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Conserved domains on  [gi|490285132|ref|WP_004180947|]
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MULTISPECIES: CDP-diacylglycerol--serine O-phosphatidyltransferase [Klebsiella]

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;
1-431 0e+00

CDP-diacylglycerol--serine O-phosphatidyltransferase;


:

Pssm-ID: 236510 [Multi-domain]  Cd Length: 451  Bit Score: 859.88  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132   1 MLSKFKRNKHQQHLAQLPKLSQSVDDVEFFYAPAEFREALLTRIAHATQRICIIALYLEQDDGGKGILQALYDAKRQRPE 80
Cdd:PRK09428   1 MLSKFKRNKHQQHLAQLPKIPQSPDDVETLYSPADFRETLLEKIASAKKRIYIVALYLEDDEAGREILDALYQAKQQNPE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132  81 LDVRVLVDWHRAQRGRIGAAASNTNADWYCRMANENPGVDIPVYGVPINTREALGVLHFKGFIIDDCVLYSGASLNDVYL 160
Cdd:PRK09428  81 LDIKVLVDWHRAQRGLIGAAASNTNADWYCEMAQEYPGVDIPVYGVPVNTREALGVLHLKGFIIDDTVLYSGASLNNVYL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132 161 HQHDKYRYDRYQCIRNGKMADIMFDWVDNNLVQGRGVNRLDRPDRPKSPEIKNDIRQYRQELRDRSYHFVGTAGDEELSV 240
Cdd:PRK09428 161 HQHDKYRYDRYHLIRNAELADSMVNFIQQNLLNSPAVNRLDQPNRPKTKEIKNDIRQFRQRLRDAAYQFQGQANNDELSV 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132 241 TPLVGLGKSSLLNKTIFHLMPCAEHKLTICTPYFNLPAVLVRNIIQLLRDGKQVEIIVGDKTANDFYIPEDQPFKIIGAL 320
Cdd:PRK09428 241 TPLVGLGKKNLLNKTIFHLMASAEQKLTICTPYFNLPAILVRNIIRLLRRGKKVEIIVGDKTANDFYIPPDEPFKIIGAL 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132 321 PYLYEINLRRFLSRLQYYVNTDQLIVRLWKDDDNSYHLKGMWVDDEWMLLTGNNLNPRAWRLDLENAILIHDPKRQLGAM 400
Cdd:PRK09428 321 PYLYEINLRRFAKRLQYYIDNGQLNVRLWKDGDNSYHLKGIWVDDRWMLLTGNNLNPRAWRLDLENALLIHDPKQELAEQ 400

                        410       420       430
                 ....*....|....*....|....*....|.
gi 490285132 401 REKELKLIRTHTTVVKHYRDLQSIADYPVKV 431
Cdd:PRK09428 401 REKELELIRTHTTRVKHYSQLESIADYPVKV 431
 
Name Accession Description Interval E-value
pssA PRK09428
CDP-diacylglycerol--serine O-phosphatidyltransferase;
1-431 0e+00

CDP-diacylglycerol--serine O-phosphatidyltransferase;


