Conserved Protein Domain Family
PLPDE_III_VanT

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cd06825: PLPDE_III_VanT 
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, VanT and similar proteins
This subfamily is composed of Enterococcus gallinarum VanT and similar proteins. VanT is a membrane-bound serine racemase (EC 5.1.1.18) that is essential for vancomycin resistance in Enterococcus gallinarum. It converts L-serine into its D-enantiomer (D-serine) for peptidoglycan synthesis. The C-terminal region of this protein contains a PLP-binding TIM-barrel domain followed by beta-sandwich domain, which is homologous to the fold type III PLP-dependent enzyme, bacterial alanine racemase (AR). AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. On the basis of this similarity, it has been suggested that dimer formation of VanT is required for its catalytic activity, and that it catalyzes the racemization of serine in a mechanistically similar manner to that of alanine by bacterial AR. Some biochemical evidence indicates that VanT also exhibits alanine racemase activity and plays a role in the racemization of L-alanine. VanT contains a unique N-terminal transmembrane domain, which may function as an L-serine transporter. VanT serine racemases are not related to eukaryotic serine racemases, which are fold type II PLP-dependent enzymes.
Statistics
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PSSM-Id: 143498
View PSSM: cd06825
Aligned: 9 rows
Threshold Bit Score: 590.865
Threshold Setting Gi: 18476140
Created: 8-Jul-2008
Updated: 2-Oct-2020
Structure
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Aligned Rows:
 
Feature 1:active site [active site]
Evidence:
  • Comment:Based on the binding of the PLP cofactor and substrate to other members of the superfamily.
  • 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                                      # #   #                                         # 
Q9X3P3       339 RAVKEFSKTALLHNLQEIQRIISpkTKVMAVVKADAYGCGAKEVAPVLEQaGIDFFAVATIDEGIRLRKNAVkSPILVLG 418 Enterococcus ga...
ZP_02862048    6 RAWIELDINNLNNNVNEFKRVLPkgCELMPAIKANAYGHGLVETAEALNKmEIYHFCVAEISEGIRLRKAGVkGEILILG 85  Anaerofustis st...
YP_001088129 345 RAWIEIDLNNLEHNVKMIQKAMPedCELMAVVKANAYGHSAFEVATCANQiGVKAFAVATIDEGIDLRRYGIlGEILILG 424 Clostridium dif...
EDQ95983      18 RAWVEIDLSKFKHNIEVIKELLHddVQIVGVVKANAYGHGDVVVAKYFESlGIKYFAVACIEEAIKLREGGIkGDIIILG 97  Clostridium bar...
ZP_02038521  346 RAWAEIDRSALVHNISQLTGLLPsgCELMAVVKANAYGHGDVLTARVCMSsGVKAFAVATLEEGIRLRQAGMkGEILILG 425 Bacteroides cap...
AAS47779      10 PSWLEIDLTRISHNIKEVQKLIPstSKIMAIVKANGYGHGDVECSRMMEQqGIDFFGVSSVDEGVRLRENGIqSPILVLG 89  Clostridium inn...
ZP_02078067    7 RSWLEIHVSRIEHNVAEIQKLLLgtNKIMGIVKANAYGHGDVVCAKELERiGIDFFGVSSVDEALSLREGGIsSPILILG 86  Eubacterium dol...
AAK58491     341 RATKEFSAPALLHNLQEIKRLIPatTKVMAVVKADAYGCDAKTVASTLERaGVDFFAVATLEEAIELRRAGIkSRLLILG 420 Enterococcus ca...
ABB17545     344 RAYLEIDLNNLEHNVKVLKRAMPqkCELMAVVKAEAYGHGLYEIATHLNKiGVKAFAVATIDEGIKLRQYGVlGEILILG 423 Enterococcus fa...
Feature 1                                                   #      #                             
Q9X3P3       419 YTspkRIKELRRYsLTQSIISeGHAVALSQrk----vaIDCHLAIDTGMHRLGVTp-----TIDSILSIFDLPFLTISGV 489 Enterococcus ga...
