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Conserved domains on  [gi|294352528|gb|ADE66584|]
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murine toxin (plasmid) [Yersinia pestis Z176003]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLDc_Ymt_2 cd09151
Putative catalytic domain, repeat 2, of Yersinia pestis murine toxin-like proteins; Putative ...
 317-580 0e+00

Putative catalytic domain, repeat 2, of Yersinia pestis murine toxin-like proteins; Putative catalytic domain, repeat 2, of Yersinia pestis murine toxin (Ymt), a plasmid-encoded phospholipase D (PLD, EC 3.1.4.4), and similar proteins. Ymt is important in order for Yersinia pestis to survive and spread. It is toxic to mice and rats but not to other animals. It is not a conventional secreted exotoxin, but a cytoplasmic protein that is released upon bacterial lysis. Ymt may be active as a dimer. The monomeric Ymt consists of two catalytic domains, each of which contains one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue). Two HKD motifs from two domains form a single active site. Ymt has PLD-like activity and has been classified into the PLD superfamily. It hydrolyzes the terminal phosphodiester bond in several phospholipids, with preference for phosphatidylethanolamine (PE) over phosphatidylcholine (PC) and phosphatidylserine (PS). Like other PLD enzymes, Ymt may 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. In terms of sequence similarity, Ymt is closely related to Streptomyces PLDs.


:

Pssm-ID: 197249  Cd Length: 264  Bit Score: 529.51  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294352528 317 DRVLSVGKYWTGPNMEHDYQRGSEIMKEQLIKNAKRIIRISQQDLVSAWKKKWKDHFTCNWIIEALLENKDLHIHVVVSA 396
Cdd:cd09151    1 TRMLSVGKYWRGPTMRTDYQGGSEIMKEQLIKNAKRSIRMSQQDLVSAWKKNWSDHVVCQWVIEALLANKSLKVEVVVSP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294352528 397 LDAAAGAAGDQYSFGSGAERTYELFKYYLTHDIDTDEVLDDPDGSRADALKRILIAPFFFTDKVPDENTIEGETYKWPDL 476
Cdd:cd09151   81 LDAAAGAAGDQYSFGSGAVRTFELFKYYLTHDVATDAVLPDPDGARKEALKRIFVAPFFFTDKVPPGDNIEGDTYKWPNL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294352528 477 EQSAYTATLKQKPLSEKPPHQGIIGSALMSAIKGSGLFYPKVPVAPGNHAKLMIIDDELYVVGSDNLYPGYLSEFDYLVE 556
Cdd:cd09151  161 PKEGYTATLKQPPLSEEPPKHGVIGSAAMSVIKASGYIYPKVPSAPGNHAKLMIIDDELYVVGSDNLYPGYLSEFDYLIE 240

                        250       260
                 ....*....|....*....|....
gi 294352528 557 GKDAVNELMKSYWEPLWKYSSPHA 580
Cdd:cd09151  241 GPDAVSELLKSYWEPLWKYSGPHA 264
PLDc_Ymt_1 cd09150
Putative catalytic domain, repeat 1, of Yersinia pestis murine toxin-like proteins; Putative ...
 20-240 8.19e-146

Putative catalytic domain, repeat 1, of Yersinia pestis murine toxin-like proteins; Putative catalytic domain, repeat 1, of Yersinia pestis murine toxin (Ymt), a plasmid-encoded phospholipase D (PLD, EC 3.1.4.4), and similar proteins. Ymt is important in order for Yersinia pestis to survive and spread. It is toxic to mice and rats but not to other animals. It is not a conventional secreted exotoxin, but a cytoplasmic protein that is released upon bacterial lysis. Ymt may be active as a dimer. The monomeric Ymt consists of two catalytic domains, each of which contains one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue). Two HKD motifs from two domains form a single active site. Ymt has PLD-like activity and has been classified into the PLD superfamily. It hydrolyzes the terminal phosphodiester bond in several phospholipids, with preference for phosphatidylethanolamine (PE) over phosphatidylcholine (PC) and phosphatidylserine (PS). Like other PLD enzymes, Ymt may 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. In terms of sequence similarity, Ymt is closely related to Streptomyces PLDs.