Pssm-ID: 236510 [Multi-domain]  Cd Length: 451  Bit Score: 859.88  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132   1 MLSKFKRNKHQQHLAQLPKLSQSVDDVEFFYAPAEFREALLTRIAHATQRICIIALYLEQDDGGKGILQALYDAKRQRPE 80
Cdd:PRK09428   1 MLSKFKRNKHQQHLAQLPKIPQSPDDVETLYSPADFRETLLEKIASAKKRIYIVALYLEDDEAGREILDALYQAKQQNPE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132  81 LDVRVLVDWHRAQRGRIGAAASNTNADWYCRMANENPGVDIPVYGVPINTREALGVLHFKGFIIDDCVLYSGASLNDVYL 160
Cdd:PRK09428  81 LDIKVLVDWHRAQRGLIGAAASNTNADWYCEMAQEYPGVDIPVYGVPVNTREALGVLHLKGFIIDDTVLYSGASLNNVYL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132 161 HQHDKYRYDRYQCIRNGKMADIMFDWVDNNLVQGRGVNRLDRPDRPKSPEIKNDIRQYRQELRDRSYHFVGTAGDEELSV 240
Cdd:PRK09428 161 HQHDKYRYDRYHLIRNAELADSMVNFIQQNLLNSPAVNRLDQPNRPKTKEIKNDIRQFRQRLRDAAYQFQGQANNDELSV 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132 241 TPLVGLGKSSLLNKTIFHLMPCAEHKLTICTPYFNLPAVLVRNIIQLLRDGKQVEIIVGDKTANDFYIPEDQPFKIIGAL 320
Cdd:PRK09428 241 TPLVGLGKKNLLNKTIFHLMASAEQKLTICTPYFNLPAILVRNIIRLLRRGKKVEIIVGDKTANDFYIPPDEPFKIIGAL 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132 321 PYLYEINLRRFLSRLQYYVNTDQLIVRLWKDDDNSYHLKGMWVDDEWMLLTGNNLNPRAWRLDLENAILIHDPKRQLGAM 400
Cdd:PRK09428 321 PYLYEINLRRFAKRLQYYIDNGQLNVRLWKDGDNSYHLKGIWVDDRWMLLTGNNLNPRAWRLDLENALLIHDPKQELAEQ 400

                        410       420       430
                 ....*....|....*....|....*....|.
gi 490285132 401 REKELKLIRTHTTVVKHYRDLQSIADYPVKV 431
Cdd:PRK09428 401 REKELELIRTHTTRVKHYSQLESIADYPVKV 431
PLDc_PSS_G_neg_2 cd09136
Catalytic domain, repeat 2, of phosphatidylserine synthases from gram-negative bacteria; ...
 238-431 5.65e-123

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: 356.53  E-value: 5.65e-123
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132 238 LSVTPLVGLGKS-SLLNKTIFHLMPCAEHKLTICTPYFNLPAVLVRNIIQLLRDGKQVEIIVGDKTANDFYIPEDQPFKI 316
Cdd:cd09136    1 LSITPLVGLGKRgNQLNRTIRQLIQSAESELIICTPYFNLPRSLVRDIARLLKRGVKVEIIVGDKTANDFYIPPEEPFKT 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132 317 IGALPYLYEINLRRFLSRLQYYVNTDQLIVRLWKDDDNSYHLKGMWVDDEWMLLTGNNLNPRAWRLDLENAILIHDPKRQ 396
Cdd:cd09136   81 IGALPYLYEINLRRFAKRLQKYIDNGQLNVRLWKDGNNSFHLKGIWVDDRYHLLTGNNLNPRAWRLDLENGLLIHDPQGQ 160

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 490285132 397 LGAMREKELKLIRTHTTVVKHYRDLQSIADYPVKV 431
Cdd:cd09136  161 LKAQFEKELEQILAHTTRIKHYSQLESIADYPEKV 195
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 9-406 3.28e-57

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: 192.85  E-value: 3.28e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132   9 KHQQHLAQLPKlsQSVDDVEFFYAPAEFREALLTRIAHATQRICIIALYLEQDDGGKGILQALYDAKRqrPELDVRVLVD 88
Cdd:COG1502    1 KAAPLAAGLPL--VGGNRVTLLVDGDEAFAALLEAIEAARRSIDLEYYIFDDDEVGRRLADALIAAAR--RGVKVRVLLD 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132  89 WhraqrgrIGAAAsnTNADWYCRManENPGVDIPVYG-VPINTREALGVLHFKGFIIDDCVLY-SGASLNDVYLHQHDKY 166
Cdd:COG1502   77 G-------IGSRA--LNRDFLRRL--RAAGVEVRLFNpVRLLFRRLNGRNHRKIVVIDGRVAFvGGANITDEYLGRDPGF 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132 167 RYDRyqcirngkmaDIMFdwvdnnLVQGRGVNRLDRpdrpkspeiknDIRQYRQELRDRSYHFVGTAGDEELSVTPLVGL 246
Cdd:COG1502  146 GPWR----------DTHV------RIEGPAVADLQA-----------VFAEDWNFATGEALPFPEPAGDVRVQVVPSGPD 198

