Conserved Protein Domain Family
PLPDE_III_AR2

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cd06826: PLPDE_III_AR2 
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme, Alanine Racemase 2
This subfamily is composed of bacterial alanine racemases (EC 5.1.1.1) with similarity to Yersinia pestis and Vibrio cholerae alanine racemase (AR) 2. ARs catalyze the interconversion between L- and D-alanine, an essential component of the peptidoglycan layer of bacterial cell walls. These proteins are similar to other bacterial ARs and are fold type III PLP-dependent enzymes containing contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist 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. Homodimer formation and the presence of the PLP cofactor are required for catalytic activity.
Statistics
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PSSM-Id: 143499
View PSSM: cd06826
Aligned: 11 rows
Threshold Bit Score: 558.497
Threshold Setting Gi: 88800370
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                                       # #   #                                         #
YP_857116     41 NAWLEVDLGAFEHNIQTLKDRLgdkgPKICAIMKADAYGHGIDLLVPSVVKaGIPCIGIASNEEARVAREKGFtGRLMRV 120 Aeromonas hydro...
ZP_02970478   34 HAWLEISQPAFEHNLAEMKKLVgp-nTQVCAVMKADAYGHGIAMLIPAISRaAIPYVGVTSNEEAAKARAAGYkGKLMRL 112 bacterium Ellin514
NP_745855     43 NAWVEVSASALQHNIRTLQAELag-kSKLCAVLKADAYGHGIGLVMPSIIAqGVPCVAVASNEEARVVRASGFtGQLVRV 121 Pseudomonas put...
NP_799227     28 NAWLEIDTQAFSNNIQLLQKDLkg-nTQICAIMKADAYGNGIAGLMPSIIAnNVACVGITSNEEARVVREHGFeGKIMRV 106 Vibrio parahaem...
Q8ZFL4        29 NAWLEISQGALDFNTKKMLTLLdn-kSTLCAILKGDAYGHDLTLVTPVMLKnNVQCIGVASNQELKTVRDLGFtGQLIRV 107 Yersinia pestis
Q9KSE5        27 NSWLEISLGQFQSNIEQFKSHMna-nTKICAIMKADAYGNGIRGLMPTIIAqGIPCVGVASNAEARAVRESGFkGELIRV 105 Vibrio cholerae
YP_001675043  41 NSWLEVNLTQFDSNIKELKNHIqs-nVKVCAIMKADAYGNGIAGLMPTVLAnNIPCIGVTSNEEIRIVRDAGFrGSLIRV 119 Shewanella hali...
YP_001084387  25 NAWIEVDTQAFEDNIKRTNQLLng-kTQLCVVMKANAYGHSIDLLMPSVMKlNVSCIGITSNAEAAMVRKHGYkGKITRL 103 Acinetobacter b...
NP_859997     39 NSFMEVDIKAFKNNIKVAKKIAg--nAKVCAVLKANAYGAGISKVLPTIIEeKIPCVAITSNEEARVIRKMKYtGEILRI 116 Helicobacter he...
ZP_01056961    8 SAWCEISPAQISQNLRHTLDRLpa-qTRLCAVIKADAYGHGIENVVPALLAqGVRHIGISANSEARAVRAAGFtGAILRL 86  Roseobacter sp....
ZP_01115936    8 TAWCEILTDRIANNLSLALSLLpe-hAEFCAVLKADAYGHGIAEVAAIVCEhRIKTVGITSNAEARLVREAGFeGTILRL 86  Reinekea sp. ME...
Feature 1                                                    #       #                           
YP_857116    121 RAATpaEVEQALPYkMEELIGSlVSAQGIADIAqrhhtnIPVHIALNSAGMSRNGIDlrLADSKEDALAMLklkGITPVG 200 Aeromonas hydro...
ZP_02970478  113 RTATpaEIEAALPYdIEELLGSlTLAEDVSVLAhrhhiiLRYHLALNSAGMSRNGIElkADAGKADALALLrlpNLRIVG 192 bacterium Ellin514
NP_745855    122 RLASlsELEDGLQYdMEELVGSaEFARQADAIAarhgktLRIHMALNSSGMSRNGVEmaTWSGRGEALQITdqkHLKLVA 201 Pseudomonas put...
NP_799227    107 RAASrnEIENGVQYeIEELIGTkMQADQIIEIAynyntvIPVHLALNTSGMGRNGLDltTYEGQVEGVEIAsdpNLKIVG 186 Vibrio parahaem...
