Conserved Protein Domain Family
PLPDE_III_PvsE_like

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cd06843: PLPDE_III_PvsE_like 
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme PvsE
This subfamily is composed of PvsE from Vibrio parahaemolyticus and similar proteins. PvsE is a vibrioferrin biosynthesis protein which is homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. It has been suggested that PvsE may be involved in the biosynthesis of the polycarboxylate siderophore vibrioferrin. It may catalyze the decarboxylation of serine to yield ethanolamine. PvsE may require homodimer formation and the presence of the PLP cofactor for activity.
Statistics
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PSSM-Id: 143510
View PSSM: cd06843
Aligned: 16 rows
Threshold Bit Score: 467.913
Threshold Setting Gi: 158312520
Created: 1-Jul-2008
Updated: 2-Oct-2020
Structure
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Aligned Rows:
 
Feature 1:active site [active site]
Evidence:
  • Comment:Based on the structures of PLP and substrate bound to ornithine and diaminopimelate decarboxylases.
  • Comment:The active site is composed of residues from both subunits of the dimer. There are two active sites in the functional dimer.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                      # #                  #                     #     
BAC16548     25 PLCAYLYDLnALEEHIKQLRHVLPKNVKLFYAAKANPSGPILNTLAPYVDGFEAASGGELTHLHQQQlDKPLIFGGPGKM 104 Vibrio parahaemo...
NP_942760    31 PLSTYVYDLeALRRHATATARGLPPGFELFYAIKANSDLPILQTLAPLAHGFEISSGGELAWVREHFaDVPLIFSGPGKT 110 Ralstonia eutrop...
YP_747942    21 SLCAYLYDLgALASHARNIKSSLPDRVNFFYAIKANSDLPILSALAEHVDGFEASSGGEIQWVRQNFpDVPLIFSGPGKL 100 Nitrosomonas eut...
ZP_01892152  22 PLCAYVYDLpELRNRAQNIVGCLPPGCEMFYAAKANPALPVLSALASFVHGFEVASGGELDWVRRHFpDTSVIFGGPGKL 101 Marinobacter alg...
NP_643489    24 PICAYVYDLaALDTHAAWMRAQLPAQCELFYAAKANAEPPILRTLAPHVDGFEAASGGELAWLHAQQpQAPLLFGGPGKL 103 Xanthomonas axon...
ZP_01858890  21 PVCAYVYDLkGLREHARRLKDSLPAFCSLYYAVKANPDNRILEALSGIVDGFDTASEGEILKVHKLS-ALPVIFAAPAKK 99  Bacillus sp. SG-1
NP_370647    17 PVCHYIYDLvGLEHHLQHITSSLPSNCQMYYAMKANSERTILDTISQYVEGFEVASQGEIAKGLAFKpANHIIFGGPGKT 96  Staphylococcus a...
NP_521985    16 PVCAYLYDLdHLRERAARLSAMLPPGCELFYAIKANSDAPVLAALDGAVAGYEVASLGEVVRAREVGaQARIVFGGPGKT 95  Ralstonia solana...
ZP_01045740  16 PVCAYLYDLaHLRRRADTLRRCLPAQCKLFYAIKANSDAPILRALLHRTDGFEVASLGEIQAVRGINdAVPVVFGGPGKT 95  Nitrobacter sp. ...
YP_561597    17 EVCAFIYDLdQLSAHIRTMTSRLPKQVDCYYAIKANSDSAILRALLPHVYGFEVASMGEIEKVRAISqNVPIAFGGPGKT 96  Shewanella denit...
Feature 1                                                #                                      
BAC16548    105 pSELQQAIELdVDAIHVESlTELQRIGALTERlNRPASIFLRMNIdig------ditLSKLAMGGKPTPFGLDesELSNA 178 Vibrio parahaemo...
NP_942760   111 dAELAGALELgVEALHVESlHELERLAWLARArGVTAPVLLRVNLaie------glqATTLMMGGKPTPFGIAgdQLPAC 184 Ralstonia eutrop...
YP_747942   101 dTELELAILN-NVTVHIESrFELERLLHIARHyQQPAEILLRVNPhfe------dlrATSLMMGGKPTQFGISveHLSDC 173 Nitrosomonas eut...
ZP_01892152 102 aSDLEKAIDQnVELIHVESlLELQRLCDIAGRrQANQDILLRINLela------dtpSTRLTMGGVPTPFGMEeaCIPDA 175 Marinobacter alg...