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132 247 GKSSLLNKTIFHLMPCAEHKLTICTPYFNLPAVLVRNIIQLLRDGKQVEIIVGDKTandfyipeDQPFKIIGALPYLYEI 326
Cdd:COG1502  199 SPRETIERALLAAIASARRRIYIETPYFVPDRSLLRALIAAARRGVDVRILLPAKS--------DHPLVHWASRSYYEEL 270

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132 327 NLRRflsrlqyyvntdqliVRLWKDDDNSYHLKGMWVDDEWMLLTGNNLNPRAWRLDLENAILIHDPK--RQLGAMREKE 404
Cdd:COG1502  271 LEAG---------------VRIYEYEPGFLHAKVMVVDDEWALVGSANLDPRSLRLNFEVNLVIYDPEfaAQLRARFEED 335


                 ..
gi 490285132 405 LK 406
Cdd:COG1502  336 LA 337
PLDc_2 pfam13091
PLD-like domain;
256-394 6.42e-21

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 88.12  E-value: 6.42e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132  256 IFHLMPCAEHKLTICTPYFNLPAVLVRNIIQLLRDGKQVEIIVGDKTAnDFYIPEDQPFKIIGALpYLYEINLRRFLSRL 335
Cdd:pfam13091   1 LIDLINSAKKSIDIATYYFVPDREIIDALIAAAKRGVDVRIILDSNKD-DAGGPKKASLKELRSL-LRAGVEIREYQSFL 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 490285132  336 qyyvntdqlivrlwkdddNSYHLKGMWVDDEWMLLTGNNLNPRAWRLDLENAILIHDPK 394
Cdd:pfam13091  79 ------------------RSMHAKFYIIDGKTVIVGSANLTRRALRLNLENNVVIKDPE 119
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
 353-379 1.26e-04

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: 38.91  E-value: 1.26e-04
                           10        20
                   ....*....|....*....|....*..
gi 490285132   353 DNSYHLKGMWVDDEWMLLTGNNLNPRA 379
Cdd:smart00155   2 DGVLHTKLMIVDDEIAYIGSANLDGRS 28
 
Name Accession Description Interval E-value
pssA PRK09428
CDP-diacylglycerol--serine O-phosphatidyltransferase;
1-431 0e+00

CDP-diacylglycerol--serine O-phosphatidyltransferase;


Pssm-ID: 236510 [Multi-domain]  Cd Length: 451  Bit Score: 859.88  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132   1 MLSKFKRNKHQQHLAQLPKLSQSVDDVEFFYAPAEFREALLTRIAHATQRICIIALYLEQDDGGKGILQALYDAKRQRPE 80
Cdd:PRK09428   1 MLSKFKRNKHQQHLAQLPKIPQSPDDVETLYSPADFRETLLEKIASAKKRIYIVALYLEDDEAGREILDALYQAKQQNPE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132  81 LDVRVLVDWHRAQRGRIGAAASNTNADWYCRMANENPGVDIPVYGVPINTREALGVLHFKGFIIDDCVLYSGASLNDVYL 160
Cdd:PRK09428  81 LDIKVLVDWHRAQRGLIGAAASNTNADWYCEMAQEYPGVDIPVYGVPVNTREALGVLHLKGFIIDDTVLYSGASLNNVYL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132 161 HQHDKYRYDRYQCIRNGKMADIMFDWVDNNLVQGRGVNRLDRPDRPKSPEIKNDIRQYRQELRDRSYHFVGTAGDEELSV 240
Cdd:PRK09428 161 HQHDKYRYDRYHLIRNAELADSMVNFIQQNLLNSPAVNRLDQPNRPKTKEIKNDIRQFRQRLRDAAYQFQGQANNDELSV 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132 241 TPLVGLGKSSLLNKTIFHLMPCAEHKLTICTPYFNLPAVLVRNIIQLLRDGKQVEIIVGDKTANDFYIPEDQPFKIIGAL 320
Cdd:PRK09428 241 TPLVGLGKKNLLNKTIFHLMASAEQKLTICTPYFNLPAILVRNIIRLLRRGKKVEIIVGDKTANDFYIPPDEPFKIIGAL 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132 321 PYLYEINLRRFLSRLQYYVNTDQLIVRLWKDDDNSYHLKGMWVDDEWMLLTGNNLNPRAWRLDLENAILIHDPKRQLGAM 400
Cdd:PRK09428 321 PYLYEINLRRFAKRLQYYIDNGQLNVRLWKDGDNSYHLKGIWVDDRWMLLTGNNLNPRAWRLDLENALLIHDPKQELAEQ 400