:

Pssm-ID: 197248  Cd Length: 215  Bit Score: 419.60  E-value: 8.19e-146
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294352528  20 NINYIRLLDTPHAWGAPFGKEIMQQSYLRQEEFAGAMTEVLRNSRYRCDISSLNSPDAEWRKVIFKAIDESLSKKMGRTQ 99
Cdd:cd09150    1 GINYVRLLDTPRVWGLPFGKEIMPQAWERQGEFERAIVEVLQKTRYRCDISSLNSPDPDWRKVILGAIDTALSKKMNRTE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294352528 100 PTQYRFLFGQSPTVFMNGLSAatngspdFVAFKSELIQLIKERGQYWEKMPEIWLGRFFRIEEGLATSFMRNVYPDFP-P 178
Cdd:cd09150   81 PTQFRFLFGQTPLVPMNGPTN-------YTAFKAALIRLIRERGHYWERMPEIWLGRFYRIEEGLLDSLQKKVLPEDFfP 153

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 294352528 179 INDTRMTWNHTKIMASDGTEALVGGHNMNMDLFRNYPPVHDVSIITHGSSAYGSQLYLNELW 240
Cdd:cd09150  154 GDDTKMTWNHTKIIAVDGLEALVGGHNLNMDLFRSYPPVHDVSVIVHGPAALGSQLYLNELW 215
 
Name Accession Description Interval E-value
PLDc_Ymt_2 cd09151
Putative catalytic domain, repeat 2, of Yersinia pestis murine toxin-like proteins; Putative ...
 317-580 0e+00

Putative catalytic domain, repeat 2, of Yersinia pestis murine toxin-like proteins; Putative catalytic domain, repeat 2, of Yersinia pestis murine toxin (Ymt), a plasmid-encoded phospholipase D (PLD, EC 3.1.4.4), and similar proteins. Ymt is important in order for Yersinia pestis to survive and spread. It is toxic to mice and rats but not to other animals. It is not a conventional secreted exotoxin, but a cytoplasmic protein that is released upon bacterial lysis. Ymt may be active as a dimer. The monomeric Ymt consists of two catalytic domains, each of which contains one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue). Two HKD motifs from two domains form a single active site. Ymt has PLD-like activity and has been classified into the PLD superfamily. It hydrolyzes the terminal phosphodiester bond in several phospholipids, with preference for phosphatidylethanolamine (PE) over phosphatidylcholine (PC) and phosphatidylserine (PS). Like other PLD enzymes, Ymt may 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. In terms of sequence similarity, Ymt is closely related to Streptomyces PLDs.


Pssm-ID: 197249  Cd Length: 264  Bit Score: 529.51  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294352528 317 DRVLSVGKYWTGPNMEHDYQRGSEIMKEQLIKNAKRIIRISQQDLVSAWKKKWKDHFTCNWIIEALLENKDLHIHVVVSA 396
Cdd:cd09151    1 TRMLSVGKYWRGPTMRTDYQGGSEIMKEQLIKNAKRSIRMSQQDLVSAWKKNWSDHVVCQWVIEALLANKSLKVEVVVSP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294352528 397 LDAAAGAAGDQYSFGSGAERTYELFKYYLTHDIDTDEVLDDPDGSRADALKRILIAPFFFTDKVPDENTIEGETYKWPDL 476
Cdd:cd09151   81 LDAAAGAAGDQYSFGSGAVRTFELFKYYLTHDVATDAVLPDPDGARKEALKRIFVAPFFFTDKVPPGDNIEGDTYKWPNL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294352528 477 EQSAYTATLKQKPLSEKPPHQGIIGSALMSAIKGSGLFYPKVPVAPGNHAKLMIIDDELYVVGSDNLYPGYLSEFDYLVE 556
Cdd:cd09151  161 PKEGYTATLKQPPLSEEPPKHGVIGSAAMSVIKASGYIYPKVPSAPGNHAKLMIIDDELYVVGSDNLYPGYLSEFDYLIE 240

