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 1264924588  68 IFQAVTNAIDDAKAFIIMDMFLFNGYYNQGE-TFPHLSDTLASKLIEKKRKHPNIAIVFITDEINTTYGSHDSKWLDSLR 146
Cdd:cd09129     1 IFDEILEIIDEAKDFIVLDMFLFNDYYDKKKgKFPPLSEELTDALIEKKKENPDLPIVVITDPINTFYGSHDNPHLKKLK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1264924588 147 LNGIKVVQTNLSKLRDSIPLYSSVWRTFVQWFGEKGNGWITNPFGTNAPKATVRAYLKLLNVKANHRKVVATDQSVIISS 226
Cdd:cd09129    81 EAGIEVVETDLDKLRDSNPLYSGIWRTFIQWFGNSGKGWLPNPFGKEAPKVTLRSYLRLLNFKANHRKVLVTENTALVTS 160

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1264924588 227 ANPHDASFYNSNMAFEVKGNIIGDVVKSEQAVSDFS 262
Cdd:cd09129   161 ANPHDASARHSNIAFEVSGPIIGDLLKSEQAVARFS 196

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 1264924588  68 IFQAVTNAIDDAKAFIIMDMFLFNGYYNQGE-TFPHLSDTLASKLIEKKRKHPNIAIVFITDEINTTYGSHDSKWLDSLR 146
Cdd:cd09129     1 IFDEILEIIDEAKDFIVLDMFLFNDYYDKKKgKFPPLSEELTDALIEKKKENPDLPIVVITDPINTFYGSHDNPHLKKLK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1264924588 147 LNGIKVVQTNLSKLRDSIPLYSSVWRTFVQWFGEKGNGWITNPFGTNAPKATVRAYLKLLNVKANHRKVVATDQSVIISS 226
Cdd:cd09129    81 EAGIEVVETDLDKLRDSNPLYSGIWRTFIQWFGNSGKGWLPNPFGKEAPKVTLRSYLRLLNFKANHRKVLVTENTALVTS 160

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1264924588 227 ANPHDASFYNSNMAFEVKGNIIGDVVKSEQAVSDFS 262
Cdd:cd09129   161 ANPHDASARHSNIAFEVSGPIIGDLLKSEQAVARFS 196

PLD-like domain;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1264924588 294 VLHDLHHAKKgdDVWLGMFYLG-DRDVIKALLKASKQGANVRLILDPNenafgRKKFGLPNRPVAAELVKKSKGDIKIRW 372
Cdd:pfam13091   1 LIDLINSAKK--SIDIATYYFVpDREIIDALIAAAKRGVDVRIILDSN-----KDDAGGPKKASLKELRSLLRAGVEIRE 73

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1264924588 373 YHTGKEQYHSKTLFIRNKknaTIIAGAANFTKRNLaDLNLETDIKVSGPfnkKVMTELNAYFDRLW 438
Cdd:pfam13091  74 YQSFLRSMHAKFYIIDGK---TVIVGSANLTRRAL-RLNLENNVVIKDP---ELAQELEKEFDRLW 132

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 1264924588 282 VQLLTEGK-IYKHVLHDLHHAKKgdDVWLGMFYLGD----RDVIKALLKASKQGANVRLILDpnenAFGRKKFglpNRPV 356
Cdd:COG1502    17 VTLLVDGDeAFAALLEAIEAARR--SIDLEYYIFDDdevgRRLADALIAAARRGVKVRVLLD----GIGSRAL---NRDF 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1264924588 357 AAELVkksKGDIKIRWYHTGKEQY-------HSKTLFIRNKknaTIIAGAANFTKRNLADL-----NLETDIKVSGPfnk 424
Cdd:COG1502    88 LRRLR---AAGVEVRLFNPVRLLFrrlngrnHRKIVVIDGR---VAFVGGANITDEYLGRDpgfgpWRDTHVRIEGP--- 158

