSNKD-DAGGPKKASLK-----------ELRSLLRA- 67

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1040489334 331 eaniasrNLSIRLWQHDSNSFHLKGIWVDKRYMLLTGNNLNPRAWKLDLENGIFIQDnyHHLTDKFQAEVDNI 403
Cdd:pfam13091  68 -------GVEIREYQSFLRSMHAKFYIIDGKTVIVGSANLTRRALRLNLENNVVIKD--PELAQELEKEFDRL 131
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
 352-374 9.87e-03

Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) isoforms are activated by ADP-ribosylation factors (ARFs). PLD produces phosphatidic acid from phosphatidylcholine, which may be essential for the formation of certain types of transport vesicles or may be constitutive vesicular transport to signal transduction pathways. PC-hydrolysing PLD is a homologue of cardiolipin synthase, phosphatidylserine synthase, bacterial PLDs, and viral proteins. Each of these appears to possess a domain duplication which is apparent by the presence of two motifs containing well-conserved histidine, lysine, aspartic acid, and/or asparagine residues which may contribute to the active site. An E. coli endonuclease (nuc) and similar proteins appear to be PLD homologues but possess only one of these motifs. The profile contained here represents only the putative active site regions, since an accurate multiple alignment of the repeat units has not been achieved.


Pssm-ID: 197546 [Multi-domain]  Cd Length: 28  Bit Score: 33.52  E-value: 9.87e-03
                           10        20
                   ....*....|....*....|...
gi 1040489334  352 HLKGIWVDKRYMLLTGNNLNPRA 374
Cdd:smart00155   6 HTKLMIVDDEIAYIGSANLDGRS 28
 
Name Accession Description Interval E-value
pssA PRK09428
CDP-diacylglycerol--serine O-phosphatidyltransferase;
4-446 0e+00

CDP-diacylglycerol--serine O-phosphatidyltransferase;


Pssm-ID: 236510 [Multi-domain]  Cd Length: 451  Bit Score: 792.47  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334   4 SRNPFIQLPTIAQNPDKFEVLLSAHEFRTRLLDEISRATTRISLVALYLEDDDAGREILTALYEAKQKNPELDVSVCVDW 83
Cdd:PRK09428   10 HQQHLAQLPKIPQSPDDVETLYSPADFRETLLEKIASAKKRIYIVALYLEDDEAGREILDALYQAKQQNPELDIKVLVDW 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334  84 HRAQRGLIGAESSEGNAAMYKEFADKYQ-HTVPVYGIPVRGKEVFGVLHLKGFIVDDSVIYSGASLNNIYLSYHDRYRFD 162
Cdd:PRK09428   90 HRAQRGLIGAAASNTNADWYCEMAQEYPgVDIPVYGVPVNTREALGVLHLKGFIIDDTVLYSGASLNNVYLHQHDKYRYD 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 163 RYHVLNNATLADSMFSYIQEQMISDIAVYDLADKNKPLTKELKPAIRQFRASLARSQYKFDSQeVSADQVAVTPLVGIGK 242
Cdd:PRK09428  170 RYHLIRNAELADSMVNFIQQNLLNSPAVNRLDQPNRPKTKEIKNDIRQFRQRLRDAAYQFQGQ-ANNDELSVTPLVGLGK 248

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 243 RrNRLNQGINQLVAQAKDEIFICTPYFNFPPSLAKEVKKALKRGVKVTIVVGDKTANDFFISPEEEFKTIGGLPYLYELN 322
Cdd:PRK09428  249 K-NLLNKTIFHLMASAEQKLTICTPYFNLPAILVRNIIRLLRRGKKVEIIVGDKTANDFYIPPDEPFKIIGALPYLYEIN 327

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 323 LRRFAKANEANIASRNLSIRLWQHDSNSFHLKGIWVDKRYMLLTGNNLNPRAWKLDLENGIFIQDNYHHLTDKFQAEVDN 402
Cdd:PRK09428  328 LRRFAKRLQYYIDNGQLNVRLWKDGDNSYHLKGIWVDDRWMLLTGNNLNPRAWRLDLENALLIHDPKQELAEQREKELEL 407

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|....
gi 1040489334 403 IVQHTQLICTYKQLDKVDSYPMEVQKLIRKITRVKADRVLKQIL 446
Cdd:PRK09428  408 IRTHTTRVKHYSQLESIADYPVKVRKLIRRLRRIRIDRLIKRIL 451
PLDc_PSS_G_neg_2 cd09136
Catalytic domain, repeat 2, of phosphatidylserine synthases from gram-negative bacteria; ...
 232-446 4.30e-127

