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: 17-Jan-2013
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:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                       # #   #                                         #
gi 117619060  41 NAWLEVDLGAFEHNIQTLKDRLgdkgPKICAIMKADAYGHGIDLLVPSVVKaGIPCIGIASNEEARVAREKGFtGRLMRV 120
gi 186460177  34 HAWLEISQPAFEHNLAEMKKLVgp-nTQVCAVMKADAYGHGIAMLIPAISRaAIPYVGVTSNEEAAKARAAGYkGKLMRL 112
gi 26990430   43 NAWVEVSASALQHNIRTLQAELag-kSKLCAVLKADAYGHGIGLVMPSIIAqGVPCVAVASNEEARVVRASGFtGQLVRV 121
gi 28899622   28 NAWLEIDTQAFSNNIQLLQKDLkg-nTQICAIMKADAYGNGIAGLMPSIIAnNVACVGITSNEEARVVREHGFeGKIMRV 106
gi 20137378   29 NAWLEISQGALDFNTKKMLTLLdn-kSTLCAILKGDAYGHDLTLVTPVMLKnNVQCIGVASNQELKTVRDLGFtGQLIRV 107
gi 20137517   27 NSWLEISLGQFQSNIEQFKSHMna-nTKICAIMKADAYGNGIRGLMPTIIAqGIPCVGVASNAEARAVRESGFkGELIRV 105
gi 167624749  41 NSWLEVNLTQFDSNIKELKNHIqs-nVKVCAIMKADAYGNGIAGLMPTVLAnNIPCIGVTSNEEIRIVRDAGFrGSLIRV 119
gi 126641403  25 NAWIEVDTQAFEDNIKRTNQLLng-kTQLCVVMKANAYGHSIDLLMPSVMKlNVSCIGITSNAEAAMVRKHGYkGKITRL 103
gi 32265965   39 NSFMEVDIKAFKNNIKVAKKIAg--nAKVCAVLKANAYGAGISKVLPTIIEeKIPCVAITSNEEARVIRKMKYtGEILRI 116
gi 86138387    8 SAWCEISPAQISQNLRHTLDRLpa-qTRLCAVIKADAYGHGIENVVPALLAqGVRHIGISANSEARAVRAAGFtGAILRL 86
gi 88800370    8 TAWCEILTDRIANNLSLALSLLpe-hAEFCAVLKADAYGHGIAEVAAIVCEhRIKTVGITSNAEARLVREAGFeGTILRL 86
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                    #       #                           
gi 117619060 121 RAATpaEVEQALPYkMEELIGSlVSAQGIADIAqrhhtnIPVHIALNSAGMSRNGIDlrLADSKEDALAMLklkGITPVG 200
gi 186460177 113 RTATpaEIEAALPYdIEELLGSlTLAEDVSVLAhrhhiiLRYHLALNSAGMSRNGIElkADAGKADALALLrlpNLRIVG 192
gi 26990430  122 RLASlsELEDGLQYdMEELVGSaEFARQADAIAarhgktLRIHMALNSSGMSRNGVEmaTWSGRGEALQITdqkHLKLVA 201
gi 28899622  107 RAASrnEIENGVQYeIEELIGTkMQADQIIEIAynyntvIPVHLALNTSGMGRNGLDltTYEGQVEGVEIAsdpNLKIVG 186
gi 20137378  108 RSATlkEMQQAMAYdVEELIGDkTVAEQLNNIAklngkvLRIHLALNSAGMSRNGLEvsKARGLNDAKTIAglkNLTIVG 187
gi 20137517  106 RSASlsEMSSALDLnIEELIGThQQALDLAELAkqsgktLKVHIALNDGGMGRNGIDmtTEAGKKEAVSIAtqpSLSVVG 185
gi 167624749 120 RSASiaEISDTLQYdVEEFVGDaNQATLLSAMAakldkpLKVHLVLNSGGMGRNGVDvsTQSGLNEAVQIAttaDLDVVG 199
gi 126641403 104 RTATdsEIINAHALnIEELLGNyDQATRISKWAeannttVHYSLALNSGGMDRNGLEmsTAQGKEQAVAITklpNLKIDG 183
gi 32265965  117 RTATmgEIKDGLKYnITEVLGNlDQAKKVDSLAktigkkLPIHIKLNSGGMDRNGIDlsTDKGKESAVKLAtlpHLKIKG 196
gi 86138387   87 RTATpeEVEDALSYnVQELIGSvGGMQAILNQLgar-glPPVHLSLNAGGMSRDGVElsTQQGRTDCGRILelgAERIVG 165
gi 88800370   87 RTATpsEIAGAVADrVQEQVSSlYTAEVIDSLTeh---sEGVHLAINAGGMSRDGLElnERDGHDTCQRIVdllGDRIVG 163
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1           #                                       ##              ####                 
gi 117619060 201 IMTHFPVEEKEDVKMGLAQFKLDSQWLLeagkLDRSKITIHAANSFATLEVPDayFDMVRPGGLLYGDSIps-ytEYKRV 279
gi 186460177 193 IMTHFPVEEVADVRAGLAAFNTESAWVIheghLDRSKLLLHTANSFATLEVPEarLDLVRPGGALYGDTVps-htEYQRV 271
gi 26990430  202 LMTHFAVEDKDDVRKGLAAFNEQTDWLIkharLDRSKLTLHAANSFATLEVPEarLDMVRTGGALFGDTVpa-rtEYKRA 280