                         170
                  ....*....|....*
gi 1264924588 425 kVMTELNAYFDRLWT 439
Cdd:COG1502   159 -AVADLQAVFAEDWN 172

cardiolipin synthetase; Reviewed

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1264924588 282 VQLLTEGK-IYKHVLHDLHHAKKgddVWLGMFY------LGDRdVIKALLKASKQGANVRLILD 338
Cdd:PRK01642  118 LRLLTNGDeTFQAIIRDIELARH---YILMEFYiwrpdgLGDQ-VAEALIAAAKRGVRVRLLYD 177

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 1264924588  68 IFQAVTNAIDDAKAFIIMDMFLFNGYYNQGE-TFPHLSDTLASKLIEKKRKHPNIAIVFITDEINTTYGSHDSKWLDSLR 146
Cdd:cd09129     1 IFDEILEIIDEAKDFIVLDMFLFNDYYDKKKgKFPPLSEELTDALIEKKKENPDLPIVVITDPINTFYGSHDNPHLKKLK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1264924588 147 LNGIKVVQTNLSKLRDSIPLYSSVWRTFVQWFGEKGNGWITNPFGTNAPKATVRAYLKLLNVKANHRKVVATDQSVIISS 226
Cdd:cd09129    81 EAGIEVVETDLDKLRDSNPLYSGIWRTFIQWFGNSGKGWLPNPFGKEAPKVTLRSYLRLLNFKANHRKVLVTENTALVTS 160

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1264924588 227 ANPHDASFYNSNMAFEVKGNIIGDVVKSEQAVSDFS 262
Cdd:cd09129   161 ANPHDASARHSNIAFEVSGPIIGDLLKSEQAVARFS 196

PLD-like domain;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1264924588 294 VLHDLHHAKKgdDVWLGMFYLG-DRDVIKALLKASKQGANVRLILDPNenafgRKKFGLPNRPVAAELVKKSKGDIKIRW 372
Cdd:pfam13091   1 LIDLINSAKK--SIDIATYYFVpDREIIDALIAAAKRGVDVRIILDSN-----KDDAGGPKKASLKELRSLLRAGVEIRE 73

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1264924588 373 YHTGKEQYHSKTLFIRNKknaTIIAGAANFTKRNLaDLNLETDIKVSGPfnkKVMTELNAYFDRLW 438
Cdd:pfam13091  74 YQSFLRSMHAKFYIIDGK---TVIVGSANLTRRAL-RLNLENNVVIKDP---ELAQELEKEFDRLW 132

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 1264924588 282 VQLLTEGK-IYKHVLHDLHHAKKgdDVWLGMFYLGD----RDVIKALLKASKQGANVRLILDpnenAFGRKKFglpNRPV 356
Cdd:COG1502    17 VTLLVDGDeAFAALLEAIEAARR--SIDLEYYIFDDdevgRRLADALIAAARRGVKVRVLLD----GIGSRAL---NRDF 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1264924588 357 AAELVkksKGDIKIRWYHTGKEQY-------HSKTLFIRNKknaTIIAGAANFTKRNLADL-----NLETDIKVSGPfnk 424
Cdd:COG1502    88 LRRLR---AAGVEVRLFNPVRLLFrrlngrnHRKIVVIDGR---VAFVGGANITDEYLGRDpgfgpWRDTHVRIEGP--- 158

                         170
                  ....*....|....*
gi 1264924588 425 kVMTELNAYFDRLWT 439
Cdd:COG1502   159 -AVADLQAVFAEDWN 172

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1264924588 292 KHVLHDLHHAKKgdDVWLGMFYLG---DRDVIKALLKASKQGANVRLILDPNENAFGrkkfglpnRPVAAELVKKSKGDI 368
Cdd:cd00138     1 EALLELLKNAKE--SIFIATPNFSfnsADRLLKALLAAAERGVDVRLIIDKPPNAAG--------SLSAALLEALLRAGV 70