NP_643489   104 dTELAQAAALpDCTVHVESlSELERLAEVASHaGRCVPVFLRMNIavp------gaqSTRLMMGGQPSPFGLDpcDLHAA 177 Xanthomonas axon...
ZP_01858890 100 dRELAYLADGsLRFMNVESeRDLYRLNRVGKEaGKALPVLIRINLqhn-------vsNSSHKMSGVPTQFGIEerKIPSI 172 Bacillus sp. SG-1
NP_370647    97 dEELRYAVSEgVQRIHVESmHELQRLNAILEDeDKTQHILLRVNLagp-------fpNATLHMAGRPTQFGISedEVDDV 169 Staphylococcus a...
NP_521985    96 dDELQGALERgVELIHVESeLQLRRLDAIACRmGRRARVLLRVNPnplsadavgkraQGTLTMGGQPTQFGIEedAVPDL 175 Ralstonia solana...
ZP_01045740  96 dAELEGALDQgVLLIHVESeHQLRRLDWIARRrNQRADILLRVNPasv-------pqQATLRMGGQATQFGIEeaQIPAL 168 Nitrobacter sp. ...
YP_561597    97 iTELTRALTLnVQLYHLESeLQLARLNQLAKEqNQLVRCLLRVNPyfd-------lpSATLQMAGQATQFGIDerELLAL 169 Shewanella denit...
Feature 1                         #  #                                     ##                   
BAC16548    179 LMLLRd-fPQVSLKGFHFHLMSHqLDVERHLALMQRYFQVVKAWQQEFEL-GELMINLGGGMGINYqnPEQHFPWMEFCD 256 Vibrio parahaemo...
NP_942760   185 LAWLRa-hPEIRLRGFHFHLMSHqLDAAAHLRLLDAYLQQVRRWRAEYGLdTLDQVNVGGGIGVNYrePERQFDWAGFAE 263 Ralstonia eutrop...
YP_747942   174 LKMVRdnsDCLYFQGFHFHLLSHqLDAAQHLRLLSAYIEQAVKWKEEFNL-VIDHINVGGGIGVNYkdIDQQFDWCHFSH 252 Nitrosomonas eut...
ZP_01892152 176 LALLAr-qGRVRLRGFHFHLMSHqLDEKRHLTLIKHYLETVRTWEAQYGL-SLTEINVGGGIGINYtqPDQQFDWSGFCT 253 Marinobacter alg...
NP_643489   178 MQRLQa-sPSLRLAGFHFHLMSHqRDATAQLHLVAAYLRTVQQWRQAYAL-GPLRVNAGGGFGVDYlaPEASFDWAGFCA 255 Xanthomonas axon...
ZP_01858890 173 LEKLSe-fPYIELNGFHFHAMSNnLNAEEHLIFVKRCLEKSLEWKKTFSL-DLGVVNIGGGIGVNYenPSESFDWTFFSE 250 Bacillus sp. SG-1
NP_370647   170 IEAALv-mPNIHLDGFHFHSISNnLDSNLHVDVVKLYFKKAKSWSEKHRF-PLKHINLGGGIGVNYadLTSQFEWDNFVE 247 Staphylococcus a...
NP_521985   176 IRLARt-lPGVEVVGLHLHALSNnLDADSHLALMRHYLSLALRLRREHGL-TLDTLNVGGGIGVDYadPSHAFDWRRFCD 253 Ralstonia solana...
ZP_01045740 169 IELALg-lPGVRLRGLHIHSISNnLDAQTHLALLEHYFDLTSTWQRRYQL-EFDWLNAGGGIGINYanPQASFDWEGFCA 246 Nitrobacter sp. ...
YP_561597   170 LPRLGd-yPNIQVEGLHFHCLSNnLDAVKHVTLVRHYLQTASTWAAQFGL-TWTTVNIGGGIGVTYq-GETEFDFPLYAE 246 Shewanella denit...
Feature 1                         ####                                                          
BAC16548    257 KLEFLIakeqvqdwTLRFECGRFITAACGYYVMEVLDIKQNLGENFVIARGGTHHFRTPAAQSHDHPFVILKSEQHhd-- 334 Vibrio parahaemo...