                        250       260
                 ....*....|....*....|....
gi 294352528 557 GKDAVNELMKSYWEPLWKYSSPHA 580
Cdd:cd09151  241 GPDAVSELLKSYWEPLWKYSGPHA 264
PLDc_Ymt_1 cd09150
Putative catalytic domain, repeat 1, of Yersinia pestis murine toxin-like proteins; Putative ...
 20-240 8.19e-146

Putative catalytic domain, repeat 1, of Yersinia pestis murine toxin-like proteins; Putative catalytic domain, repeat 1, of Yersinia pestis murine toxin (Ymt), a plasmid-encoded phospholipase D (PLD, EC 3.1.4.4), and similar proteins. Ymt is important in order for Yersinia pestis to survive and spread. It is toxic to mice and rats but not to other animals. It is not a conventional secreted exotoxin, but a cytoplasmic protein that is released upon bacterial lysis. Ymt may be active as a dimer. The monomeric Ymt consists of two catalytic domains, each of which contains one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue). Two HKD motifs from two domains form a single active site. Ymt has PLD-like activity and has been classified into the PLD superfamily. It hydrolyzes the terminal phosphodiester bond in several phospholipids, with preference for phosphatidylethanolamine (PE) over phosphatidylcholine (PC) and phosphatidylserine (PS). Like other PLD enzymes, Ymt may 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. In terms of sequence similarity, Ymt is closely related to Streptomyces PLDs.


Pssm-ID: 197248  Cd Length: 215  Bit Score: 419.60  E-value: 8.19e-146
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294352528  20 NINYIRLLDTPHAWGAPFGKEIMQQSYLRQEEFAGAMTEVLRNSRYRCDISSLNSPDAEWRKVIFKAIDESLSKKMGRTQ 99
Cdd:cd09150    1 GINYVRLLDTPRVWGLPFGKEIMPQAWERQGEFERAIVEVLQKTRYRCDISSLNSPDPDWRKVILGAIDTALSKKMNRTE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294352528 100 PTQYRFLFGQSPTVFMNGLSAatngspdFVAFKSELIQLIKERGQYWEKMPEIWLGRFFRIEEGLATSFMRNVYPDFP-P 178
Cdd:cd09150   81 PTQFRFLFGQTPLVPMNGPTN-------YTAFKAALIRLIRERGHYWERMPEIWLGRFYRIEEGLLDSLQKKVLPEDFfP 153

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 294352528 179 INDTRMTWNHTKIMASDGTEALVGGHNMNMDLFRNYPPVHDVSIITHGSSAYGSQLYLNELW 240
Cdd:cd09150  154 GDDTKMTWNHTKIIAVDGLEALVGGHNLNMDLFRSYPPVHDVSVIVHGPAALGSQLYLNELW 215
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
 524-547 1.03e-05

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: 42.38  E-value: 1.03e-05
                           10        20
                   ....*....|....*....|....
gi 294352528   524 NHAKLMIIDDELYVVGSDNLYPGY 547
Cdd:smart00155   5 LHTKLMIVDDEIAYIGSANLDGRS 28
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
 186-209 1.77e-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: 1.77e-04
                           10        20
                   ....*....|....*....|....
gi 294352528   186 WNHTKIMASDGTEALVGGHNMNMD 209
Cdd:smart00155   4 VLHTKLMIVDDEIAYIGSANLDGR 27
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 176-240 1.33e-03

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: 41.47  E-value: 1.33e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 294352528 176 FPPINDTRMTWN---HTKIMASDGTEALVGGHNMN---MDLFRNYPPVHDVSIITHGSSAYGSQLYLNELW 240
Cdd:COG1502  101 FNPVRLLFRRLNgrnHRKIVVIDGRVAFVGGANITdeyLGRDPGFGPWRDTHVRIEGPAVADLQAVFAEDW 171
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 525-578 5.13e-03

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: 39.54  E-value: 5.13e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 294352528 525 HAKLMIIDDELYVVGSDNLYPGYLS---EFDYLVEGKDAVNELMKSYWEpLWKYSSP 578
Cdd:COG1502  286 HAKVMVVDDEWALVGSANLDPRSLRlnfEVNLVIYDPEFAAQLRARFEE-DLAHSRE 341
PLDc_2 pfam13091
PLD-like domain;
492-573 6.43e-03

