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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 660560972  29 SIETGYSPEGTALQLVLKTIDSAQQEIRLMGYSFTSPEVAGALVRAKRRGVDVKVVLDWKANTGKQnqaslAAMNLLVNT 108
Cdd:cd09170    1 TVEVYFSPEGGARELILDVIDSARRSIDVAAYSFTSPPIARALIAAKKRGVDVRVVLDKSQAGGKY-----SALNYLANA 75

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 660560972 109 GIPVRTVSQYKIMHDKVIIADGRNVEVGSFNFTRSADRGNSENVLVVWDDPVVAQRYLQHWQTRWE 174
Cdd:cd09170   76 GIPVRIDDNYAIMHNKVMVIDGKTVITGSFNFTASAEKRNAENLLVIRNPPELAQQYLQEWQRRWA 141

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 660560972  29 SIETGYSPEGTALQLVLKTIDSAQQEIRLMGYSFTSPEVAGALVRAKRRGVDVKVVLDWKANTGKQnqaslAAMNLLVNT 108
Cdd:cd09170    1 TVEVYFSPEGGARELILDVIDSARRSIDVAAYSFTSPPIARALIAAKKRGVDVRVVLDKSQAGGKY-----SALNYLANA 75

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 660560972 109 GIPVRTVSQYKIMHDKVIIADGRNVEVGSFNFTRSADRGNSENVLVVWDDPVVAQRYLQHWQTRWE 174
Cdd:cd09170   76 GIPVRIDDNYAIMHNKVMVIDGKTVITGSFNFTASAEKRNAENLLVIRNPPELAQQYLQEWQRRWA 141

Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and metabolism]; Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase is part of the Pathway/BioSystem: Phospholipid biosynthesis

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 660560972  35 SPEGTALQLVLKTIDSAQQEIRLMGYSFT-SPEVAGALVRAKRRGVDVKVVLDWKANTGKQNQASLAAMNLLVNTGIPVR 113
Cdd:COG1502  199 SPRETIERALLAAIASARRRIYIETPYFVpDRSLLRALIAAARRGVDVRILLPAKSDHPLVHWASRSYYEELLEAGVRIY 278

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 660560972 114 tvsQYK--IMHDKVIIADGRNVEVGSFNFTRSADRGNSENVLVVwDDPVVAQRYLQHWQTRWE 174
Cdd:COG1502  279 ---EYEpgFLHAKVMVVDDEWALVGSANLDPRSLRLNFEVNLVI-YDPEFAAQLRARFEEDLA 337

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.

                           10        20
                   ....*....|....*....|....*
gi 660560972   120 IMHDKVIIADGRNVEVGSFNFTRSA 144
Cdd:smart00155   4 VLHTKLMIVDDEIAYIGSANLDGRS 28

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 660560972  29 SIETGYSPEGTALQLVLKTIDSAQQEIRLMGYSFTSPEVAGALVRAKRRGVDVKVVLDWKANTGKQnqaslAAMNLLVNT 108
Cdd:cd09170    1 TVEVYFSPEGGARELILDVIDSARRSIDVAAYSFTSPPIARALIAAKKRGVDVRVVLDKSQAGGKY-----SALNYLANA 75

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 660560972 109 GIPVRTVSQYKIMHDKVIIADGRNVEVGSFNFTRSADRGNSENVLVVWDDPVVAQRYLQHWQTRWE 174
Cdd:cd09170   76 GIPVRIDDNYAIMHNKVMVIDGKTVITGSFNFTASAEKRNAENLLVIRNPPELAQQYLQEWQRRWA 141

PLD-like domain;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 660560972   44 VLKTIDSAQQEIRL-MGYSFTSPEVAGALVRAKRRGVDVKVVLD-WKANTGKQNQASLAAMNLLVNTGIPVR-TVSQYKI 120
Cdd:pfam13091   1 LIDLINSAKKSIDIaTYYFVPDREIIDALIAAAKRGVDVRIILDsNKDDAGGPKKASLKELRSLLRAGVEIReYQSFLRS 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 660560972  121 MHDKVIIADGRNVEVGSFNFTRSADRGNSENvLVVWDDPVVAQRYLQHWQTRW 173
Cdd:pfam13091  81 MHAKFYIIDGKTVIVGSANLTRRALRLNLEN-NVVIKDPELAQELEKEFDRLW 132