                        410       420       430
                 ....*....|....*....|....*....|.
gi 490285132 401 REKELKLIRTHTTVVKHYRDLQSIADYPVKV 431
Cdd:PRK09428 401 REKELELIRTHTTRVKHYSQLESIADYPVKV 431
PLDc_PSS_G_neg_2 cd09136
Catalytic domain, repeat 2, of phosphatidylserine synthases from gram-negative bacteria; ...
 238-431 5.65e-123

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: 356.53  E-value: 5.65e-123
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132 238 LSVTPLVGLGKS-SLLNKTIFHLMPCAEHKLTICTPYFNLPAVLVRNIIQLLRDGKQVEIIVGDKTANDFYIPEDQPFKI 316
Cdd:cd09136    1 LSITPLVGLGKRgNQLNRTIRQLIQSAESELIICTPYFNLPRSLVRDIARLLKRGVKVEIIVGDKTANDFYIPPEEPFKT 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132 317 IGALPYLYEINLRRFLSRLQYYVNTDQLIVRLWKDDDNSYHLKGMWVDDEWMLLTGNNLNPRAWRLDLENAILIHDPKRQ 396
Cdd:cd09136   81 IGALPYLYEINLRRFAKRLQKYIDNGQLNVRLWKDGNNSFHLKGIWVDDRYHLLTGNNLNPRAWRLDLENGLLIHDPQGQ 160

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 490285132 397 LGAMREKELKLIRTHTTVVKHYRDLQSIADYPVKV 431
Cdd:cd09136  161 LKAQFEKELEQILAHTTRIKHYSQLESIADYPEKV 195
PLDc_CDP-OH_P_transf_II_2 cd09103
Catalytic domain, repeat 2, of CDP-alcohol phosphatidyltransferase class-II family members; ...
 238-420 3.83e-113

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: 330.34  E-value: 3.83e-113
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132 238 LSVTPLVGLGKS-SLLNKTIFHLMPCAEHKLTICTPYFNLPAVLVRNIIQLLRDGKQVEIIVGDKTANDFYIPEDQPFKI 316
Cdd:cd09103    1 LSITPLVGLGKRgNILNRTIEQLITSAESKIILCTPYFNLPQALMRDILRLLKRGVKVEIIVGDKTANDFYIPPEEPFKV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132 317 IGALPYLYEINLRRFLSRLQYYVNTDQLIVRLWKDDDNSYHLKGMWVDDEWMLLTGNNLNPRAWRLDLENAILIHDPKRQ 396
Cdd:cd09103   81 IGALPYLYEINLRRFAKRLQKYIDQGQLNVRLWKDGDNSFHLKGIWVDDRYTLLTGNNLNPRAWRLDLENGLLIHDPQKQ 160

                        170       180
                 ....*....|....*....|....
gi 490285132 397 LGAMREKELKLIRTHTTVVKHYRD 420
Cdd:cd09103  161 LQQQLEKELEQILLHTTRISHYTQ 184
PLDc_PSS_G_neg_1 cd09134
Catalytic domain, repeat 1, of phosphatidylserine synthases from gram-negative bacteria; ...
 17-190 5.19e-101

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: 298.78  E-value: 5.19e-101
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132  17 LPKLSQSVDDVEFFYAPAEFREALLTRIAHATQRICIIALYLEQDDGGKGILQALYDAKRQRPELDVRVLVDWHRAQRGR 96
Cdd:cd09134    1 LPKIPQQPEDIDVLYSPKDFRARLLELISNAKKRIYIVALYLEDDEAGREILDALYEAKANNPGLDIKVLVDWHRAQRGL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132  97 IGAAASNTNADWYCRMANENPgVDIPVYGVPINTREALGVLHFKGFIIDDCVLYSGASLNDVYLHQHDKYRYDRYQCIRN 176
Cdd:cd09134   81 IGAKKSLGNADWYRKIAQRYG-HDVPIYGVPVKTRELFGVLHLKGFIIDDTVLYSGASLNNVYLHQFDKYRYDRYHLIYN 159