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 37.27  E-value: 6.43e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294352528  492 EKPPHQGIIGSALMSAIKgsglFYPKVPVAPGNHAKLMIIDDELYVVGSDNLYPGYLS---EFDYLVEGKDAVNELMKSY 568
Cdd:pfam13091  53 PKKASLKELRSLLRAGVE----IREYQSFLRSMHAKFYIIDGKTVIVGSANLTRRALRlnlENNVVIKDPELAQELEKEF 128


                  ....*
gi 294352528  569 WEpLW 573
Cdd:pfam13091 129 DR-LW 132
 
Name Accession Description Interval E-value
PLDc_Ymt_2 cd09151
Putative catalytic domain, repeat 2, of Yersinia pestis murine toxin-like proteins; Putative ...
 317-580 0e+00

Putative catalytic domain, repeat 2, of Yersinia pestis murine toxin-like proteins; Putative catalytic domain, repeat 2, of Yersinia pestis murine toxin (Ymt), a plasmid-encoded phospholipase D (PLD, EC 3.1.4.4), and similar proteins. Ymt is important in order for Yersinia pestis to survive and spread. It is toxic to mice and rats but not to other animals. It is not a conventional secreted exotoxin, but a cytoplasmic protein that is released upon bacterial lysis. Ymt may be active as a dimer. The monomeric Ymt consists of two catalytic domains, each of which contains one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue). Two HKD motifs from two domains form a single active site. Ymt has PLD-like activity and has been classified into the PLD superfamily. It hydrolyzes the terminal phosphodiester bond in several phospholipids, with preference for phosphatidylethanolamine (PE) over phosphatidylcholine (PC) and phosphatidylserine (PS). Like other PLD enzymes, Ymt may 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. In terms of sequence similarity, Ymt is closely related to Streptomyces PLDs.


Pssm-ID: 197249  Cd Length: 264  Bit Score: 529.51  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294352528 317 DRVLSVGKYWTGPNMEHDYQRGSEIMKEQLIKNAKRIIRISQQDLVSAWKKKWKDHFTCNWIIEALLENKDLHIHVVVSA 396
Cdd:cd09151    1 TRMLSVGKYWRGPTMRTDYQGGSEIMKEQLIKNAKRSIRMSQQDLVSAWKKNWSDHVVCQWVIEALLANKSLKVEVVVSP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294352528 397 LDAAAGAAGDQYSFGSGAERTYELFKYYLTHDIDTDEVLDDPDGSRADALKRILIAPFFFTDKVPDENTIEGETYKWPDL 476
Cdd:cd09151   81 LDAAAGAAGDQYSFGSGAVRTFELFKYYLTHDVATDAVLPDPDGARKEALKRIFVAPFFFTDKVPPGDNIEGDTYKWPNL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294352528 477 EQSAYTATLKQKPLSEKPPHQGIIGSALMSAIKGSGLFYPKVPVAPGNHAKLMIIDDELYVVGSDNLYPGYLSEFDYLVE 556
Cdd:cd09151  161 PKEGYTATLKQPPLSEEPPKHGVIGSAAMSVIKASGYIYPKVPSAPGNHAKLMIIDDELYVVGSDNLYPGYLSEFDYLIE 240

                        250       260
                 ....*....|....*....|....
gi 294352528 557 GKDAVNELMKSYWEPLWKYSSPHA 580
Cdd:cd09151  241 GPDAVSELLKSYWEPLWKYSGPHA 264
PLDc_Ymt_1 cd09150
Putative catalytic domain, repeat 1, of Yersinia pestis murine toxin-like proteins; Putative ...
 20-240 8.19e-146