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: 366.54  E-value: 4.30e-127
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 232 VAVTPLVGIGKRRNRLNQGINQLVAQAKDEIFICTPYFNFPPSLAKEVKKALKRGVKVTIVVGDKTANDFFISPEEEFKT 311
Cdd:cd09136     1 LSITPLVGLGKRGNQLNRTIRQLIQSAESELIICTPYFNLPRSLVRDIARLLKRGVKVEIIVGDKTANDFYIPPEEPFKT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 312 IGGLPYLYELNLRRFAKANEANIASRNLSIRLWQHDSNSFHLKGIWVDKRYMLLTGNNLNPRAWKLDLENGIFIQDNYHH 391
Cdd:cd09136    81 IGALPYLYEINLRRFAKRLQKYIDNGQLNVRLWKDGNNSFHLKGIWVDDRYHLLTGNNLNPRAWRLDLENGLLIHDPQGQ 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1040489334 392 LTDKFQAEVDNIVQHTQLICTYKQLDKVDSYPMEVQKLIRKITRVKADRVLKQIL 446
Cdd:cd09136   161 LKAQFEKELEQILAHTTRIKHYSQLESIADYPEKVQKLLRRIRRVRADRLLKRIL 215
PLDc_CDP-OH_P_transf_II_2 cd09103
Catalytic domain, repeat 2, of CDP-alcohol phosphatidyltransferase class-II family members; ...
 232-415 3.37e-106

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: 312.24  E-value: 3.37e-106
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 232 VAVTPLVGIGKRRNRLNQGINQLVAQAKDEIFICTPYFNFPPSLAKEVKKALKRGVKVTIVVGDKTANDFFISPEEEFKT 311
Cdd:cd09103     1 LSITPLVGLGKRGNILNRTIEQLITSAESKIILCTPYFNLPQALMRDILRLLKRGVKVEIIVGDKTANDFYIPPEEPFKV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 312 IGGLPYLYELNLRRFAKANEANIASRNLSIRLWQHDSNSFHLKGIWVDKRYMLLTGNNLNPRAWKLDLENGIFIQDNYHH 391
Cdd:cd09103    81 IGALPYLYEINLRRFAKRLQKYIDQGQLNVRLWKDGDNSFHLKGIWVDDRYTLLTGNNLNPRAWRLDLENGLLIHDPQKQ 160

                         170       180
                  ....*....|....*....|....
gi 1040489334 392 LTDKFQAEVDNIVQHTQLICTYKQ 415
Cdd:cd09103   161 LQQQLEKELEQILLHTTRISHYTQ 184
PLDc_PSS_G_neg_1 cd09134
Catalytic domain, repeat 1, of phosphatidylserine synthases from gram-negative bacteria; ...
 11-183 7.15e-104

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: 306.10  E-value: 7.15e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334  11 LPTIAQNPDKFEVLLSAHEFRTRLLDEISRATTRISLVALYLEDDDAGREILTALYEAKQKNPELDVSVCVDWHRAQRGL 90
Cdd:cd09134     1 LPKIPQQPEDIDVLYSPKDFRARLLELISNAKKRIYIVALYLEDDEAGREILDALYEAKANNPGLDIKVLVDWHRAQRGL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334  91 IGAESSEGNAAMYKEFADKYQHTVPVYGIPVRGKEVFGVLHLKGFIVDDSVIYSGASLNNIYLSYHDRYRFDRYHVLNNA 170
Cdd:cd09134    81 IGAKKSLGNADWYRKIAQRYGHDVPIYGVPVKTRELFGVLHLKGFIIDDTVLYSGASLNNVYLHQFDKYRYDRYHLIYNP 160

                         170
                  ....*....|...
gi 1040489334 171 TLADSMFSYIQEQ 183
Cdd:cd09134   161 ELADSMVNFIQDY 173
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 15-436 8.28e-50

