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: 2-Oct-2020
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:
Feature 1                                     # #   #                                        #   
1RCQ_A         3 PARALIDLQALRHNYRLAREATG-ARALAVIKADAYGHGAVRCAEALAAeADGFAVACIEEGLELREAGirqPILLLEGF 81  Pseudomonas aer...
YP_001155699  12 PILASIHTQAFRHNLNRVRELAPeSKIWSVIKARAYGHCFDAALKGLSS-TDGFALLDIQDAVWLREHGwegRVLLLEGL 90  Polynucleobacte...
ZP_02960807    4 PISAVIHLQNFTHNLSVVRQHVGhAKIWSVMKADAYGHSIKHVWKALAA-SDGFAILDLNEAILLREQGwkgPILLLEGF 82  Providencia stu...
NP_929796      4 PISATIHLDALENNLAIIRNKVGnSKIWAVVKANAYGHGLHCIWRSLDQ-ADGFALLDFHEAILLREQGwqgAILLLEGF 82  Photorhabdus lu...
YP_002151239   4 PAKISINLDALSHNLSVIKSKAQgSKVWSVVKADAYGHGLSCVWPALSH-TDGFALIELDKAIMLREQGwvgPILLLEGF 82  Proteus mirabil...
P29012         4 PIQASLDLQALKQNLSIVRQAAThARVWSVVKANAYGHGIERIWSAIGA-TDGFALLNLEEAITLRERGwkgPILMLEGF 82  Escherichia col...
Q2SLB1         3 PSRALIDLDALRHNIRLLNSIAHnARCAAVIKADAYGHGAVEIARALKGeAPKLAVACYDEAVSLREAGvttPLLVLEGF 82  Hahella chejuen...
ZP_01914394    4 PIRAVVKPAAISANINRIKELLGnVVMMPVVKANGYGHGLERIIDGLWQ-ADALAILEIEGAARLRCMGwnkPIVLLEGC 82  Limnobacter sp....
A1U388         4 PTVARIDLDALKHNFRRARELAGtAYAMAVVKADGYGHGIRSVADALAPeTSRFAVACIEEAIAIRGAGhrhSVVLLQGT 83  Marinobacter aq...
Q8D2H8         4 KTTIRISSNALASNLRTIKNYANkSKVWSVIKSNAYGHTIKAALKGLKE-TSGFAVLELNEAVLLRENGwngPILLLEGF 82  Wigglesworthia ...
Feature 1                                                        #      #                        
1RCQ_A        82 FeasELELIVAHd-FWCVVHCaWQLEAIEras-------larPLNVWLXMDsGMHRVGFFPeDFRAAHERLRas---gKV 150 Pseudomonas aer...
YP_001155699  91 FhenELELAQELs-CDLVVHCeAQVEWLEkyie-----qghkPFSIFLKMNtGMNRLGFKPeAYRTAFHRLHa-----FG 159 Polynucleobacte...
ZP_02960807   83 FqpdDLKVIDQYq-LTTAVHSyWQLDAIEnrh-------fqnPISVYVKLNsGMNRLGFEPpEYAQVVHRLSam---eNV 151 Providencia stu...
NP_929796     83 FkpeDLPIIDEYq-LTTVVHShWQLEAIEaan-------lskPINIYLKLNsGMNRLGFPAdQYSAVLSLARgi---rQI 151 Photorhabdus lu...
YP_002151239  83 FkpdDVYLLERYs-LTTVVHAdWQFEAIEqaq-------lerPINIYLKLNsGMNRLGYRPeDYQQAIQRAKgi---tNI 151 Proteus mirabil...
P29012        83 FhaqDLEIYDQHr-LTTCVHSnWQLKALQnar-------lkaPLDIYLKVNsGMNRLGFQPdRVLTVWQQLRam---aNV 151 Escherichia col...
Q2SLB1        83 YsseELADSTRWcdIEWVVHDmEQLDMLSevaplrkagpdstRMQTWIKLNtGMNRLGLPLnKLAHVAEKLQqf---pGL 159 Hahella chejuen...
ZP_01914394   83 FdqtDLLKAMELr-CDWVVHNqNQLNDLAaiaqw----qpahKPQIFLKLNtGMNRLGFQPaQAQAAIQWLDeftlkhQW 157 Limnobacter sp....
A1U388        84 HqkdDLAECERSg-FEPVLHCqQQLSWLGag----------rSPRFWIKVNtGMNRLGFRPeELPEVMAGLEea--glKH 150 Marinobacter aq...
Q8D2H8        83 FeesDLLEICQYk-ITTVIHNdWQLNYIKqyd-------iksPIDVYLKLNsGMNRLGFNEkDFIRTWYDLSnl---kKI 151 Wigglesworthia ...
Feature 1             # #                                        ###             ####            
1RCQ_A       151 AKIVMMSHFSRADEld----cPRTEEQLAAFSAASQg---LEGEISLRNSPAVLGWPkvPSDWVRPGILLYGATPferah 223 Pseudomonas aer...
YP_001155699 160 CRMHHMTHFANADQad---qrPTVGEQQEVFERTIDg---LSGPTSLANSAAILWHRnaLGGWIRPGIMLYGASPtgiya 233 Polynucleobacte...
ZP_02960807  152 ETVTLMTHFANSDLs------TGTDKPHAIIKQFID----GQFPVCIANSGATLWHPktHYDWVRSGVILYGASPsgrwq 221 Providencia stu...
NP_929796    152 GQITLMSHFANADKdn---keISVTEQLNVIHSVSQg---LDISQCLANSAASLWYPqtHRDWVRPGIVLYGASPsgkwk 225 Photorhabdus lu...