Putative catalytic domain, repeat 1, of Yersinia pestis murine toxin-like proteins; Putative catalytic domain, repeat 1, of Yersinia pestis murine toxin (Ymt), a plasmid-encoded phospholipase D (PLD, EC 3.1.4.4), and similar proteins. Ymt is important in order for Yersinia pestis to survive and spread. It is toxic to mice and rats but not to other animals. It is not a conventional secreted exotoxin, but a cytoplasmic protein that is released upon bacterial lysis. Ymt may be active as a dimer. The monomeric Ymt consists of two catalytic domains, each of which contains one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue). Two HKD motifs from two domains form a single active site. Ymt has PLD-like activity and has been classified into the PLD superfamily. It hydrolyzes the terminal phosphodiester bond in several phospholipids, with preference for phosphatidylethanolamine (PE) over phosphatidylcholine (PC) and phosphatidylserine (PS). Like other PLD enzymes, Ymt may 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. In terms of sequence similarity, Ymt is closely related to Streptomyces PLDs.


Pssm-ID: 197248  Cd Length: 215  Bit Score: 419.60  E-value: 8.19e-146
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294352528  20 NINYIRLLDTPHAWGAPFGKEIMQQSYLRQEEFAGAMTEVLRNSRYRCDISSLNSPDAEWRKVIFKAIDESLSKKMGRTQ 99
Cdd:cd09150    1 GINYVRLLDTPRVWGLPFGKEIMPQAWERQGEFERAIVEVLQKTRYRCDISSLNSPDPDWRKVILGAIDTALSKKMNRTE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294352528 100 PTQYRFLFGQSPTVFMNGLSAatngspdFVAFKSELIQLIKERGQYWEKMPEIWLGRFFRIEEGLATSFMRNVYPDFP-P 178
Cdd:cd09150   81 PTQFRFLFGQTPLVPMNGPTN-------YTAFKAALIRLIRERGHYWERMPEIWLGRFYRIEEGLLDSLQKKVLPEDFfP 153

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 294352528 179 INDTRMTWNHTKIMASDGTEALVGGHNMNMDLFRNYPPVHDVSIITHGSSAYGSQLYLNELW 240
Cdd:cd09150  154 GDDTKMTWNHTKIIAVDGLEALVGGHNLNMDLFRSYPPVHDVSVIVHGPAALGSQLYLNELW 215
PLDc_PMFPLD_like_2 cd09109
Catalytic domain, repeat 2, of phospholipase D from Streptomyces Sp. Strain PMF and similar ...
 317-576 2.46e-91

Catalytic domain, repeat 2, of phospholipase D from Streptomyces Sp. Strain PMF and similar proteins; Catalytic domain, repeat 2, of phospholipases D (PLD, EC 3.1.4.4) from Streptomyces Sp. Strain PMF (PMFPLD) and similar proteins, which are generally extracellular and bear N-terminal signal sequences. PMFPLD hydrolyzes the terminal phosphodiester bond of phospholipids with the formation of phosphatidic acid and alcohols. Phosphatidic acid is an essential compound involved in signal transduction. It also catalyzes a transphosphatidylation of phospholipids to acceptor alcohols, by which various phospholipids can be synthesized. In contrast to eukaryotic PLDs, PMFPLD has a compact structure, which consists of two catalytic domains, but lacks the regulatory domains. Each catalytic domain contains one copy of the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the PLD superfamily. Two HKD motifs from two domains form a single active site. Like other PLD enzymes, PMFPLD may 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. A calcium-dependent PLD from Streptomyce chromofuscus is excluded from this family, since it displays very little sequence homology with other Streptomyces PLDs. Moreover, it does not contain the conserved HKD motif and hydrolyzes the phospholipids via a different mechanism.


Pssm-ID: 197208  Cd Length: 212  Bit Score: 279.95  E-value: 2.46e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294352528 317 DRVLSVGKYWTGPNME---HDYQRGSEIMKEQLIKNAKRIIRISQQDLVSAWKKKWKDHFTCNWIIEALLENKDLHIHVV 393
Cdd:cd09109    1 VPVIAVGGLGVGINDDdrdYDTVNPEEFALRILIASAKIHIEISQQDLNATCPLPRYDIFTYNFIAVSLAASTGVKVRIV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294352528 394 VSALDAAAGAAGdqysfgsgaertyelfkyylthdidTDEVLDDPDGSRADALKRILIAPFFFTDkvpdentiegeTYKW 473
Cdd:cd09109   81 VSDPDNRGAVGS-------------------------GGYVQIKSLTEIADTLSRRLAILTSVGN-----------LSKD 124