Putative catalytic domain, repeat 1, of uncharacterized hypothetical proteins similar to Nuc, an endonuclease from Salmonella typhimurium; Putative catalytic domain, repeat 1, of uncharacterized hypothetical proteins, which show high sequence homology to the endonuclease from Salmonella typhimurium and vertebrate phospholipase D6. 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 characterizes the PLD superfamily and is essential for catalysis. Nuc and PLD6 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. However, proteins in this subfamily have two HKD motifs in a single polypeptide chain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 660560972  40 ALQLVLKTIDSAQQEIRLMGYSFTSPEVAGALVRAKRRGVDVKVVLDWKANTGKQNQASLAAMNLLVNTGIPVRTVSQyK 119
Cdd:cd09172   10 ALLAFLDEARSAGSSIRLAIYELDDPEIIDALKAAKDRGVRVRIILDDSSVTGDPTEESAAATLSKGPGALVKRRHSS-G 88

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 660560972 120 IMHDKVIIADGRNVEV----GSFNFTRSADRGNSENVLVVwDDPVVAQRYLQHWQT 171
Cdd:cd09172   89 LMHNKFLVVDRKDGPNrvltGSTNFTTSGLYGQSNNVLIF-RNPAFAAAYLAYWNT 143

Putative catalytic domain, repeat 1, of uncharacterized phospholipase D-like proteins; Putative catalytic domain, repeat 1, 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 660560972  42 QLVLKTIDSAQQEIRLMGYSFTSPEVAGALVRAKRRGVDVKVVLDwKANTGKQNQASlAAMNLLVNTGIPVRTVS---QY 118
Cdd:cd09127   11 APVVDAIASAKRSILLKMYEFTDPALEKALAAAAKRGVRVRVLLE-GGPVGGISRAE-KLLDYLNEAGVEVRWTNgtaRY 88

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 660560972 119 KIMHDKVIIADGRNVEVGSFNFTRSADRGNSENVLVVWDDPVVAQ 163
Cdd:cd09127   89 RYTHAKYIVVDDERALVLTENFKPSGFTGTRGFGVVTDDPAVVAE 133

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 660560972  35 SPeGTALQLVLKTIDSAQQEIRLMGYSFTS-PEVAGALVRAKRRGVDVKVVLDWKANTGKQNQASLAAMNllvNTGIPVR 113
Cdd:cd09128    7 SP-DNAREALLALIDSAEESLLIQNEEMGDdAPILDALVDAAKRGVDVRVLLPSAWSAEDERQARLRALE---GAGVPVR 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 660560972 114 TVSQYKI-MHDKVIIADGRNVEVGSFNFTRSADRGNSENVLVVWDDPVVAqrYLQHW 169
Cdd:cd09128   83 LLKDKFLkIHAKGIVVDGKTALVGSENWSANSLDRNREVGLIFDDPEVAA--YLQAV 137

nuclease NucT; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 660560972  40 ALQLVLKTIDSAQQEIRLMGYSFTSPEVAGALVRAKRRGVDVKVVLDWKANTgKQNQASLAAMNLLVNT------GIPVR 113
Cdd:PRK13912  34 ALNKLVSLISNARSSIKIAIYSFTHKDIAKALKSAAKRGVKISIIYDYESNH-NNDQSTIGYLDKYPNIkvcllkGLKAK 112

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 660560972 114 TVSQYKIMHDKVIIADGRNVEVGSFNFTRSADRGNSENVLVVwDDPVVAQRYLQHWQ 170
Cdd:PRK13912 113 NGKYYGIMHQKVAIIDDKIVVLGSANWSKNAFENNYEVLLIT-DDTETILKAKEYFQ 168

Putative catalytic domain, repeat 2, of uncharacterized hypothetical proteins similar to Nuc, an endonuclease from Salmonella typhimurium; Putative catalytic domain, repeat 2, of uncharacterized hypothetical proteins, which show high sequence homology to the endonuclease from Salmonella typhimurium and vertebrate phospholipase D6. 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 characterizes the PLD superfamily and is essential for catalysis. Nuc and PLD6 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. However, proteins in this subfamily have two HKD motifs in a single polypeptide chain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 660560972  37 EGTALQLVLKTIDSAQQEIRLMGYSFTSPEVAGALVRAKRRGVDVKVVLDwkANTGKQNQASLAAMNLL-------VNTG 109
Cdd:cd09173    7 GNADLALIAELVAKAKSSVLFALFDFSDGALLDALLAAADAGLFVRGLVD--KRFGGRYYSAAADMGGIdpvypaaLAPD 84