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: 173.20  E-value: 8.28e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334  15 AQNPDKFEVLLSAHEFRTRLLDEISRATTRISLVALYLEDDDAGREILTALYEAKQknPELDVSVCVDWhraqrglIGae 94
Cdd:COG1502    11 LVGGNRVTLLVDGDEAFAALLEAIEAARRSIDLEYYIFDDDEVGRRLADALIAAAR--RGVKVRVLLDG-------IG-- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334  95 SSEGNAAMYKEFAD---KYQHTVPVYGIPVRgkeVFGVLHLKGFIVDDSVIY-SGASLNNIYLSYHDR--YRFDRYHVLN 168
Cdd:COG1502    80 SRALNRDFLRRLRAagvEVRLFNPVRLLFRR---LNGRNHRKIVVIDGRVAFvGGANITDEYLGRDPGfgPWRDTHVRIE 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 169 NATLADsmfsyIQEQMISDIavYDLADKNKPLTKELKPAIRQFraslarsqykfdsqevsadqVAVTPlvgiGKRRNRLN 248
Cdd:COG1502   157 GPAVAD-----LQAVFAEDW--NFATGEALPFPEPAGDVRVQV--------------------VPSGP----DSPRETIE 205

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 249 QGINQLVAQAKDEIFICTPYFNFPPSLAKEVKKALKRGVKVTIVVGDKtaNDFFispeeeFKTIGGLPYLYELnlrrfak 328
Cdd:COG1502   206 RALLAAIASARRRIYIETPYFVPDRSLLRALIAAARRGVDVRILLPAK--SDHP------LVHWASRSYYEEL------- 270

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 329 aneaniasRNLSIRLWQHDSNSFHLKGIWVDKRYMLLTGNNLNPRAWKLDLENGIFIQDnyHHLTDKFQAEVDNIVQHTQ 408
Cdd:COG1502   271 --------LEAGVRIYEYEPGFLHAKVMVVDDEWALVGSANLDPRSLRLNFEVNLVIYD--PEFAAQLRARFEEDLAHSR 340

                         410       420
                  ....*....|....*....|....*...
gi 1040489334 409 LIctykQLDKVDSYPMevQKLIRKITRV 436
Cdd:COG1502   341 EV----TLEEWRKRPL--RRLRERLARL 362
PLDc_CDP-OH_P_transf_II_1 cd09102
Catalytic domain, repeat 1, of CDP-alcohol phosphatidyltransferase class-II family members; ...
 22-181 8.68e-42

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: 145.81  E-value: 8.68e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334  22 EVLLSAHEFRTRLLDEISRATTRISLVALYLEDDDAGREILTALYEAKQKNPELDVSVCVDWHRAQRGLIGAES-SEGNA 100
Cdd:cd09102     3 RFLGSPAEFKTQIIELIRNAKRRVYVASLYWGKDEAGQEILDEIYSVKQENPNLDVSVLIDWHRAQRNLLGSETkSATNA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 101 AMYKEFADKYQ-HTVPV-----YGIPVRGKEVFGVLHLKGFIVDDSVIYSGASLNNIYLSY-HDRYRFdryhVLNNATLA 173
Cdd:cd09102    83 DWYCEQRQTSQlHLLPDdgn*fFGVPINTNEVFGVLHVKGYVFDDTVLLSGANLSNVYFHYrYDRYVK----ITHGAELA 158


                  ....*...
gi 1040489334 174 DSMFSYIQ 181
Cdd:cd09102   159 DS*VNLIN 166
PLDc_PGS1_euk_1 cd09135
Catalytic domain, repeat 1, of eukaryotic PhosphatidylGlycerophosphate Synthases; Catalytic ...
 22-181 6.30e-28

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: 108.79  E-value: 6.30e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334  22 EVLLSAHEFRTRLLDEISRATTRISLVALYLEDDDAGREILTALYEAKQKNPELDVSVCVDWHRAQRGLIGAESSEGNAA 101
Cdd:cd09135     3 RILRTPSEFYNTLLDKIRNAKRRIVLSSLYIGTGPLEQELVDALQEALERNPNLKVSILLDYLRGTRGEPNSRTASLLLP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 102 MYKEFADKYQ----HTVPVYG-----IPVRGKEVFGVLHLKGFIVDDSVIYSGASLNNIYLsyhdRYRFDRYHVLNNA-T 171
Cdd:cd09135    83 LLKLFPDRVRvslyHTPNLRGllkklLPERFNEIIGLQHMKLYIFDDDVILSGANLSDDYF----TNRQDRYMLIENCpE 158

                         170
                  ....*....|
gi 1040489334 172 LADSMFSYIQ 181
Cdd:cd09135   159 LADFYHDLIK 168
PLDc_2 pfam13091
PLD-like domain;
251-403 1.05e-24