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294352528 474 PDLEQSAYTATLkqKPLSEKPPHQGIIGSAlmsaikgsglfypKVPVAPGNHAKLMIIDDELYVVGSDNLYPGYLSEFDY 553
Cdd:cd09109  125 PGSDQMARRALC--KNLQLAPPRSSGAGKW-------------ADGAPYALHAKLVIVDGKLFYIGSDNLYPSWLQEFGY 189

                        250       260
                 ....*....|....*....|...
gi 294352528 554 LVEGKDAVNELMKSYWEPLWKYS 576
Cdd:cd09109  190 IVEDPDAAKQLEDGYLDPLWKYS 212
PLDc_PMFPLD_like_1 cd09108
Catalytic domain, repeat 1, of phospholipase D from Streptomyces Sp. Strain PMF and similar ...
 49-240 4.26e-24

Catalytic domain, repeat 1, of phospholipase D from Streptomyces Sp. Strain PMF and similar proteins; Catalytic domain, repeat 1, of phospholipases D (PLD, EC 3.1.4.4) from Streptomyces Sp. Strain PMF (PMFPLD) and similar proteins, which are generally extracellular and bear N-terminal signal sequences. PMFPLD hydrolyzes the terminal phosphodiester bond of phospholipids with the formation of phosphatidic acid and alcohols. Phosphatidic acid is an essential compound involved in signal transduction. It also catalyzes a transphosphatidylation of phospholipids to acceptor alcohols, by which various phospholipids can be synthesized. In contrast to eukaryotic PLDs, PMFPLD has a compact structure, which consists of two catalytic domains, but lacks the regulatory domains. Each catalytic domain contains one copy of the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the PLD superfamily. Two HKD motifs from two domains form a single active site. Like other PLD enzymes, PMFPLD may 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. A calcium-dependent PLD from Streptomyce chromofuscus is excluded from this family, since it displays very little sequence homology with other Streptomyces PLDs. Moreover, it does not contain the conserved HKD motif and hydrolyzes the phospholipids via a different mechanism.


Pssm-ID: 197207 [Multi-domain]  Cd Length: 210  Bit Score: 100.59  E-value: 4.26e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294352528  49 QEEFAGAMTEVLRNSRYRCD-----ISSLNSPDAEWRKV--IFKAIDESLSKKMGRT--QPTQYRFLFGQSPTvfmngls 119
Cdd:cd09108    4 SDELEGAVWELTDGNRLDCScgnafISLLQTPGPWGATAclIDGAGDDELLEKMADNigSLPNARRIVGITTL------- 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294352528 120 AATNGSPDfvAFKSELIQLIKERGQY-WEKMPEIWLGRFFRIEEGLATSFMRNVYPDFPPIND-------------TRMT 185
Cdd:cd09108   77 APFPAFLA--AAVAGLKRRVSAHESYgEGITVRILVGNFPRYHLGQVVSAVRDLLTAGLPLDDpasgwtlsvanmtYFLP 154

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 294352528 186 WNHTKIMASDGTEALVGGHNMNMDLFRN-YPPVHDVSIITHGSSAYGSQLYLNELW 240
Cdd:cd09108  155 WNHAKLLVVDGEELLTGGYNLWDDHYLDgGNPVHDLSLVVRGPAARSGVRFFDDLW 210
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
 524-547 1.03e-05

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: 42.38  E-value: 1.03e-05
                           10        20
                   ....*....|....*....|....
gi 294352528   524 NHAKLMIIDDELYVVGSDNLYPGY 547
Cdd:smart00155   5 LHTKLMIVDDEIAYIGSANLDGRS 28
PLDc_vPLD1_2_like_bac_2 cd09143
Catalytic domain, repeat 2, of uncharacterized bacterial proteins with similarity to ...
 512-543 8.97e-05