                        170
                 ....*....|....
gi 490285132 177 GKMADIMFDWVDNN 190
Cdd:cd09134  160 PELADSMVNFIQDY 173
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 9-406 3.28e-57

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: 192.85  E-value: 3.28e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132   9 KHQQHLAQLPKlsQSVDDVEFFYAPAEFREALLTRIAHATQRICIIALYLEQDDGGKGILQALYDAKRqrPELDVRVLVD 88
Cdd:COG1502    1 KAAPLAAGLPL--VGGNRVTLLVDGDEAFAALLEAIEAARRSIDLEYYIFDDDEVGRRLADALIAAAR--RGVKVRVLLD 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132  89 WhraqrgrIGAAAsnTNADWYCRManENPGVDIPVYG-VPINTREALGVLHFKGFIIDDCVLY-SGASLNDVYLHQHDKY 166
Cdd:COG1502   77 G-------IGSRA--LNRDFLRRL--RAAGVEVRLFNpVRLLFRRLNGRNHRKIVVIDGRVAFvGGANITDEYLGRDPGF 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132 167 RYDRyqcirngkmaDIMFdwvdnnLVQGRGVNRLDRpdrpkspeiknDIRQYRQELRDRSYHFVGTAGDEELSVTPLVGL 246
Cdd:COG1502  146 GPWR----------DTHV------RIEGPAVADLQA-----------VFAEDWNFATGEALPFPEPAGDVRVQVVPSGPD 198

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132 247 GKSSLLNKTIFHLMPCAEHKLTICTPYFNLPAVLVRNIIQLLRDGKQVEIIVGDKTandfyipeDQPFKIIGALPYLYEI 326
Cdd:COG1502  199 SPRETIERALLAAIASARRRIYIETPYFVPDRSLLRALIAAARRGVDVRILLPAKS--------DHPLVHWASRSYYEEL 270

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132 327 NLRRflsrlqyyvntdqliVRLWKDDDNSYHLKGMWVDDEWMLLTGNNLNPRAWRLDLENAILIHDPK--RQLGAMREKE 404
Cdd:COG1502  271 LEAG---------------VRIYEYEPGFLHAKVMVVDDEWALVGSANLDPRSLRLNFEVNLVIYDPEfaAQLRARFEED 335


                 ..
gi 490285132 405 LK 406
Cdd:COG1502  336 LA 337
PLDc_CDP-OH_P_transf_II_1 cd09102
Catalytic domain, repeat 1, of CDP-alcohol phosphatidyltransferase class-II family members; ...
 27-188 1.88e-41

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: 145.04  E-value: 1.88e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132  27 VEFFYAPAEFREALLTRIAHATQRICIIALYLEQDDGGKGILQALYDAKRQRPELDVRVLVDWHRAQRGRIGAAA-SNTN 105
Cdd:cd09102    2 IRFLGSPAEFKTQIIELIRNAKRRVYVASLYWGKDEAGQEILDEIYSVKQENPNLDVSVLIDWHRAQRNLLGSETkSATN 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132 106 ADWYCRMAN----ENPGVDIPV-YGVPINTREALGVLHFKGFIIDDCVLYSGASLNDVYLHqhdkYRYDRYQCIRNG-KM 179
Cdd:cd09102   82 ADWYCEQRQtsqlHLLPDDGN*fFGVPINTNEVFGVLHVKGYVFDDTVLLSGANLSNVYFH----YRYDRYVKITHGaEL 157


                 ....*....
gi 490285132 180 ADIMFDWVD 188
Cdd:cd09102  158 ADS*VNLIN 166
PLDc_PGS1_euk_1 cd09135
Catalytic domain, repeat 1, of eukaryotic PhosphatidylGlycerophosphate Synthases; Catalytic ...
 26-188 8.92e-22