ZP_02862048   86 YThlsNINLVKKYdLTQTVIDyRYASSLDEck----lnIKVHIKIDTGMHRLGEHf----eNITNIIRILSFKNIDVKGV 157 Anaerofustis st...
YP_001088129 425 YTnpiRAKELHKYnLTQSVIDlNHAISLNKqk----ynIKSHIKIDTGMHRLGFDv----nDVRSILKAFKLKYLDICGI 496 Clostridium dif...
EDQ95983      98 WTpscQKDDLIKYdLCQTLANeAYAEELSKlp----gtVRGYVKLNTGMNRLGEPk----eHMDLIEKIYTLDNIKVEGI 169 Clostridium bar...
ZP_02038521  426 WTppeQAQQLTRWrLSQAVVSrTYAEELSHsa----hrVKVHLAVDTGMHRLGLSw----dDGDGLLAVCRLKQLRVTGL 497 Bacteroides cap...
AAS47779      90 YTppvHFHYLNEAsLIQTLVSkEYAEKLNAyakeqnvvVKAHAKVNTGMSRIGIShrimhiISRISKALVRLKHLNVSGI 169 Clostridium inn...
ZP_02078067   87 YTppvHFPLLKKYrLTQTILSlEYAKKLNAyalahdecIDVHVKLDTGMSRIGIVtqshayHIEEVKAVYALKGLHACGI 166 Eubacterium dol...
AAK58491     421 YTsaqRAKELKHYsLIQTIVSeAHGHALAQts----ipIECHLAVDTGMHRLGVAp-----DLETVTGLYALPSLKITRI 491 Enterococcus ca...
ABB17545     424 YTapaRAKELRKYdLTQTLIDyKYALLLDKqg----ydVMTHIKVDTGMHRLGFDa----kDIEKISAVFSMKHIKVSGI 495 Enterococcus fa...
Feature 1          #                                           ##               ####             
Q9X3P3       490 YSHLGSADRLnPDSMIRTQKQIACFDQILLELDQRQI-SYGITHLQSSYGILNYPDl-nYDYVRPGILLTGSLSdtnep- 566 Enterococcus ga...
ZP_02862048  158 FSHLCVSDSIdKKDIEFTKLQINHFNNIVKVLKENGY-TNLKFHIQGSYGVLNYPDl-kYDYARVGIALYGVLSkksdk- 234 Anaerofustis st...
YP_001088129 497 FTHLCVSDSLkDEDVDFTNKQIECFYKLIDFLLKKGI-KIPKVHIQSSYGFFNYPNl-kCNYVRIGIALYGILSspndt- 573 Clostridium dif...
EDQ95983     170 FSHLSRSDSKlEADIVFTKQQIANFDYVINKLKADGF-ELGNVHLQNSYGIVTYRDl-hYDLARPGIILYGVPSdplddt 247 Clostridium bar...
ZP_02038521  498 FTHLAFSESLePDAVGHTREQLHRFYQAADLVISAGY-GPVALHALSSYGLLNCPKqagMAYARPGIALYGVLSrpdeq- 575 Bacteroides cap...
AAS47779     170 FSHFSVSDCLdEENCAFTNHQIALFERVLADLRPEGLtPVQRICRQLWNFKLSEPA---LDYVRPGLLWMGVPAmm---- 242 Clostridium inn...
ZP_02078067  167 FSHFPVSDDLgEDAQAFTKHQIELFEQVLADLKQAGI-EVGLRHIQNSYGILNYPDl-dYDYARPGLLWMGITSddeia- 243 Eubacterium dol...
AAK58491     492 FSHLGSSDQLdTASILRTQAQITCFDDLLAGLSARNI-AYGLTHLQSSYGILNYPEk-hYDYVRPGILLTGSLSvpnep- 568 Enterococcus ca...
ABB17545     496 YTHLCAADSVdEKDIFFTNVQIESFYNLLNQLKEKGI-TIPKIHIQSSYGLLNYPEl-kCDYVRVGVSLYGVLSspndr- 572 Enterococcus fa...