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 98.52  E-value: 1.05e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 251 INQLVAQAKDEIFICTPYFNFPPSLAKEVKKALKRGVKVTIVVGDKTAnDFFISPEEEFKtigglpylyelNLRRFAKAn 330
Cdd:pfam13091   1 LIDLINSAKKSIDIATYYFVPDREIIDALIAAAKRGVDVRIILDSNKD-DAGGPKKASLK-----------ELRSLLRA- 67

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1040489334 331 eaniasrNLSIRLWQHDSNSFHLKGIWVDKRYMLLTGNNLNPRAWKLDLENGIFIQDnyHHLTDKFQAEVDNI 403
Cdd:pfam13091  68 -------GVEIREYQSFLRSMHAKFYIIDGKTVIVGSANLTRRALRLNLENNVVIKD--PELAQELEKEFDRL 131
PLDc_PGS1_euk_2 cd09137
Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases; Catalytic ...
 259-416 1.81e-19

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: 85.71  E-value: 1.81e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 259 KDEIFICTPYFNFPPSLakeVKKALKRGVKVTIVVGDKTANDFFispeeEFKTI-GGLPYLYELNLRRFAKANEANIASR 337
Cdd:cd09137    31 GSSLTLASGYFNLTPEY---LNLLLNSSANLDVLTASPEANGFY-----GSKGVsGYIPPAYTYIARQFLKRVRKNGKQP 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 338 NLSIRLWQHDSNSFHLKGIWVDK---RYMLLT--GN-NLNPRAWKLDLENGIFIQDNYHHLTDKFQAEVDNIVQHTQLiC 411
Cdd:cd09137   103 RIKLFEYKRPGWTFHAKGLWIYLpgtDLPSLTliGSsNYGYRSVHRDLEAQFLIVTNNPKLQQQLKEELENLFEYSKP-V 181


                  ....*
gi 1040489334 412 TYKQL 416
Cdd:cd09137   182 TPETF 186
PLDc_SF cd00138
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ...
 251-385 6.17e-12

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: 62.53  E-value: 6.17e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 251 INQLVAQAKDEIFICTPYFNFP--PSLAKEVKKALKRGVKVTIVVGDKTANDFFISPeeefktigglpylyelnlrrfak 328
Cdd:cd00138     3 LLELLKNAKESIFIATPNFSFNsaDRLLKALLAAAERGVDVRLIIDKPPNAAGSLSA----------------------- 59

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 329 ANEANIASRNLSIRLW---QHDSNSFHLKGIWVDKRYMLLTGNNLNPRAWKLDLENGIFI 385
Cdd:cd00138    60 ALLEALLRAGVNVRSYvtpPHFFERLHAKVVVIDGEVAYVGSANLSTASAAQNREAGVLV 119
PLDc_EcCLS_like_2 cd09158
Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase and similar proteins; ...
 239-435 4.93e-06

Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase and similar proteins; Catalytic domain, repeat 2, of Escherichia coli cardiolipin (CL) synthase and similar proteins. Escherichia coli CL synthase (EcCLS), specified by the cls gene, is the prototype of this family. EcCLS is a multi-pass membrane protein that catalyzes reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form cardiolipin (CL) and glycerol. The monomer of EcCLS consists of two catalytic domains. Each catalytic domain contains one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. Two HKD motifs from two domains form a single active site involved in phosphatidyl group transfer. EcCLS can be stimulated by phosphate and inhibited by CL, the product of the reaction, and by phosphatidate. Phosphate stimulation may be unique to enzymes with CL synthase activity belonging to the PLD superfamily. Like other PLD enzymes, EcCLS utilizes a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group.


Pssm-ID: 197255 [Multi-domain]  Cd Length: 174  Bit Score: 46.80  E-value: 4.93e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 239 GIGKRRNRLNQGINQLVAQAKDEIFICTPYFNFPPSLAKEVKKALKRGVKVTIVVgDKTANDFFISPEEEfktigglPYL 318
Cdd:cd09158     4 GPDYPTENIPQLLLSAIHAARRRVVITTPYFVPDESLLQALCTAALRGVEVTLIL-PAKNDSFLVGAASR-------SYY 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 319 YELnLRrfakaneaniasrnLSIRLWQHDSNSFHLKGIWVDKRYMLLTGNNLNPRAWKLDLENGIFIQDnyhhltDKFQA 398
Cdd:cd09158    76 EEL-LE--------------AGVKIYLYRGGLLHAKTVTVDDEVALVGSSNFDIRSFALNFEISLILYD------KEFTA 134

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1040489334 399 EVDNIVQHTQLICTYKQLDKVDSYPMeVQKLIRKITR 435
Cdd:cd09158   135 QLRAIQERYLARSDPLTLEEWKKRPL-WRRLLENLAR 170
PLDc_unchar1_2 cd09128
Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; ...
 254-387 6.66e-06

Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; Putative catalytic domain, repeat 2, of uncharacterized phospholipase D (PLD, EC 3.1.4.4)-like proteins. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze transphosphatidylation of phospholipids to acceptor alcohols. Members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the PLD superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer.