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: 91.84  E-value: 8.92e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132  26 DVEFFYAPAEFREALLTRIAHATQRICIIALYLeqddgGKGIL-----QALYDAKRQRPELDVRVLVDWHRAQRGRIGAA 100
Cdd:cd09135    1 QIRILRTPSEFYNTLLDKIRNAKRRIVLSSLYI-----GTGPLeqelvDALQEALERNPNLKVSILLDYLRGTRGEPNSR 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132 101 ASNTNAdwycRMANE-NPGVDIPVYGVPiNTR------------EALGVLHFKGFIIDDCVLYSGASLNDVYLHQhdkyR 167
Cdd:cd09135   76 TASLLL----PLLKLfPDRVRVSLYHTP-NLRgllkkllperfnEIIGLQHMKLYIFDDDVILSGANLSDDYFTN----R 146

                        170       180
                 ....*....|....*....|..
gi 490285132 168 YDRYQCIRNGK-MADIMFDWVD 188
Cdd:cd09135  147 QDRYMLIENCPeLADFYHDLIK 168
PLDc_2 pfam13091
PLD-like domain;
256-394 6.42e-21

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 88.12  E-value: 6.42e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132  256 IFHLMPCAEHKLTICTPYFNLPAVLVRNIIQLLRDGKQVEIIVGDKTAnDFYIPEDQPFKIIGALpYLYEINLRRFLSRL 335
Cdd:pfam13091   1 LIDLINSAKKSIDIATYYFVPDREIIDALIAAAKRGVDVRIILDSNKD-DAGGPKKASLKELRSL-LRAGVEIREYQSFL 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 490285132  336 qyyvntdqlivrlwkdddNSYHLKGMWVDDEWMLLTGNNLNPRAWRLDLENAILIHDPK 394
Cdd:pfam13091  79 ------------------RSMHAKFYIIDGKTVIVGSANLTRRALRLNLENNVVIKDPE 119
PLDc_PGS1_euk_2 cd09137
Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases; Catalytic ...
 264-415 1.36e-16

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: 77.62  E-value: 1.36e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132 264 EHKLTICTPYFNLPavlvRNIIQLLRDGK-QVEIIVGDKTANDFYipedqPFKII-GALPYLYEINLRRFLSRLQYYVNT 341
Cdd:cd09137   31 GSSLTLASGYFNLT----PEYLNLLLNSSaNLDVLTASPEANGFY-----GSKGVsGYIPPAYTYIARQFLKRVRKNGKQ 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132 342 DQLIVRLWKDDDNSYHLKGMWV---DDEWMLLT--GN-NLNPRAWRLDLENAILI--HDP--KRQLgamrEKELKLIRTH 411
Cdd:cd09137  102 PRIKLFEYKRPGWTFHAKGLWIylpGTDLPSLTliGSsNYGYRSVHRDLEAQFLIvtNNPklQQQL----KEELENLFEY 177


                 ....
gi 490285132 412 TTVV 415
Cdd:cd09137  178 SKPV 181
PLDc_SF cd00138
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ...
 258-390 2.65e-10

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: 57.53  E-value: 2.65e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132 258 HLMPCAEHKLTICTPYFNLPAV--LVRNIIQLLRDGKQVEIIVGDKTANDFYIPEDQPFKIIGALpylyeINLRRFLSRL 335
Cdd:cd00138    5 ELLKNAKESIFIATPNFSFNSAdrLLKALLAAAERGVDVRLIIDKPPNAAGSLSAALLEALLRAG-----VNVRSYVTPP 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 490285132 336 QYyvntdqlivrlwkddDNSYHLKGMWVDDEWMLLTGNNLNPRAWRLDLENAILI 390
Cdd:cd00138   80 HF---------------FERLHAKVVVIDGEVAYVGSANLSTASAAQNREAGVLV 119
PLDc_CLS_unchar1_2 cd09162
Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial ...
 250-394 9.97e-07

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: 48.80  E-value: 9.97e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132 250 SLLNKTIFHlmpcAEHKLTICTPYFNLPAVLVRNIIQLLRDGKQVEIIVgdktandfyiPEDQPFKIIgalpylyeiNLR 329
Cdd:cd09162   14 EALLSAIFE----AEHRIWIVTPYFVPDEVLLRALRLAARRGVDVRLIV----------PKRSNHRIA---------DLA 70