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 660560972 110 IPVRTVSQYK-----IMHDKVIIAD--GRN--VEVGSFNFTRSADRGNSENVLVVwDDPVVAQRYLQHW 169
Cdd:cd09173   85 EPEKFVGEPLlgvgdKLHHKFMVIDpfGDDpvVITGSHNFSGAANDNNDENLLVI-RDPAIADAYAIEF 152

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 660560972  39 TALQLVLKTIDSAQQEIRL-MGYSFTSPEVAGALVRAKRRGVDVKVVLDWKANTGKQNQASLAAMNLLVNTGIPVRtvsQ 117
Cdd:cd09159   11 SIRRAYLVAIAAARRRIWIaNAYFVPDRRLRRALIEAARRGVDVRLLLPGKSDDPLTVAASRALYGKLLRAGVRIF---E 87

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 660560972 118 YK--IMHDKVIIADGRNVEVGSFNF-TRSAdRGNSENVLVVwDDPVVAQRYLQHWQ 170
Cdd:cd09159   88 YQpsMLHAKTAVIDGDWATVGSSNLdPRSL-RLNLEANLVV-EDPAFAAQLEELFE 141

Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Catalytic domain, repeat 1, of bacterial cardiolipin (CL) synthase and a few homologs found in eukaryotes and archaea. Bacterial CL synthases catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. The monomer of bacterial CL synthase 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. 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 belonging to the PLD superfamily. Like other PLD enzymes, bacterial CL synthases 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 660560972  45 LKTIDSAQQEIRLMGYSFTSPEVAG----ALVRAKRRGVDVKVVLDWkANTGKQNQASLAAmnlLVNTGIPVRT---VSQ 117
Cdd:cd09110   11 LEAIRAARHSIHLEYYIFRDDEIGRrfrdALIEKARRGVEVRLLYDG-FGSLGLSRRFLRE---LREAGVEVRAfnpLSF 86

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 660560972 118 YKI-------MHDKVIIADGRNVEVGSFNFTR---SADRGNSEnvlvvWDD-------PVVAQ---RYLQHWQ 170
Cdd:cd09110   87 PLFllrlnyrNHRKILVIDGKIAFVGGFNIGDeylGKDPGFGP-----WRDthvriegPAVADlqaAFLEDWY 154

Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins; Putative catalytic domain, repeat 1, 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 660560972  40 ALQLVLKTIDSAQQEIRLMGYSFTSPE----VAGALVRAKRRGVDVKVVLDwKANTGKQNQAsLAAMNLLVNtgIPVR-- 113
Cdd:cd09111    7 ALAARLALIRSAERSIDLQYYIWHDDEsgrlLLGELLEAADRGVRVRLLLD-DLGTSGRDRL-LAALDAHPN--IEVRlf 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 660560972 114 --TVSQYKI--------------MHDKVIIAD-------GRNV 133
Cdd:cd09111   83 npFRNRGGRllefltdfsrlnrrMHNKLFIVDgavaivgGRNI 125

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 660560972  35 SPEGTALQLVLKTIDSAQQEIRLMGYSFTSPEVAGALVRAKRRGVDVKVVL--------DWKANTGKQNQASLAAMnLLV 106
Cdd:cd09105    4 SGEFEIADAYLKAIRNARRYIYIEDQYLWSPELLDALAEALKANPGLRVVLvlpalpdaVAFGADDGLDALALLAL-LLL 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 660560972 107 NTGIPVR-----------TVSQYKIM--HDKVIIADGRNVEVGSFNFTRSADRGNSENVLVVWD 157
Cdd:cd09105   83 ADAAPDRvavfslathrrGLLGGPPIyvHSKVVIVDDEWATVGSANLNRRSMTWDTELNLAVVD 146

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 660560972  36 PEGTALQLVLKTIDSAQQEIRLMGYSFTSPEV-AGALVRAKRRGVDVKVVLDWKANTGKQNQASLAAMNLLVNTGIPVRT 114
Cdd:cd09162    8 PGDPLYEALLSAIFEAEHRIWIVTPYFVPDEVlLRALRLAARRGVDVRLIVPKRSNHRIADLARGSYLRDLQEAGAEIYL 87

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 660560972 115 VsQYKIMHDKVIIADGRNVEVGSFNF-TRSADRgNSENVLVVWDDPVVAQryLQHW 169
Cdd:cd09162   88 Y-QPGMLHAKAVVVDDKLALVGSANLdMRSLFL-NYEVAVFFYSPADIKE--LSDW 139