Pssm-ID: 197226 [Multi-domain]  Cd Length: 142  Bit Score: 45.73  E-value: 6.66e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 254 LVAQAKDEIFICTPYFNFPPSLAKEVKKALKRGVKVTIVVGDKtandffispeeefktigglPYLYELNLRRFAKANEAN 333
Cdd:cd09128    18 LIDSAEESLLIQNEEMGDDAPILDALVDAAKRGVDVRVLLPSA-------------------WSAEDERQARLRALEGAG 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1040489334 334 IAsrnlsIRLWQHDSNSFHLKGIWVDKRYMLLTGNNLNPRAWKLDLENGIFIQD 387
Cdd:cd09128    79 VP-----VRLLKDKFLKIHAKGIVVDGKTALVGSENWSANSLDRNREVGLIFDD 127
PLDc_like_TrmB_middle cd09124
Middle phospholipase D-like domain of the transcriptional regulator TrmB and similar proteins; ...
 242-316 3.47e-05

Middle phospholipase D-like domain of the transcriptional regulator TrmB and similar proteins; Middle phospholipase D (PLD)-like domain of the transcriptional regulator TrmB and similar proteins. TrmB acts as a bifunctional sugar-sensing transcriptional regulator which controls two operons encoding maltose/trehalose and maltodextrin ABC transporters of Pyrococcus fruiosus. It functions as a dimer. Full length TrmB includes an N-terminal DNA-binding domain, a C-terminal sugar-binding domain and middle region that has been named as a PLD-like domain. The middle domain displays homology to PLD enzymes, which contain one or two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) per chain. The HKD motif characterizes the PLD superfamily. Due to the lack of key residues related to PLD activity in the PLD-like domain, members of this subfamily are unlikely to carry PLD activity.


Pssm-ID: 197223 [Multi-domain]  Cd Length: 126  Bit Score: 43.08  E-value: 3.47e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1040489334 242 KRRNRLNQGINQLVAQAKDEIFICTPYFNFPPsLAKEVKKALKRGVKVTIVVGDKTANDFFISPEEEFKTIGGLP 316
Cdd:cd09124     6 KGEENILAKIREMINSAKEEIYISLPSEELEE-LLEELEKAAERGVKVVIIIFGDDDLDDLDSPAIEVRVREGGG 79
PLDc_CLS_2 cd09112
catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; This CD ...
 249-387 3.52e-05

catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; This CD corresponds to the catalytic domain repeat 2 of bacterial cardiolipin synthase (CL synthase, EC 2.7.8.-) and a few homologs found in eukaryotes and archea. Bacterial CL synthases catalyze reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form cardiolipin (CL) and glycerol. The monomer of bacterial CL synthase consists of two catalytic domains. Each catalytic domain contains one copy of conserved HKD motifs (H-X-K-X(4)-D, X represents any amino acid residue) that are the characteristic of the phospholipase D (PLD) superfamily. Two HKD motifs from two domains together form a single active site involving in phosphatidyl group transfer. Bacterial CL synthases can be stimulated by phosphate and inhibited by CL, the product of the reaction, and by phosphatidate. Phosphate stimulation may be unique to enzymes with CL synthase activity in PLD superfamily. Like other PLD enzymes, bacterial CL synthase utilize a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid stabilizing the leaving group.