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490285132 330 R--FLSRLQYyvntdqLIVRLWKDDDNSYHLKGMWVDDEWMLLTGNNLNPRAWRLDLENAILIHDPK 394
Cdd:cd09162   71 RgsYLRDLQE------AGAEIYLYQPGMLHAKAVVVDDKLALVGSANLDMRSLFLNYEVAVFFYSPA 131
PLDc_PaCLS_like_2 cd09161
Putative catalytic domain, repeat 2, of Pseudomonas aeruginosa cardiolipin synthase and ...
 255-406 5.70e-06

Putative catalytic domain, repeat 2, of Pseudomonas aeruginosa cardiolipin synthase and similar proteins; Putative catalytic domain, repeat 2, of Pseudomonas aeruginosa cardiolipin (CL) synthase (PaCLS) and similar proteins. Although PaCLS and similar proteins have not been functionally characterized, members in 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, PaCLS and other 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: 197258 [Multi-domain]  Cd Length: 176  Bit Score: 46.51  E-value: 5.70e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132 255 TIFHLMPCAEHKLTICTPYFnLPAVLVRNIIQL--LRdGKQVEIIVGDKTandfyipeDQPfkiigaLPYLyeinlrrfl 332
Cdd:cd09161   15 FFVQAINAAQKRLWIASPYF-VPDEGVLAALQLaaLR-GVDVRILIPERP--------DHL------LVYL--------- 69

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490285132 333 SRLQYYVNTDQLIVRLWKDDDNSYHLKGMWVDDEWMLLTGNNLNPRAWRLDLENAILIHDPK--RQLGAMREKELK 406
Cdd:cd09161   70 ASFSYLPELIRAGVKVYRYQPGFLHQKVVLVDDELAAVGTANLDNRSFRLNFEITALVADPGfaQEVEAMLEADFA 145
PLDc_SF cd00138
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ...
 38-162 1.26e-05

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: 44.43  E-value: 1.26e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132  38 EALLTRIAHATQRICIIALYLEQDDGGKgILQALYDAKRQrpELDVRVLVDWHRAQRGRIGAA--ASNTNADWYCRMANe 115
Cdd:cd00138    1 EALLELLKNAKESIFIATPNFSFNSADR-LLKALLAAAER--GVDVRLIIDKPPNAAGSLSAAllEALLRAGVNVRSYV- 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 490285132 116 npgvdipvygvpiNTREALGVLHFKGFIIDDCVLY-SGASLNDVYLHQ 162
Cdd:cd00138   77 -------------TPPHFFERLHAKVVVIDGEVAYvGSANLSTASAAQ 111
PLDc pfam00614
Phospholipase D Active site motif; Phosphatidylcholine-hydrolysing phospholipase D (PLD) ...
 353-379 1.59e-05

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: 41.64  E-value: 1.59e-05
                          10        20
                  ....*....|....*....|....*..
gi 490285132  353 DNSYHLKGMWVDDEWMLLTGNNLNPRA 379
Cdd:pfam00614   2 DGRLHRKIVVVDDELAYIGGANLDGRS 28
PLDc_CLS_unchar2_2 cd09163
Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial ...
 262-400 3.29e-05

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: 197260 [Multi-domain]  Cd Length: 176  Bit Score: 44.47  E-value: 3.29e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132 262 CAEHKLTICTPYFNLPAVLVRNIIQLLRDGKQVEIIVGDKtaNDfyipedqpfkiigaLPYLyeinlrRFLSRLQYyvnt 341
Cdd:cd09163   22 AARHSIRIMTPYFLPDRTLITALQAAALRGVEVDIVLPER--NN--------------LPLV------DWAMRANL---- 75

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490285132 342 DQLI---VRLWKDDDNSYHLKGMWVDDEWMLLTGNNLNPRAWRLDLENAILIHDPK--RQLGAM 400
Cdd:cd09163   76 WELLehgVRIYLQPPPFDHSKLMVVDGAWALIGSANWDPRSLRLNFELNLEVYDTAlaGQLDAL 139
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
 353-379 1.26e-04

