1RCQ,2ODO,2RJG


Conserved Protein Domain Family
PLPDE_III_AR_proteobact

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cd06827: PLPDE_III_AR_proteobact 
Click on image for an interactive view with Cn3D
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases
This subfamily is composed mainly of proteobacterial alanine racemases (EC 5.1.1.1), fold type III PLP-dependent enzymes that catalyze the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. hese 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: 143500
View PSSM: cd06827
Aligned: 64 rows
Threshold Bit Score: 496.248
Threshold Setting Gi: 198284522
Created: 8-Jul-2008
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 16 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:
  • Comment:The active site is composed of residues from both subunits of the dimer. There are two active sites in the functional dimer. Only one subunit of the dimer is shown in the 1RCQ structure.
  • Structure:1RCQ_A; Pseudomonas aeruginosa alanine racemase binds PLP and a guest substrate (D-lysine); defined at 4A contacts.
    View structure with Cn3D
  • Structure:2RJG_AB; Escherichia coli alanine racemase dimer binds two PLP molecules and two sulfate ions in two active sites; defined at 4A contacts.
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                     # #   #                                        #   
1RCQ_A         3 PARALIDLQALRHNYRLAREATG-ARALAVIKADAYGHGAVRCAEALAAeADGFAVACIEEGLELREAGirqPILLLEGF 81
gi 145589102  12 PILASIHTQAFRHNLNRVRELAPeSKIWSVIKARAYGHCFDAALKGLSS-TDGFALLDIQDAVWLREHGwegRVLLLEGL 90
gi 183599314   4 PISAVIHLQNFTHNLSVVRQHVGhAKIWSVMKADAYGHSIKHVWKALAA-SDGFAILDLNEAILLREQGwkgPILLLEGF 82
gi 37526452    4 PISATIHLDALENNLAIIRNKVGnSKIWAVVKANAYGHGLHCIWRSLDQ-ADGFALLDFHEAILLREQGwqgAILLLEGF 82
gi 197285367   4 PAKISINLDALSHNLSVIKSKAQgSKVWSVVKADAYGHGLSCVWPALSH-TDGFALIELDKAIMLREQGwvgPILLLEGF 82
gi 2506172     4 PIQASLDLQALKQNLSIVRQAAThARVWSVVKANAYGHGIERIWSAIGA-TDGFALLNLEEAITLRERGwkgPILMLEGF 82
gi 123534099   3 PSRALIDLDALRHNIRLLNSIAHnARCAAVIKADAYGHGAVEIARALKGeAPKLAVACYDEAVSLREAGvttPLLVLEGF 82
gi 149926132   4 PIRAVVKPAAISANINRIKELLGnVVMMPVVKANGYGHGLERIIDGLWQ-ADALAILEIEGAARLRCMGwnkPIVLLEGC 82
gi 166969416   4 PTVARIDLDALKHNFRRARELAGtAYAMAVVKADGYGHGIRSVADALAPeTSRFAVACIEEAIAIRGAGhrhSVVLLQGT 83
gi 31339945    4 KTTIRISSNALASNLRTIKNYANkSKVWSVIKSNAYGHTIKAALKGLKE-TSGFAVLELNEAVLLRENGwngPILLLEGF 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                        #      #                        
1RCQ_A        82 FeasELELIVAHd-FWCVVHCaWQLEAIEras-------larPLNVWLXMDsGMHRVGFFPeDFRAAHERLRas---gKV 150
gi 145589102  91 FhenELELAQELs-CDLVVHCeAQVEWLEkyie-----qghkPFSIFLKMNtGMNRLGFKPeAYRTAFHRLHa-----FG 159
gi 183599314  83 FqpdDLKVIDQYq-LTTAVHSyWQLDAIEnrh-------fqnPISVYVKLNsGMNRLGFEPpEYAQVVHRLSam---eNV 151
gi 37526452   83 FkpeDLPIIDEYq-LTTVVHShWQLEAIEaan-------lskPINIYLKLNsGMNRLGFPAdQYSAVLSLARgi---rQI 151
gi 197285367  83 FkpdDVYLLERYs-LTTVVHAdWQFEAIEqaq-------lerPINIYLKLNsGMNRLGYRPeDYQQAIQRAKgi---tNI 151
gi 2506172    83 FhaqDLEIYDQHr-LTTCVHSnWQLKALQnar-------lkaPLDIYLKVNsGMNRLGFQPdRVLTVWQQLRam---aNV 151
gi 123534099  83 YsseELADSTRWcdIEWVVHDmEQLDMLSevaplrkagpdstRMQTWIKLNtGMNRLGLPLnKLAHVAEKLQqf---pGL 159
gi 149926132  83 FdqtDLLKAMELr-CDWVVHNqNQLNDLAaiaqw----qpahKPQIFLKLNtGMNRLGFQPaQAQAAIQWLDeftlkhQW 157
gi 166969416  84 HqkdDLAECERSg-FEPVLHCqQQLSWLGag----------rSPRFWIKVNtGMNRLGFRPeELPEVMAGLEea--glKH 150