Pssm-ID: 197211 [Multi-domain]  Cd Length: 174  Bit Score: 44.01  E-value: 3.52e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 249 QGINQLVAQAKDEIFICTPYFNFPPSLAKEVKKALKRGVKVTIVVGDKTANdffispeeefktigglPYLYELNLRRFAK 328
Cdd:cd09112    14 QAYLKAINSAKKSIYIQTPYFIPDESLLEALKTAALSGVDVRIMIPGKPDH----------------KLVYWASRSYFEE 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1040489334 329 ANEANiasrnlsIRLWQHDSNSFHLKGIWVDKRYMLLTGNNLNPRAWKLDLENGIFIQD 387
Cdd:cd09112    78 LLKAG-------VKIYEYNKGFLHSKTLIVDDEIASVGTANLDIRSFELNFEVNAVIYD 129
PLDc_ybhO_like_2 cd09159
Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; ...
 253-410 4.16e-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: 4.16e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 253 QLVAQAKDEIFICTPYFNFPPSLAKEVKKALKRGVKVTIVVGDKTANDFFISpeeefktigGLPYLYelnlRRFAKANea 332
Cdd:cd09159    18 VAIAAARRRIWIANAYFVPDRRLRRALIEAARRGVDVRLLLPGKSDDPLTVA---------ASRALY----GKLLRAG-- 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1040489334 333 niasrnlsIRLWQHDSNSFHLKGIWVDKRYMLLTGNNLNPRAWKLDLENGIFIQDnyHHLTDKFQAEVDNIVQHTQLI 410
Cdd:cd09159    83 --------VRIFEYQPSMLHAKTAVIDGDWATVGSSNLDPRSLRLNLEANLVVED--PAFAAQLEELFEEDLARSREI 150
PLDc_unchar4 cd09132
Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic ...
 249-385 1.07e-04

Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic domain of uncharacterized phospholipase D (PLD, EC 3.1.4.4)-like proteins. Members of this subfamily contain one copy of HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the PLD superfamily.


Pssm-ID: 197230 [Multi-domain]  Cd Length: 122  Bit Score: 41.88  E-value: 1.07e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 249 QGINQLVAQAKDEIFICTPYFNFPPSLAKEVKKALKRGVKVTIVVGDKTAND--FFISPEEEFKTIGGLPYLYELN--LR 324
Cdd:cd09132     2 QVLLELIEGAERSLLIVGYSAYKVSELLQALAAALERGVQVRVVVESSEKAGsvLSLDEDELMWPKLAGATLYVWPekKR 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1040489334 325 RFAKAneaniasrnlsirlwqhdsnSFHLKGIWVDKRYMLLTGNNLNPRAWKLDLENGIFI 385
Cdd:cd09132    82 PGKRA--------------------SLHAKVIVADRRRLLVTSANLTGAGMERNIEAGVLV 122
PLDc_2 pfam13091
PLD-like domain;
34-149 1.21e-04

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 41.89  E-value: 1.21e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334  34 LLDEISRATTRISLVALYLEDDdagREILTALYEAKQKNpeLDVSVCVDWHRAQRGLIgaessegNAAMYKEFADKYQHT 113
Cdd:pfam13091   1 LIDLINSAKKSIDIATYYFVPD---REIIDALIAAAKRG--VDVRIILDSNKDDAGGP-------KKASLKELRSLLRAG 68

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1040489334 114 VPVYgipvRGKEVFGVLHLKGFIVDDSVIYSGaSLN 149
Cdd:pfam13091  69 VEIR----EYQSFLRSMHAKFYIIDGKTVIVG-SAN 99
PLDc_ymdC_like_2 cd09113
Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and ...
 237-387 1.99e-04

Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins; Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins. In Escherichia coli, there are two genes, f413 (ybhO) and o493 (ymdC), which are homologous to gene cls that encodes the Escherichia coli cardiolipin (CL) synthase. The prototype of this subfamily is an uncharacterized protein ymdC specified by the o493 (ymdC) gene. Although the functional characterization of ymdC and similar proteins remains unknown, members of this subfamily show high sequence homology to bacterial CL synthases, which catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. Moreover, ymdC and its similar proteins contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characteriszes the phospholipase D (PLD) superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer.


Pssm-ID: 197212 [Multi-domain]  Cd Length: 218  Bit Score: 42.59  E-value: 1.99e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 237 LVGIGKRRNRLNQGINQLVAQAKDEIFICTPYFNFPPSLAKEVKKALKRGVKVTIVVGDKTANDFFI--SpeeefktiGG 314
Cdd:cd09113     8 ALKEAGPEPVLAYQLAELLKNAKREVLIVSPYFVPGDEGVALLAELARRGVRVRILTNSLAATDVPAvhS--------GY 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 315 LPY----------LYELnlrrfakanEANIASRNLSIRLWQHDSNSFHLKGIWVDKRyMLLTGN-NLNPRAWKLDLENGI 383
Cdd:cd09113    80 ARYrkrllkagveLYEL---------KPDAAKRKRLRGLFGSSRASLHAKSFVIDDR-LVFVGSfNLDPRSAYLNTEMGL 149