Q8ZFL4       108 RSATlkEMQQAMAYdVEELIGDkTVAEQLNNIAklngkvLRIHLALNSAGMSRNGLEvsKARGLNDAKTIAglkNLTIVG 187 Yersinia pestis
Q9KSE5       106 RSASlsEMSSALDLnIEELIGThQQALDLAELAkqsgktLKVHIALNDGGMGRNGIDmtTEAGKKEAVSIAtqpSLSVVG 185 Vibrio cholerae
YP_001675043 120 RSASiaEISDTLQYdVEEFVGDaNQATLLSAMAakldkpLKVHLVLNSGGMGRNGVDvsTQSGLNEAVQIAttaDLDVVG 199 Shewanella hali...
YP_001084387 104 RTATdsEIINAHALnIEELLGNyDQATRISKWAeannttVHYSLALNSGGMDRNGLEmsTAQGKEQAVAITklpNLKIDG 183 Acinetobacter b...
NP_859997    117 RTATmgEIKDGLKYnITEVLGNlDQAKKVDSLAktigkkLPIHIKLNSGGMDRNGIDlsTDKGKESAVKLAtlpHLKIKG 196 Helicobacter he...
ZP_01056961   87 RTATpeEVEDALSYnVQELIGSvGGMQAILNQLgar-glPPVHLSLNAGGMSRDGVElsTQQGRTDCGRILelgAERIVG 165 Roseobacter sp....
ZP_01115936   87 RTATpsEIAGAVADrVQEQVSSlYTAEVIDSLTeh---sEGVHLAINAGGMSRDGLElnERDGHDTCQRIVdllGDRIVG 163 Reinekea sp. ME...
Feature 1           #                                       ##              ####                 
YP_857116    201 IMTHFPVEEKEDVKMGLAQFKLDSQWLLeagkLDRSKITIHAANSFATLEVPDayFDMVRPGGLLYGDSIps-ytEYKRV 279 Aeromonas hydro...
ZP_02970478  193 IMTHFPVEEVADVRAGLAAFNTESAWVIheghLDRSKLLLHTANSFATLEVPEarLDLVRPGGALYGDTVps-htEYQRV 271 bacterium Ellin514
NP_745855    202 LMTHFAVEDKDDVRKGLAAFNEQTDWLIkharLDRSKLTLHAANSFATLEVPEarLDMVRTGGALFGDTVpa-rtEYKRA 280 Pseudomonas put...
NP_799227    187 MMTHFPNEGLDEIRRKVDRFKVETKWLMdsagLKRKDITLHVANSYITLNLPEahLDMVRPGGMLYGDYPat--lPYERI 264 Vibrio parahaem...
Q8ZFL4       188 IMSHYPVEDASEIKADLARFQQQAKDVIavtgLKREKIKLHVANTFATLAVPDswLDMVRVGGVFYGDTIas--tEYKRV 265 Yersinia pestis
Q9KSE5       186 IMTHFPNYNADEVRAKLAQFKESSTWLMqqanLKREEITLHVANSYTALNVPEaqLDMVRPGGVLFGDLPtn--pEYPSI 263 Vibrio cholerae
YP_001675043 200 IMTHFPSYDRDDVLVKSKSFYNSALNIIeesgLKRDSVTIHSGNSYVALNVPEahFDMVRPGGVLYGDQPtn--pEFPSI 277 Shewanella hali...
YP_001084387 184 IMTHYAVEDEKYVRERLAQFNEQTAWLIkkakLNRKELTLHTANSFATVNVPEshLDMVRAGAIIYGDFPnh--pEYKRM 261 Acinetobacter b...
NP_859997    197 LMTHFPYDDTSKVKENLKHFEEDTDFLIskakLDRNKLVLHAAASYAAVQVPQsrLDMIRPGKLIYGYGGgdenlPIQQI 276 Helicobacter he...
ZP_01056961  166 LCTHFPSNSFDELADNIARFQQDLAWVFanssLRREDILTHAGSTLTLAAGQDpkVDMMRCGAILFGIAGag--pEFRPA 243 Roseobacter sp....
ZP_01115936  164 ICTHHPSGSEQDLQLSDQHFRSDLNWIFsntaLKREQVNVHAGSSLSLISSTPieTDFYRCGAILYGILKpe--lGFEHT 241 Reinekea sp. ME...
Feature 1                            #                  #                           ##           
YP_857116    280 MAFKTQVASVNHYPAGNTVGYDRTFTLKRDSWLANLPLGYSDGYRRAlsNKAYVLIQGQKVPVVGKTSMNTIMVDVTDLk 359 Aeromonas hydro...