NP_942760   264 GLPALSaqr--dglTVRLECGRYITAFCGYYAMEVIDVKHAFDRAFVVACGGTHHFRTPYAQGHSHPFRVLPVESWryp- 340 Ralstonia eutrop...
YP_747942   253 GLNNLLigaaknipKIRFEMGRYVSAFCGVYVAEVIDIKTSGNGTYVVVKGGTHHFRTPYAQNHSHPFKVIPVSTWkkp- 331 Nitrosomonas eut...
ZP_01892152 254 GLDELLqayvdrawRIRFECGRFITAPCGYYVGEVLDVKRCGEEWFAVCRGGTHHFRTPAAQAHNHPFDILPTNNTda-- 331 Marinobacter alg...
NP_643489   256 GLPALLreha-tdlRLRLEPGRYVSASCGWYLMEVLDLKRSHGAWFAIARGGTHHFRTPAAQGHDHPFRVLRGERA---- 330 Xanthomonas axon...
ZP_01858890 251 GLHQMQeefeanqlELIMELGRYLTAQCGFYITEVIDLKQNYDEWFPLVRGGTHHLRLPAAWKMSHPFSVYPVTEWkeap 330 Bacillus sp. SG-1
NP_370647   248 NFKTLIveqemedvTLNFECGRFIVAHIGYYVTEVLDIKKVHGAWYAILRGGTQQFRLPVSWQHNHPFEIYRYKDNpys- 326 Staphylococcus a...
NP_521985   254 GLGVLLaeag-agcRIVFECGRFIAADCGYYVTEVVDLKRNHGRWFAVLRGGTHHFRLPASWQHNHPFAILPNARWdyp- 331 Ralstonia solana...
ZP_01045740 247 GLAALIaarq-prfQLVFECGRFLTADCGYYLADVTDLKHTHGKHFAILRGGSHHFRLPASWQHNHPFVVLPREAWpyp- 324 Nitrobacter sp. ...
YP_561597   247 QLTLLCrdy--pqlHLATECGRYISADCGVYLTEVTDIKLSHNEYFAVLRGGTHHFRLPSSWQHSHPFKIYPRETWhyp- 323 Shewanella denit...
Feature 1                        ##                           #   #    #           
BAC16548    335 -isHPIQHAQATFVGQLCTPKDVLARNQHVAHVDIGDYVVFTLAGAYAWNISHQNFLMHEPPIFHYF 400 Vibrio parahaemolyticus
NP_942760   341 farPGVRDARVSVVGQLCTPKDVLAQDAPVDSVRAGDMVVFPYAGAYAWHISHHDFLRHPHPQHCYL 407 Ralstonia eutropha H16
YP_747942   332 ysrPGLRHGKVNIVGQLCTPKDLLAFDEMVGEIRVGDIVLFSHAGAYAWHISHHDFLRHAHPQHIYL 398 Nitrosomonas eutropha C91
ZP_01892152 332 -atPCVTDHSVTLVGQLCTPKDVFARQVHIASLGVGDLVVFRYAGAYAWNISHQAFLMHPHPEEYFI 397 Marinobacter algicola DG893
NP_643489   331 ---PVLRDTPVTLVGQLCTPKDVLARDQHVAALAPGDCLAFPLAGAYAWNISHQRFLMHPAPQMVFL 394 Xanthomonas axonopodis pv. ci...
ZP_01858890 331 lprPAVKGERITIAGELCTPNDLLVRKQYVDDLKVGDLVMFHLSGAYGWTISHHDFLSHPAPDFHYL 397 Bacillus sp. SG-1
NP_370647   327 fekVSISRQDTTLVGQLCTPKDVFAREVQIDAISTGDVIVFKYAGAYGWSISHHDFLSHPHPEFIYL 393 Staphylococcus aureus subsp. ...
NP_521985   332 ferPSVLAQAVTLCGELCTPKDVLARDVVVDRLRVGDRIVFQLAGAYGWHISHHDFLSHPHPERRFV 398 Ralstonia solanacearum GMI1000
ZP_01045740 325 fsrPAVHETPVTLCGELCTPKDTLACDVRVERLRAGDCIAFLLAGAYGWHISHHDFLSHPHPERVYL 391 Nitrobacter sp. Nb-311A
YP_561597   324 ftrPSVTDTAITLCGELCTPKDVLAKNVHVAQLKVADVIVFQKAGAYGWHISHHDFLSHPHPQRLYI 390 Shewanella denitrificans OS217

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