                  ....
gi 1040489334 384 FIQD 387
Cdd:cd09113   150 VIDS 153
YrhO COG1378
Sugar-specific transcriptional regulator TrmB [Transcription];
251-316 3.18e-04

Sugar-specific transcriptional regulator TrmB [Transcription];


Pssm-ID: 440988 [Multi-domain]  Cd Length: 238  Bit Score: 41.93  E-value: 3.18e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1040489334 251 INQLVAQAKDEIFI-CTPYFNFPPSLAKEVKKALKRGVKVTIVVGDKTANDF--FISPEEEFKTIGGLP 316
Cdd:COG1378   122 LRELIASAEEEILIvLSPPELLLEELEEALEEALERGVKVRVLVSPEVLEVPerLEEEGEEVRVLPGLP 190
PLDc_CLS_unchar1_2 cd09162
Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial ...
 244-385 4.51e-04

Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial cardiolipin synthase; Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial cardiolipin (CL) synthases, which catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. Members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer.


Pssm-ID: 197259 [Multi-domain]  Cd Length: 172  Bit Score: 40.71  E-value: 4.51e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 244 RNRLNQGINQLVAQAKDEIFICTPYFNFPPSLAKEVKKALKRGVKVTIVVgdktandffisPEEEFKTIGGLP---YLYE 320
Cdd:cd09162     9 GDPLYEALLSAIFEAEHRIWIVTPYFVPDEVLLRALRLAARRGVDVRLIV-----------PKRSNHRIADLArgsYLRD 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1040489334 321 LnlrrfakaNEANiasrnlsIRLWQHDSNSFHLKGIWVDKRYMLLTGNNLNPRAWKLDLENGIFI 385
Cdd:cd09162    78 L--------QEAG-------AEIYLYQPGMLHAKAVVVDDKLALVGSANLDMRSLFLNYEVAVFF 127
PLDc pfam00614
Phospholipase D Active site motif; Phosphatidylcholine-hydrolysing phospholipase D (PLD) ...
 352-374 9.80e-04

Phospholipase D Active site motif; Phosphatidylcholine-hydrolysing phospholipase D (PLD) isoforms are activated by ADP-ribosylation factors (ARFs). PLD produces phosphatidic acid from phosphatidylcholine, which may be essential for the formation of certain types of transport vesicles or may be constitutive vesicular transport to signal transduction pathways. PC-hydrolysing PLD is a homolog of cardiolipin synthase, phosphatidylserine synthase, bacterial PLDs, and viral proteins. Each of these appears to possess a domain duplication which is apparent by the presence of two motifs containing well-conserved histidine, lysine, and/or asparagine residues which may contribute to the active site. aspartic acid. An E. coli endonuclease (nuc) and similar proteins appear to be PLD homologs but possess only one of these motifs. The profile contained here represents only the putative active site regions, since an accurate multiple alignment of the repeat units has not been achieved.


Pssm-ID: 395489 [Multi-domain]  Cd Length: 28  Bit Score: 36.24  E-value: 9.80e-04
                          10        20
                  ....*....|....*....|...
gi 1040489334 352 HLKGIWVDKRYMLLTGNNLNPRA 374
Cdd:pfam00614   6 HRKIVVVDDELAYIGGANLDGRS 28
PLDc_SMU_988_like_2 cd09160
Putative catalytic domain, repeat 2, of Streptococcus mutans uncharacterized protein SMU_988 ...
 253-293 1.64e-03

Putative catalytic domain, repeat 2, of Streptococcus mutans uncharacterized protein SMU_988 and similar proteins; Putative catalytic domain, repeat 2, of Streptococcus mutans uncharacterized protein SMU_988 and similar proteins. Although SMU_988 and similar proteins have not been functionally characterized, members in this subfamily show high sequence homology to bacterial cardiolipin (CL) synthases, which catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. Members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer.


Pssm-ID: 197257 [Multi-domain]  Cd Length: 176  Bit Score: 39.40  E-value: 1.64e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1040489334 253 QLVAQAKDEIFICTPYFNFPPSLAKEVKKALKRGVKVTIVV 293
Cdd:cd09160    18 DLINQAKDYVYITTPYLILDDEMLDALCLAAKRGVDVRIIT 58
PLDc_vPLD1_2_like_2 cd09105
Catalytic domain, repeat 2, of vertebrate phospholipases, PLD1 and PLD2, and similar proteins; ...
 254-387 2.84e-03