gi 31339945   83 FeesDLLEICQYk-ITTVIHNdWQLNYIKqyd-------iksPIDVYLKLNsGMNRLGFNEkDFIRTWYDLSnl---kKI 151
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1             # #                                        ###             ####            
1RCQ_A       151 AKIVMMSHFSRADEld----cPRTEEQLAAFSAASQg---LEGEISLRNSPAVLGWPkvPSDWVRPGILLYGATPferah 223
gi 145589102 160 CRMHHMTHFANADQad---qrPTVGEQQEVFERTIDg---LSGPTSLANSAAILWHRnaLGGWIRPGIMLYGASPtgiya 233
gi 183599314 152 ETVTLMTHFANSDLs------TGTDKPHAIIKQFID----GQFPVCIANSGATLWHPktHYDWVRSGVILYGASPsgrwq 221
gi 37526452  152 GQITLMSHFANADKdn---keISVTEQLNVIHSVSQg---LDISQCLANSAASLWYPqtHRDWVRPGIVLYGASPsgkwk 225
gi 197285367 152 GSIVQMSHFANADTg------LNMATQKQIIDSSMV----NDLPRCLANSAAILFEPqtHHSWVRPGIILYGVSPsgvwq 221
gi 2506172   152 GEMTLMSHFAEAEHp------DGISGAMARIEQAAEg---LECRRSLSNSAATLWHPeaHFDWVRPGIILYGASPsgqwr 222
gi 123534099 160 SVIGLMTHFACADEld----sLLQQRQWRAFQAGMQaagaNGWSYSSANSAALLQYPetHLDWVRPGIAMYGASPmadkt 235
gi 149926132 158 PTPVLMTHFANADEaeprarlPFAQRQHQILMDLKP----DHWRSSLANSAGSLNFPmlAGDIARPGIAIYGATPgpna- 232
gi 166969416 151 LAIGFVTHFACADDsd----sEMTGLQTRIFERAVAp--wPDLMRSVGNSAAHFRPNqpLYEWSRPGIMLYGASPmegkt 224
gi 31339945  152 SSLTLMSHFSLGFSt------KTVNKQMNIIRKIFKi---LNPTLCLANSTAIIFHTytHKDWIRPGIILYGILPkenkk 222
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                        
1RCQ_A       224 -pladRLRPVMTLESKVISVRDLPAGEPVGYGARYsTERRQRIGVVAMGYADGYPRHAa-DGTLVFID-------GKPGR 294
gi 145589102 234 diehaHLKAVMQLQSEIIDIQELKAGDGVGYGGRYqAPEAMRIGIVACGYADGYPRTAk-DGTPVWVSigaedgnGIVCP 312
gi 183599314 222 diadkDLRATMTLQSQIIATHEIAAGESIGYGSKFtAPYPMKIATVACGYADGYPRHAp-TGTPIWLN-------GTRCP 293
gi 37526452  226 diadiGLKAVMSLQSEIIAIQNLKAGDKIGYGSEYtAPGPMRVGTVACGYADGYPRCAm-TGTPIIVD-------GVRTQ 297
gi 197285367 222 diadfDLQPVMTFNSEVLAIQSVKKGEQIGYGSRYtAQRDMRIAVVACGYADGYPRHAp-DGTPVIVK-------GHKTQ 293
gi 2506172   223 diantGLRPVMTLSSEIIGVQTLKAGERVGYGGRYtARDEQRIGIVAAGYADGYPRHAp-TGTPVLVD-------GVRTM 294
gi 123534099 236 -gadfGLKPVMTFESRLIATRELQAGDSIGYGAAWtADAPTRMGVVAVGYGDGYPRQMq-NGAPVAVC-------GKRTK 306
gi 149926132 233 -aanyGLKAAMIFSSEIIAIQEVKQGDRVGYGSRWeASDSGRIAVVACGYADGYPRHAp-DGTPTYVE-------GHVAP 303
gi 166969416 225 -gaelGLCPAMTLQAPLITTRVVRAGESVGYGASWtASQDTRMGMVAIGYADGYPRHAg-TGTPAAVR-------GQRIR 295
gi 31339945  223 iskkfNLKPVMTLESRIISIQNIKSKEYIGYGKNYySNKSNLIGIVSCGYADGYPFSVpfSGTPVFVN-------GTRTQ 295
                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
Feature 1                                                      #               
1RCQ_A       295 LVGRVSMDMLTVDLTdhpqAGLGSRVELWGpnVPVGALAAQFGSIPYQLLCNLK-RVPRVYS 355
gi 145589102 313 IVGRVSMDMLTIDLRnapqAKIGSVVELWGdrIPVDEVARMSDTIGYELLCAVApRVPVAIK 374
gi 183599314 294 LLGTVSMDMLTIDVSecptAKIGDRVELWGknLPIDDVAQAAGTIGYELMCALAkRVPVVYE 355
gi 37526452  298 VLGTVSMDMLSVDLTpcpqAQIGSPVELWGqnLPVDDVAESSGTIGYELLCALAnRVPVSIP 359
gi 197285367 294 LVGRISMDMLTIDVTdlpdVEHGSPVELWGnqLPVDEVALACGTIGYELLCAIApRVAVEVT 355
gi 2506172   295 TVGTVSMDMLAVDLTpcpqAGIGTPVELWGkeIKIDDVAAAAGTVGYELMCALAlRVPVVTV 356
gi 123534099 307 IIGRVSMDMLTVDIShipeARIGSEVELWGgtVSADEVAGYASTISYTLFTGMTsRVPRVYI 368
gi 149926132 304 VAGRVSMDMMTIDVShipnAKVGSTVELWGehIPVDVVADRCGTIGYELLCAIApRVPFLEA 365
gi 166969416 296 LLGRVSMDMLAVDLSavpeAREGDMVELWGktVSVDEVATCAGTIGYELLTGVTsRVPRVHE 357
gi 31339945  296 IIGSVCMDMLTIDLNdcpnAKIGSKVELWGnnISINEISKLANTTSYELMCRISsRVLVKIE 357

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