Putative catalytic domain, repeat 1, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral envelope proteins K4 and p37, and similar proteins; Putative catalytic domain, repeat 1, of vertebrate phospholipases D, PLD3, PLD4, and PLD5 (EC 3.1.4.4), viral envelope proteins (vaccinia virus proteins K4 and p37), and similar proteins. Most family members contain two copies of the HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue), and have been classified into the phospholipase D (PLD) superfamily. Proteins in this subfamily are associated with Golgi membranes, altering their lipid content by the conversion of phospholipids into phosphatidic acid, which is thought to be involved in the regulation of lipid movement. ADP ribosylation factor (ARF), a small guanosine triphosphate binding protein, might be required activity. The vaccinia virus p37 protein, encoded by the F13L gene, is also associated with Golgi membranes and is required for the envelopment and spread of the extracellular enveloped virus (EEV). The vaccinia virus protein K4, encoded by the HindIII K4L gene, remains to be characterized. Sequence analysis indicates that the vaccinia virus proteins K4 and p37 might have evolved from one or more captured eukaryotic genes involved in cellular lipid metabolism. Up to date, no catalytic activity of PLD3 has been shown. Furthermore, due to the lack of functional important histidine and lysine residues in the HKD motif, mammalian PLD5 has been characterized as an inactive PLD. The poxvirus p37 proteins may also lack PLD enzymatic activity, since they contain only one partially conserved HKD motif (N-x-K-x(4)-D).

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 660560972  70 ALVRAKRRGVDVKVVLDwKANTGKQNQASLAAMNLLvntGIPVRTVSQYK-----IMHDKVIIADGRNVEVGSFNFT-RS 143
Cdd:cd09106   64 ALLEAAKRGVKIRILQD-KPSKDKPDEDDLELAALG---GAEVRSLDFTKligggVLHTKFWIVDGKHFYLGSANLDwRS 139

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 660560972  43 LVLKTIDSAQQEIRLMG-YSFTSPEVAGALVRAKRRGVDVKVVLDWKANTGKQNQASLAAMNLLVNTGIPVRtvsqYKIM 121
Cdd:cd09163   15 TLLGAISAARHSIRIMTpYFLPDRTLITALQAAALRGVEVDIVLPERNNLPLVDWAMRANLWELLEHGVRIY----LQPP 90

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 660560972 122 ---HDKVIIADGRNVEVGSFNF-TRSAdRGNSENVLVVWdDPVVAQRYLQHWQTRWETGK 177
Cdd:cd09163   91 pfdHSKLMVVDGAWALIGSANWdPRSL-RLNFELNLEVY-DTALAGQLDALFDSKIAKSR 148

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 660560972  36 PEGTALQLVLKTIDSAQQEIRLmgysfTSP------EVAGALVRAKRRGVDVKVVLDWKANtgkQNQASLAAMNL---LV 106
Cdd:cd09158    8 PTENIPQLLLSAIHAARRRVVI-----TTPyfvpdeSLLQALCTAALRGVEVTLILPAKND---SFLVGAASRSYyeeLL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 660560972 107 NTGIPVRtvsQYK--IMHDKVIIADGRNVEVGSFNFTRSADRGNSENVLVVWDDPVVAQ------RY--------LQHWQ 170
Cdd:cd09158   80 EAGVKIY---LYRggLLHAKTVTVDDEVALVGSSNFDIRSFALNFEISLILYDKEFTAQlraiqeRYlarsdpltLEEWK 156

                 ...
gi 660560972 171 TRW 173
Cdd:cd09158  157 KRP 159

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 660560972  45 LKTIDSAQQEIRLmgysfTSP------EVAGALVRAKRRGVDVKVVLDWKANTGKQNQASLAAMNLLVNTGIPVrtvSQY 118
Cdd:cd09161   17 VQAINAAQKRLWI-----ASPyfvpdeGVLAALQLAALRGVDVRILIPERPDHLLVYLASFSYLPELIRAGVKV---YRY 88

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 660560972 119 K--IMHDKVIIADGRNVEVGSFNFTRSADRGNSENVLVVWDDPVVAQ 163
Cdd:cd09161   89 QpgFLHQKVVLVDDELAAVGTANLDNRSFRLNFEITALVADPGFAQE 135