Catalytic domain, repeat 2, of vertebrate phospholipases, PLD1 and PLD2, and similar proteins; Catalytic domain, repeat 2, of phospholipase D (PLD, EC 3.1.4.4) found in yeast, plants, and vertebrates, and their bacterial homologs. PLDs are involved in signal transduction, vesicle formation, protein transport, and mitosis by participating in phospholipid metabolism. They hydrolyze the terminal phosphodiester bond of phospholipids resulting in the formation of phosphatidic acid and alcohols. Phosphatidic acid is an essential compound involved in signal transduction. PLDs also catalyze the transphosphatidylation of phospholipids to acceptor alcohols, by which various phospholipids can be synthesized. Both prokaryotic and eukaryotic PLDs have two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. PLDs are active as bi-lobed monomers. Each monomer contains two domains, each of which carries one copy of the HKD motif. Two HKD motifs from two domains form a single active site. PLDs utilize a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group.


Pssm-ID: 197204 [Multi-domain]  Cd Length: 146  Bit Score: 38.05  E-value: 2.84e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 254 LVAQAKDEIFICTPYFnFPPSLAKEVKKALK--RGVKVTIVVGDKTANDFFISPEeefktigGLPYLYELNLRRFAKANE 331
Cdd:cd09105    16 AIRNARRYIYIEDQYL-WSPELLDALAEALKanPGLRVVLVLPALPDAVAFGADD-------GLDALALLALLLLADAAP 87

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1040489334 332 ANIAsrNLSIRlwQHDSNSFHLKGIWV-------DKRYMLLTGNNLNPRAWKLDLENGIFIQD 387
Cdd:cd09105    88 DRVA--VFSLA--THRRGLLGGPPIYVhskvvivDDEWATVGSANLNRRSMTWDTELNLAVVD 146
PLDc_Nuc_like cd09116
Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar ...
 251-388 3.34e-03

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: 37.66  E-value: 3.34e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334 251 INQLVAQAKDEIFICTPYFNFPPsLAKEVKKALKRGVKVTIVVgDKTANdffispeeefktigglpyLYELNLRRFAKAN 330
Cdd:cd09116    14 IVALIANAKSSIDVAMYALTDPE-IAEALKRAAKRGVRVRIIL-DKDSL------------------ADNLSITLLALLS 73

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1040489334 331 EANIASRNLSirlwqhDSNSFHLKGIWVDKRyMLLTGN-NLNPRAWKLDLENGIFIQDN 388
Cdd:cd09116    74 NLGIPVRTDS------GSKLMHHKFIIIDGK-IVITGSaNWTKSGFHRNDENLLIIDDP 125
PLDc_Nuc_like cd09116
Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar ...
 27-149 9.34e-03

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: 36.50  E-value: 9.34e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040489334  27 AHEFRTRLLDEISRATTRISLVALYLEDddagREILTALYEAKQKNpeLDVSVCVD-WHRAQRGLIGAESSEGNAamyke 105
Cdd:cd09116     7 QDNLERLIVALIANAKSSIDVAMYALTD----PEIAEALKRAAKRG--VRVRIILDkDSLADNLSITLLALLSNL----- 75

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1040489334 106 fadkyqhtvpvyGIPVRGKEVFGVLHLKGFIVDDSVIYSGaSLN 149
Cdd:cd09116    76 ------------GIPVRTDSGSKLMHHKFIIIDGKIVITG-SAN 106
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
 352-374 9.87e-03

Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) isoforms are activated by ADP-ribosylation factors (ARFs). PLD produces phosphatidic acid from phosphatidylcholine, which may be essential for the formation of certain types of transport vesicles or may be constitutive vesicular transport to signal transduction pathways. PC-hydrolysing PLD is a homologue of cardiolipin synthase, phosphatidylserine synthase, bacterial PLDs, and viral proteins. Each of these appears to possess a domain duplication which is apparent by the presence of two motifs containing well-conserved histidine, lysine, aspartic acid, and/or asparagine residues which may contribute to the active site. An E. coli endonuclease (nuc) and similar proteins appear to be PLD homologues but possess only one of these motifs. The profile contained here represents only the putative active site regions, since an accurate multiple alignment of the repeat units has not been achieved.


Pssm-ID: 197546 [Multi-domain]  Cd Length: 28  Bit Score: 33.52  E-value: 9.87e-03
                           10        20
                   ....*....|....*....|...
gi 1040489334  352 HLKGIWVDKRYMLLTGNNLNPRA 374
Cdd:smart00155   6 HTKLMIVDDEIAYIGSANLDGRS 28
 
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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