Catalytic domain, repeat 2, of uncharacterized bacterial proteins with similarity to vertebrate phospholipases, PLD1 and PLD2; Catalytic domain, repeat 2, of uncharacterized bacterial counterparts of vertebrate, yeast and plant phospholipase D (PLD, EC 3.1.4.4). PLDs hydrolyze the terminal phosphodiester bond of phospholipids with the formation of phosphatidic acid and alcohols. They also catalyze the transphosphatidylation of phospholipids to acceptor alcohols, by which various phospholipids can be synthesized. Instead of the regulatory C2 (calcium-activated lipid binding) domain in plants and the adjacent Phox (PX) and the Pleckstrin homology (PH) N-terminal domains in most mammalian and yeast PLDs, many members in this subfamily contain a SNARE associated C-terminal domain, whose functional role is unclear. Like other PLD enzymes, members in this subfamily contain two copies of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue), that may play an important role in the catalysis.


Pssm-ID: 197241 [Multi-domain]  Cd Length: 142  Bit Score: 42.90  E-value: 8.97e-05
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 294352528 512 GLFYPKVPVAPGN----HAKLMIIDDELYVVGSDNL 543
Cdd:cd09143   90 RVYYPVTAGGGGRpiyvHSKLMIVDDRLLRVGSANL 125
PLDc smart00155
Phospholipase D. Active site motifs; Phosphatidylcholine-hydrolyzing phospholipase D (PLD) ...
 186-209 1.77e-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: 1.77e-04
                           10        20
                   ....*....|....*....|....
gi 294352528   186 WNHTKIMASDGTEALVGGHNMNMD 209
Cdd:smart00155   4 VLHTKLMIVDDEIAYIGSANLDGR 27
PLDc_vPLD1_2_like_2 cd09105
Catalytic domain, repeat 2, of vertebrate phospholipases, PLD1 and PLD2, and similar proteins; ...
 525-543 4.88e-04

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: 40.75  E-value: 4.88e-04
                         10
                 ....*....|....*....
gi 294352528 525 HAKLMIIDDELYVVGSDNL 543
Cdd:cd09105  111 HSKVVIVDDEWATVGSANL 129
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 176-240 1.33e-03

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: 41.47  E-value: 1.33e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 294352528 176 FPPINDTRMTWN---HTKIMASDGTEALVGGHNMN---MDLFRNYPPVHDVSIITHGSSAYGSQLYLNELW 240
Cdd:COG1502  101 FNPVRLLFRRLNgrnHRKIVVIDGRVAFVGGANITdeyLGRDPGFGPWRDTHVRIEGPAVADLQAVFAEDW 171
Cls COG1502
Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and ...
 525-578 5.13e-03

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: 39.54  E-value: 5.13e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 294352528 525 HAKLMIIDDELYVVGSDNLYPGYLS---EFDYLVEGKDAVNELMKSYWEpLWKYSSP 578
Cdd:COG1502  286 HAKVMVVDDEWALVGSANLDPRSLRlnfEVNLVIYDPEFAAQLRARFEE-DLAHSRE 341
PLDc_2 pfam13091
PLD-like domain;
492-573 6.43e-03

PLD-like domain;


Pssm-ID: 463784 [Multi-domain]  Cd Length: 132  Bit Score: 37.27  E-value: 6.43e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294352528  492 EKPPHQGIIGSALMSAIKgsglFYPKVPVAPGNHAKLMIIDDELYVVGSDNLYPGYLS---EFDYLVEGKDAVNELMKSY 568
Cdd:pfam13091  53 PKKASLKELRSLLRAGVE----IREYQSFLRSMHAKFYIIDGKTVIVGSANLTRRALRlnlENNVVIKDPELAQELEKEF 128


                  ....*
gi 294352528  569 WEpLW 573
Cdd:pfam13091 129 DR-LW 132
PLDc pfam00614
Phospholipase D Active site motif; Phosphatidylcholine-hydrolysing phospholipase D (PLD) ...
 524-547 9.53e-03

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: 33.93  E-value: 9.53e-03
                          10        20
                  ....*....|....*....|....
gi 294352528  524 NHAKLMIIDDELYVVGSDNLYPGY 547
Cdd:pfam00614   5 LHRKIVVVDDELAYIGGANLDGRS 28
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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