gi 28899622  187 MMTHFPNEGLDEIRRKVDRFKVETKWLMdsagLKRKDITLHVANSYITLNLPEahLDMVRPGGMLYGDYPat--lPYERI 264
gi 20137378  188 IMSHYPVEDASEIKADLARFQQQAKDVIavtgLKREKIKLHVANTFATLAVPDswLDMVRVGGVFYGDTIas--tEYKRV 265
gi 20137517  186 IMTHFPNYNADEVRAKLAQFKESSTWLMqqanLKREEITLHVANSYTALNVPEaqLDMVRPGGVLFGDLPtn--pEYPSI 263
gi 167624749 200 IMTHFPSYDRDDVLVKSKSFYNSALNIIeesgLKRDSVTIHSGNSYVALNVPEahFDMVRPGGVLYGDQPtn--pEFPSI 277
gi 126641403 184 IMTHYAVEDEKYVRERLAQFNEQTAWLIkkakLNRKELTLHTANSFATVNVPEshLDMVRAGAIIYGDFPnh--pEYKRM 261
gi 32265965  197 LMTHFPYDDTSKVKENLKHFEEDTDFLIskakLDRNKLVLHAAASYAAVQVPQsrLDMIRPGKLIYGYGGgdenlPIQQI 276
gi 86138387  166 LCTHFPSNSFDELADNIARFQQDLAWVFanssLRREDILTHAGSTLTLAAGQDpkVDMMRCGAILFGIAGag--pEFRPA 243
gi 88800370  164 ICTHHPSGSEQDLQLSDQHFRSDLNWIFsntaLKREQVNVHAGSSLSLISSTPieTDFYRCGAILYGILKpe--lGFEHT 241
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                            #                  #                           ##           
gi 117619060 280 MAFKTQVASVNHYPAGNTVGYDRTFTLKRDSWLANLPLGYSDGYRRAlsNKAYVLIQGQKVPVVGKTSMNTIMVDVTDLk 359
gi 186460177 272 LSFKSRVAAINAYPKGNTICYDRTFTLTRDSRLANIPVGYSDGYRRVfsNKANVLIHGHRCPIVGRVTMNTVMVDVTDLa 351
gi 26990430  281 MQFKSHVAAVHSYPAGNTVGYDRTFTLARDSRLANITVGYSDGYRRVftNKGHVLINGHRVPVVGKVSMNTLMVDVTDFp 360
gi 28899622  265 VSFKTRIASLHFFPAGSTIGYGSTKVLERDSILANLPIGYSDGFARSlsNKADVLINGQRARVMGKASMNTTMVDVTDIi 344
gi 20137378  266 MTFKSNIASLNNYPKGGTVGYDRTYTLKRDSLLANIPVGYADGYRRVfsNAGHVIIQGQRLPVLGKTSMNTVIVDVTDLk 345
gi 20137517  264 VSFKTRVSSLHHLPKDSTVGYDSTFTTSRDSVLANLPVGYSDGYPRKmgNKAEVLINGQRAKVVGVTSMNTTVVDVTEIk 343
gi 167624749 278 VTFKTRIASLVDLPKGATVGYDSTIKLERESLLANLPVGYSDSFPRKmgNTADVLVNGQRAKVMGVISMNTSMIDVTDLs 357
gi 126641403 262 MAFKTQIAAVNNYLKGSTVGYDQTYTLTRDSKLANLPVGYSDGYRRSfsNKAFVLVNGQKAPVVGRVSMNTVMVDVTDIp 341
gi 32265965  277 MSLKSQVAVINEYPKGSKVSYDGTHTLTRDSKLANIPVGYYDGYAKSlsNQGKVLIRGHKVPVVGRVTKNTFMVDVTDYp 356
gi 86138387  244 MQLKSRVISLGTYPKGSTVGYDRTCVLPDDRLLASVAMGYANGYSRQmsKGAQVLIRGQICPVMGAISMNTLVVDVTEVp 323
gi 88800370  242 MQLKAQITNITTYPQGSTIGYDRTTTLTRDSRVANIALGYANGFRRNyfGRSHVLIRGQLVPVLGKVSMNTIVADVTDIp 321
                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*...
Feature 1                                           #            
gi 117619060 360 gvkpGDEVVLFGRQGEAEVkQADLEEYNGALLADMYTIWGYTNPKKIK 407
gi 186460177 352 dvqkGDEVVLFGKQGAAEItQTELEDISGTILVELYAVWGRVNPTFLV 399
gi 26990430  361 dvkgGNEVVLFGKQAGGEItQAEMEEINGALLADLYTVWGNSNPKILV 408
gi 28899622  345 gvqaNDEVVVFGRQGFEEItAEETEEKSGRILPEHYTIWGATNPRVYR 392
gi 20137378  346 kvslGDEVVLFGKQGNAEIqAEEIEDLSGALFTEMSILWGATNKRILV 393
gi 20137517  344 gvlpGQEVVLFGQQQKQSIaVSEMENNAELIFPELYTLWGTSNPRFYV 391
gi 167624749 358 gvkeGDEVVLFGYQGKESIlAPEFEKNADVIFPEIYTQWGQTNPRIYV 405
gi 126641403 342 eakaGDEVVLFGRQGNAEVqSSDLTSLTGHILTEAYTPWSNSNPQVIK 389
gi 32265965  357 dikaGDEVVLFGKQCGNEItQAEFEKGTGTILSETLGYWGSANPIFIK 404
gi 86138387  324 gvaiGDEVVAFGSQGGCEIgAAAIEGGSGTILADLFSDWGQRNPRLTK 371
gi 88800370  322 vvevEDEVVIFGHQGTGKIdIKRIEMQADTIMADIYAEWGQRNPRVYI 369

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