Catalytic domain of type II restriction endonucleases BfiI and NgoFVII, and uncharacterized proteins with a DEAD domain; Catalytic domain of type II restriction endonucleases BfiI and NgoFVII, uncharacterized type III restriction endonuclease Res subunit, and uncharacterized DNA/RNA helicase superfamily II members. Proteins in this family are found mainly in prokaryotes. They contain one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) in a single polypeptide chain, and have been classified as members of the phospholipase D (PLD, EC 3.1.4.4) superfamily. BfiI consists of two discrete domains with distinct functions: an N-terminal catalytic domain with non-specific nuclease activity and dimerization function that is more closely related to Nuc, an EDTA-resistant nuclease from the phospholipase D (PLD) superfamily; and a C-terminal domain that specifically recognizes its target sequences, 5'-ACTGGG-3'. BfiI forms a functionally active homodimer which has two DNA-binding surfaces located at the C-terminal domains but only one active site, located at the dimer interface between the two N-terminal catalytic domains that contain the two HKD motifs from both subunits. BfiI utilizes a single active site to cut both DNA strands, which represents a novel mechanism for the scission of double-stranded DNA. It uses a histidine residue from the HKD motif in one subunit as the nucleophile for the cleavage of the target phosphodiester bond in both of the anti-parallel DNA strands, while the symmetrically-related histidine residue from the HKD motif of the opposite subunit acts as the proton donor/acceptor during both strand-scission events.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 660560972  62 FTSPEVAGALVRAKRRGVDVKVVLDwkANTGKQNQASLAAMNLLVNTGIPVRTVSQYKIMHDKVIIADGRNVE---VGSF 138
Cdd:cd09117   23 FASAGGAIKLLDKFREGKKIRLIVG--LDFGGTSPADFALKLLLALGNLNVRIFDAGPLLHAKLYLFENDDPTraiVGSA 100

                         90
                 ....*....|....*..
gi 660560972 139 NFTRSADRGNSENVLVV 155
Cdd:cd09117  101 NLTQGGLSGNIEAAVVI 117

Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial cardiolipin synthase; Putative catalytic domain, repeat 1, 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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 660560972  45 LKTIDSAQQEIRLMGYSFTSPEV----AGALVRAKRRGVDVKVVLD 86
Cdd:cd09157   11 LEAIDAARHSIALSSYIFDNDGVgrefVDALAEAVARGVDVRVLID 56

Putative catalytic domain, repeat 2, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral envelope proteins K4 and p37, and similar proteins; Putative catalytic domain, repeat 2, of vertebrate phospholipases D, PLD3, PLD4, and PLD5 (EC 3.1.4.4), viral envelope proteins (vaccinia virus proteins K4 and p37), and similar proteins. Most family members contain two copies of the HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue), and have been classified into the phospholipase D (PLD) superfamily. Proteins in this subfamily are associated with Golgi membranes, altering their lipid content by the conversion of phospholipids into phosphatidic acid, which is thought to be involved in the regulation of lipid movement. ADP ribosylation factor (ARF), a small guanosine triphosphate binding protein, might be required activity. The vaccinia virus p37 protein, encoded by the F13L gene, is also associated with Golgi membranes and is required for the envelopment and spread of the extracellular enveloped virus (EEV). The vaccinia virus protein K4, encoded by the HindIII K4L gene, remains to be characterized. Sequence analysis indicates that the vaccinia virus proteins K4 and p37 might have evolved from one or more captured eukaryotic genes involved in cellular lipid metabolism. Up to date, no catalytic activity of PLD3 has been shown. Furthermore, due to the lack of functional important histidine and lysine residues in the HKD motif, mammalian PLD5 has been characterized as an inactive PLD. The poxvirus p37 proteins may also lack PLD enzymatic activity, since they contain only one partially conserved HKD motif (N-x-K-x(4)-D).

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 660560972  41 LQLVLKTIDSAQQEIR--LMGYSFTS---------PEVAGALVRA-KRRGVDVKV-VLDWKaNTGKQNQASLA---AMNL 104
Cdd:cd09107   18 LDALLSTIDSAKKFIDisVMDYVPLSryadprkywPVIDNALRRAaVDRGVKVRLlVSNWK-HTDPSMDAFLKslqLLKS 96

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 660560972 105 LVNTG--------IPvRTVSQYK----IMHDKVIIADgRNVEVGSFNFtrSADR-GNSENVLVVWDDPVVAQR 164
Cdd:cd09107   97 GVGNGdievkiftVP-GDQSTKIpfarVNHAKYMVTD-ERAYIGTSNW--SGDYfYNTAGVSLVINDPAIVQQ 165

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.

                           10        20
                   ....*....|....*....|....*
gi 660560972   120 IMHDKVIIADGRNVEVGSFNFTRSA 144
Cdd:smart00155   4 VLHTKLMIVDDEIAYIGSANLDGRS 28