Feature 1                                            #                     #                     
Q9X3P3       567 ---tkqrvSLQPILTLKAQLITKRVVAKG---EAIGYGQTAV---ANQETTVGVVSIGYCDGLPRSLSNqEFCLSYRGQS 637 Enterococcus ga...
ZP_02862048  235 ---ikldlDLKPVLSLKARVEVVRELMKN---ETVGYGLDFK---AEKKCKIAVVSIGYADGISRKLSNnNGFVLINGIK 305 Anaerofustis st...
YP_001088129 574 ---tklqlDLRPVLSLKSQVILIRKIQKD---DSFGYGRVFI---ASRDSVIAILSIGYADGIPRNLSCgKSYVIINGCR 644 Clostridium dif...
EDQ95983     248 ldnlpngmKFEAPLSLRCKVAMVKDVTPG---QSVGYGNNFT---ATETIKVATVTIGYADGLSRLVSKkDMKVLVNGKY 321 Clostridium bar...
ZP_02038521  576 ---vgtlpDLRPVLSLRAKIARIHNLEPG---DCAGYDGAFA---PSASARVAAVTIGYADGYPRSLSNgKGKVLIRGKF 646 Bacteroides cap...
AAS47779     243 -------hWQFARHRSFSPHGMEGKCFPGkgySARCYGQLRPsfqAEVCTRVATLAVGYADGFPRSVSNqGACVLLHGRR 315 Clostridium inn...
ZP_02078067  244 ---iktnpDFLPVMEWKANVSLVKTIEKG---VTVSYGRHYK---ASETRRIATLSVGYADGYPRSLSNtHAYVLIHGKR 314 Eubacterium dol...
AAK58491     569 ---tkqkiNVQPILTLKALLVDKKTVAAG---EAIGYGLGTV---FDRPATIGIVSIGYCDGVPRALSNqGFQLSYQGAL 639 Enterococcus ca...
ABB17545     573 ---tklhlDLRPVLSLKSRVILLREIKKG---ESVGYSRSFV---ANRDSLIALLPVGYADGYPRNLSCgKSYVLINGHQ 643 Enterococcus fa...
Feature 1               ##                                           #               
Q9X3P3       638 LPQIGLICMDMLLIDLSHCPTIpiESEIEILTd-------WSDTAEQVQTITNELICRIGPRVSARIK 698 Enterococcus gallinarum
ZP_02862048  306 VPIIARICMDQLFIDVSKVDDVkrDDEVVFIGqsgneeisAEDMANNLDTITNEILSRLGERLKRIYK 373 Anaerofustis stercorihomini...
YP_001088129 645 AAIVGRICMDQLAVDITDIPNVevGNTAIIIGrdnlselsASEVANNSCSISNELLSRVGRRLNVIKK 712 Clostridium difficile 630
EDQ95983     322 ARQIGNVCMDQMMIDVSGIDVKe-GDTVTLIGqdgdnylsVNQISLLSNTITNETLSVIGERVKRVYH 388 Clostridium bartlettii DSM ...
ZP_02038521  647 APVAGLICMDQLLVDVTGIPEAqeDDTVTLIGrdgeniltAEEVARDAGTITNELLSRLGERVTRVVI 714 Bacteroides capillosus ATCC...
AAS47779     316 VPIIGNICMDQMMVDITGLDGVseGDVATLIGcdgdevlsVDELSRLAHTINNETLCWISQRVPRIYK 383 Clostridium innocuum
ZP_02078067  315 AEIIGNICMDQMMVDVSDIEDVkeGDVATLFGcdgeeclsIDTLSRNAHTINNETLCRISARVPRIYK 382 Eubacterium dolichum DSM 3991
AAK58491     640 LPQIGLVCMDMLLIDLTDYPELavESSLEVISd-------WTTTAYQAQTITNELISRLGSRITSSSK 700 Enterococcus casseliflavus
ABB17545     644 APVVGKICMDQLAVDVTDIPNVktGSIATLIGkdgkeeitAPMVAESAESITNELLSRMGHRLNIIRR 711 Enterococcus faecalis

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