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1264924588 369 KIRWYHTGK---EQYHSKTLFIrnkKNATIIAGAANFTKRNlADLNLETDIKV 418
Cdd:cd00138    71 NVRSYVTPPhffERLHAKVVVI---DGEVAYVGSANLSTAS-AAQNREAGVLV 119

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 1264924588 312 FYLGDRDVIKALLKASKqGANVRLILDPNEnafgrkKFGLPNRPVAAELVKKSKGDIKIRWYhtgKEQYHSKTLFIRNKK 391
Cdd:cd09117    22 AFASAGGAIKLLDKFRE-GKKIRLIVGLDF------GGTSPADFALKLLLALGNLNVRIFDA---GPLLHAKLYLFENDD 91

                          90       100
                  ....*....|....*....|....*..
gi 1264924588 392 NATIIAGAANFTKRNLADlNLETDIKV 418
Cdd:cd09117    92 PTRAIVGSANLTQGGLSG-NIEAAVVI 117

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 1264924588 316 DRDVIKALLKASKQGANVRLILDPNenafgrKKFGLPNRPVAAELVKKSKGDIKIRWYhtGKEQYHSKTLFIRNKKNAT- 394
Cdd:cd09172    34 DPEIIDALKAAKDRGVRVRIILDDS------SVTGDPTEESAAATLSKGPGALVKRRH--SSGLMHNKFLVVDRKDGPNr 105

                          90
                  ....*....|....*....
gi 1264924588 395 IIAGAANFTKRNLA-DLNL 412
Cdd:cd09172   106 VLTGSTNFTTSGLYgQSNN 124

cardiolipin synthetase; Reviewed

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1264924588  63 VSEQHIFQAVTNAIDDAKAFIIMDMFLF-NGyynqgetfpHLSDTLASKLIEKKRKhpNIAIVFITDEInttyGSHD--- 138
Cdd:PRK01642  122 TNGDETFQAIIRDIELARHYILMEFYIWrPD---------GLGDQVAEALIAAAKR--GVRVRLLYDSI----GSFAffr 186

                          90
                  ....*....|....*.
gi 1264924588 139 SKWLDSLRLNGIKVVQ 154
Cdd:PRK01642  187 SPYPEELRNAGVEVVE 202

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 1264924588 287 EGKIYKHVLHDLHHAKKgdDVWLGMFYLGDRDVIKALLKASKQGANVRLILDPNENAFGRKkfglpnrpvAAELVKKSKG 366
Cdd:cd09170     9 EGGARELILDVIDSARR--SIDVAAYSFTSPPIARALIAAKKRGVDVRVVLDKSQAGGKYS---------ALNYLANAGI 77

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1264924588 367 DIKI-RWYHTgkeqYHSKTLFIRNKknaTIIAGAANFTK 404
Cdd:cd09170    78 PVRIdDNYAI----MHNKVMVIDGK---TVITGSFNFTA 109

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1264924588  70 QAVTNAIDDAKAFIIMDMFLFNGYYnqgetfphlSDTLASKLIEKKRKHpnIAIVFITDEINTTYGSHDSKWLDSLrlng 149
Cdd:cd00138     1 EALLELLKNAKESIFIATPNFSFNS---------ADRLLKALLAAAERG--VDVRLIIDKPPNAAGSLSAALLEAL---- 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1264924588 150 ikvvqtnlsklrdsiplyssvwrtfvqwfgekgngwitnpfgtNAPKATVRAY-LKLLNVKANHRKVVATDQS-VIISSA 227
Cdd:cd00138    66 -------------------------------------------LRAGVNVRSYvTPPHFFERLHAKVVVIDGEvAYVGSA 102

                         170
                  ....*....|.
gi 1264924588 228 NPHDASFYNSN 238
Cdd:cd00138   103 NLSTASAAQNR 113