YP_002151239 152 GSIVQMSHFANADTg------LNMATQKQIIDSSMV----NDLPRCLANSAAILFEPqtHHSWVRPGIILYGVSPsgvwq 221 Proteus mirabil...
P29012       152 GEMTLMSHFAEAEHp------DGISGAMARIEQAAEg---LECRRSLSNSAATLWHPeaHFDWVRPGIILYGASPsgqwr 222 Escherichia col...
Q2SLB1       160 SVIGLMTHFACADEld----sLLQQRQWRAFQAGMQaagaNGWSYSSANSAALLQYPetHLDWVRPGIAMYGASPmadkt 235 Hahella chejuen...
ZP_01914394  158 PTPVLMTHFANADEaeprarlPFAQRQHQILMDLKP----DHWRSSLANSAGSLNFPmlAGDIARPGIAIYGATPgpna- 232 Limnobacter sp....
A1U388       151 LAIGFVTHFACADDsd----sEMTGLQTRIFERAVAp--wPDLMRSVGNSAAHFRPNqpLYEWSRPGIMLYGASPmegkt 224 Marinobacter aq...
Q8D2H8       152 SSLTLMSHFSLGFSt------KTVNKQMNIIRKIFKi---LNPTLCLANSTAIIFHTytHKDWIRPGIILYGILPkenkk 222 Wigglesworthia ...
Feature 1                                                                                        
1RCQ_A       224 -pladRLRPVMTLESKVISVRDLPAGEPVGYGARYsTERRQRIGVVAMGYADGYPRHAa-DGTLVFID-------GKPGR 294 Pseudomonas aer...
YP_001155699 234 diehaHLKAVMQLQSEIIDIQELKAGDGVGYGGRYqAPEAMRIGIVACGYADGYPRTAk-DGTPVWVSigaedgnGIVCP 312 Polynucleobacte...
ZP_02960807  222 diadkDLRATMTLQSQIIATHEIAAGESIGYGSKFtAPYPMKIATVACGYADGYPRHAp-TGTPIWLN-------GTRCP 293 Providencia stu...
NP_929796    226 diadiGLKAVMSLQSEIIAIQNLKAGDKIGYGSEYtAPGPMRVGTVACGYADGYPRCAm-TGTPIIVD-------GVRTQ 297 Photorhabdus lu...
YP_002151239 222 diadfDLQPVMTFNSEVLAIQSVKKGEQIGYGSRYtAQRDMRIAVVACGYADGYPRHAp-DGTPVIVK-------GHKTQ 293 Proteus mirabil...
P29012       223 diantGLRPVMTLSSEIIGVQTLKAGERVGYGGRYtARDEQRIGIVAAGYADGYPRHAp-TGTPVLVD-------GVRTM 294 Escherichia col...
Q2SLB1       236 -gadfGLKPVMTFESRLIATRELQAGDSIGYGAAWtADAPTRMGVVAVGYGDGYPRQMq-NGAPVAVC-------GKRTK 306 Hahella chejuen...
ZP_01914394  233 -aanyGLKAAMIFSSEIIAIQEVKQGDRVGYGSRWeASDSGRIAVVACGYADGYPRHAp-DGTPTYVE-------GHVAP 303 Limnobacter sp....
A1U388       225 -gaelGLCPAMTLQAPLITTRVVRAGESVGYGASWtASQDTRMGMVAIGYADGYPRHAg-TGTPAAVR-------GQRIR 295 Marinobacter aq...
Q8D2H8       223 iskkfNLKPVMTLESRIISIQNIKSKEYIGYGKNYySNKSNLIGIVSCGYADGYPFSVpfSGTPVFVN-------GTRTQ 295 Wigglesworthia ...
Feature 1                                                      #               
1RCQ_A       295 LVGRVSMDMLTVDLTdhpqAGLGSRVELWGpnVPVGALAAQFGSIPYQLLCNLK-RVPRVYS 355 Pseudomonas aeruginosa
YP_001155699 313 IVGRVSMDMLTIDLRnapqAKIGSVVELWGdrIPVDEVARMSDTIGYELLCAVApRVPVAIK 374 Polynucleobacter sp. QLW-P1DMWA-1
ZP_02960807  294 LLGTVSMDMLTIDVSecptAKIGDRVELWGknLPIDDVAQAAGTIGYELMCALAkRVPVVYE 355 Providencia stuartii ATCC 25827
NP_929796    298 VLGTVSMDMLSVDLTpcpqAQIGSPVELWGqnLPVDDVAESSGTIGYELLCALAnRVPVSIP 359 Photorhabdus luminescens subsp. l...
YP_002151239 294 LVGRISMDMLTIDVTdlpdVEHGSPVELWGnqLPVDEVALACGTIGYELLCAIApRVAVEVT 355 Proteus mirabilis HI4320
P29012       295 TVGTVSMDMLAVDLTpcpqAGIGTPVELWGkeIKIDDVAAAAGTVGYELMCALAlRVPVVTV 356 Escherichia coli K12
Q2SLB1       307 IIGRVSMDMLTVDIShipeARIGSEVELWGgtVSADEVAGYASTISYTLFTGMTsRVPRVYI 368 Hahella chejuensis KCTC 2396
ZP_01914394  304 VAGRVSMDMMTIDVShipnAKVGSTVELWGehIPVDVVADRCGTIGYELLCAIApRVPFLEA 365 Limnobacter sp. MED105
A1U388       296 LLGRVSMDMLAVDLSavpeAREGDMVELWGktVSVDEVATCAGTIGYELLTGVTsRVPRVHE 357 Marinobacter aquaeolei VT8
Q8D2H8       296 IIGSVCMDMLTIDLNdcpnAKIGSKVELWGnnISINEISKLANTTSYELMCRISsRVLVKIE 357 Wigglesworthia glossinidia endosy...

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