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: 38.91  E-value: 1.26e-04
                           10        20
                   ....*....|....*....|....*..
gi 490285132   353 DNSYHLKGMWVDDEWMLLTGNNLNPRA 379
Cdd:smart00155   2 DGVLHTKLMIVDDEIAYIGSANLDGRS 28
PLDc_2 pfam13091
PLD-like domain;
40-156 5.39e-04

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 39.97  E-value: 5.39e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132   40 LLTRIAHATQRICIIALYLEQDdggKGILQALYDAKRqRPeLDVRVLVDWHRAQRGrigaAASNTNADWYCRMANEnpGV 119
Cdd:pfam13091   1 LIDLINSAKKSIDIATYYFVPD---REIIDALIAAAK-RG-VDVRIILDSNKDDAG----GPKKASLKELRSLLRA--GV 69

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 490285132  120 DIPVYGVpintreALGVLHFKGFIIDDCVLYSGaSLN 156
Cdd:pfam13091  70 EIREYQS------FLRSMHAKFYIIDGKTVIVG-SAN 99
PLDc_CLS_2 cd09112
catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; This CD ...
 250-406 9.15e-04

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


Pssm-ID: 197211 [Multi-domain]  Cd Length: 174  Bit Score: 40.15  E-value: 9.15e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132 250 SLLNKTIFHLMPCAEHKLTICTPYFNLPAVLVRNIIQLLRDGKQVEIIVGDKTandfyipeDQPFKIIGALPYLyeinlr 329
Cdd:cd09112   10 SSIEQAYLKAINSAKKSIYIQTPYFIPDESLLEALKTAALSGVDVRIMIPGKP--------DHKLVYWASRSYF------ 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132 330 rflsrlqyyvntDQLI---VRLWKDDDNSYHLKGMWVDDEWMLLTGNNLNPRAWRLDLENAILIHDPK--RQLGAMREKE 404
Cdd:cd09112   76 ------------EELLkagVKIYEYNKGFLHSKTLIVDDEIASVGTANLDIRSFELNFEVNAVIYDKEvaKKLEEIFEED 143


                 ..
gi 490285132 405 LK 406
Cdd:cd09112  144 LK 145
PLDc_Nuc cd09170
Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar ...
 37-156 3.94e-03

Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar proteins; Catalytic domain of an EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar proteins. Nuc is an endonuclease cleaving both single- and double-stranded DNA. It is the smallest known member of the phospholipase D (PLD, EC 3.1.4.4) superfamily that includes a diverse group of proteins with various catalytic functions. Most members of this superfamily have two copies of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) in a single polypeptide chain and both are required for catalytic activity. However, Nuc only has one copy of the HKD motif per subunit but form a functionally active homodimer (it is most likely also active in solution as a multimeric protein), which has a single active site at the dimer interface containing the HKD motifs from both subunits. Due to the lack of a distinct domain for DNA binding, Nuc cuts DNA non-specifically. It utilizes 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.


Pssm-ID: 197267 [Multi-domain]  Cd Length: 142  Bit Score: 37.50  E-value: 3.94e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490285132  37 REALLTRIAHATQRICIIALYLEQDDggkgILQALYDAKRQrpELDVRVLVDwhRAQRGRIGAAASntnadwycRMANEn 116
Cdd:cd09170   13 RELILDVIDSARRSIDVAAYSFTSPP----IARALIAAKKR--GVDVRVVLD--KSQAGGKYSALN--------YLANA- 75

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 490285132 117 pgvdipvyGVPINTREALGVLHFKGFIIDDCVLYSGaSLN 156
Cdd:cd09170   76 --------GIPVRIDDNYAIMHNKVMVIDGKTVITG-SFN 106
PLDc_vPLD1_2_like_2 cd09105
Catalytic domain, repeat 2, of vertebrate phospholipases, PLD1 and PLD2, and similar proteins; ...
 357-392 7.29e-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: 36.89  E-value: 7.29e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 490285132 357 HLKGMWVDDEWMLLTGNNLNPRAWRLDLENAILIHD 392
Cdd:cd09105  111 HSKVVIVDDEWATVGSANLNRRSMTWDTELNLAVVD 146
 
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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