ZP_02970478  272 LSFKSRVAAINAYPKGNTICYDRTFTLTRDSRLANIPVGYSDGYRRVfsNKANVLIHGHRCPIVGRVTMNTVMVDVTDLa 351 bacterium Ellin514
NP_745855    281 MQFKSHVAAVHSYPAGNTVGYDRTFTLARDSRLANITVGYSDGYRRVftNKGHVLINGHRVPVVGKVSMNTLMVDVTDFp 360 Pseudomonas put...
NP_799227    265 VSFKTRIASLHFFPAGSTIGYGSTKVLERDSILANLPIGYSDGFARSlsNKADVLINGQRARVMGKASMNTTMVDVTDIi 344 Vibrio parahaem...
Q8ZFL4       266 MTFKSNIASLNNYPKGGTVGYDRTYTLKRDSLLANIPVGYADGYRRVfsNAGHVIIQGQRLPVLGKTSMNTVIVDVTDLk 345 Yersinia pestis
Q9KSE5       264 VSFKTRVSSLHHLPKDSTVGYDSTFTTSRDSVLANLPVGYSDGYPRKmgNKAEVLINGQRAKVVGVTSMNTTVVDVTEIk 343 Vibrio cholerae
YP_001675043 278 VTFKTRIASLVDLPKGATVGYDSTIKLERESLLANLPVGYSDSFPRKmgNTADVLVNGQRAKVMGVISMNTSMIDVTDLs 357 Shewanella hali...
YP_001084387 262 MAFKTQIAAVNNYLKGSTVGYDQTYTLTRDSKLANLPVGYSDGYRRSfsNKAFVLVNGQKAPVVGRVSMNTVMVDVTDIp 341 Acinetobacter b...
NP_859997    277 MSLKSQVAVINEYPKGSKVSYDGTHTLTRDSKLANIPVGYYDGYAKSlsNQGKVLIRGHKVPVVGRVTKNTFMVDVTDYp 356 Helicobacter he...
ZP_01056961  244 MQLKSRVISLGTYPKGSTVGYDRTCVLPDDRLLASVAMGYANGYSRQmsKGAQVLIRGQICPVMGAISMNTLVVDVTEVp 323 Roseobacter sp....
ZP_01115936  242 MQLKAQITNITTYPQGSTIGYDRTTTLTRDSRVANIALGYANGFRRNyfGRSHVLIRGQLVPVLGKVSMNTIVADVTDIp 321 Reinekea sp. ME...
Feature 1                                           #            
YP_857116    360 gvkpGDEVVLFGRQGEAEVkQADLEEYNGALLADMYTIWGYTNPKKIK 407 Aeromonas hydrophila subsp. hydrophila ATCC 7966
ZP_02970478  352 dvqkGDEVVLFGKQGAAEItQTELEDISGTILVELYAVWGRVNPTFLV 399 bacterium Ellin514
NP_745855    361 dvkgGNEVVLFGKQAGGEItQAEMEEINGALLADLYTVWGNSNPKILV 408 Pseudomonas putida KT2440
NP_799227    345 gvqaNDEVVVFGRQGFEEItAEETEEKSGRILPEHYTIWGATNPRVYR 392 Vibrio parahaemolyticus RIMD 2210633
Q8ZFL4       346 kvslGDEVVLFGKQGNAEIqAEEIEDLSGALFTEMSILWGATNKRILV 393 Yersinia pestis
Q9KSE5       344 gvlpGQEVVLFGQQQKQSIaVSEMENNAELIFPELYTLWGTSNPRFYV 391 Vibrio cholerae
YP_001675043 358 gvkeGDEVVLFGYQGKESIlAPEFEKNADVIFPEIYTQWGQTNPRIYV 405 Shewanella halifaxensis HAW-EB4
YP_001084387 342 eakaGDEVVLFGRQGNAEVqSSDLTSLTGHILTEAYTPWSNSNPQVIK 389 Acinetobacter baumannii ATCC 17978
NP_859997    357 dikaGDEVVLFGKQCGNEItQAEFEKGTGTILSETLGYWGSANPIFIK 404 Helicobacter hepaticus ATCC 51449
ZP_01056961  324 gvaiGDEVVAFGSQGGCEIgAAAIEGGSGTILADLFSDWGQRNPRLTK 371 Roseobacter sp. MED193
ZP_01115936  322 vvevEDEVVIFGHQGTGKIdIKRIEMQADTIMADIYAEWGQRNPRVYI 369 Reinekea sp. MED297

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