1L6G,1RCQ,1SFT,1XFC,2DY3,3CO8,2VD9,1VFH,2RJG,2ODO


Conserved Protein Domain Family
PLPDE_III_AR

?
cd00430: PLPDE_III_AR 
Click on image for an interactive view with Cn3D
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase
This family includes predominantly bacterial alanine racemases (AR), some serine racemases (SerRac), and putative bifunctional enzymes containing N-terminal UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase (murF) and C-terminal AR domains. These proteins are fold type III PLP-dependent enzymes that play essential roles in peptidoglycan biosynthesis. AR catalyzes the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. SerRac converts L-serine into its D-enantiomer (D-serine) for peptidoglycan synthesis. murF catalyzes the addition of D-Ala-D-Ala to UDPMurNAc-tripeptide, the final step in the synthesis of the cytoplasmic precursor of bacterial cell wall peptidoglycan. Members of this family contain 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. AR and other members of this family require dimer formation and the presence of the PLP cofactor for catalytic activity. Fungal ARs and eukaryotic serine racemases, which are fold types I and II PLP-dependent enzymes respectively, are excluded from this family.
Statistics
?
PSSM-Id: 143481
View PSSM: cd00430
Aligned: 162 rows
Threshold Bit Score: 251.647
Threshold Setting Gi: 148557035
Created: 6-Mar-2002
Updated: 2-Oct-2020
Structure
?
Program:
Drawing:
Aligned Rows:
 
Conserved site includes 18 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:1L6G_AB; Geobacillus stearothermophilus alanine racemase dimer binds two cofactor-substrate complexes, PLP-D-alanine; defined at 4A contacts.
    View structure with Cn3D

Sequence Alignment
?
Format: Row Display: Color Bits: Type Selection:
Feature 1                                      # #   #                                           
1L6G_A         7 DTWAEVDLDAIYDNVENLRRLLpddTHIMAVVKANAYGHGDVQVARTALEa-gASRLAVAFLDEALALREKGie------ 79  Geobacillus ste...
1RCQ_A         3 PARALIDLQALRHNYRLAREATg--ARALAVIKADAYGHGAVRCAEALAAe--ADGFAVACIEEGLELREAGir------ 72  Pseudomonas aer...
YP_897976      4 SPIVEINSKLVKSNIEYLRNKNp-hSKIMFIVKANAYGVGIENIYKVTNNl--VDAYGIARIEEYYVLKSLGct------ 74  Francisella tul...
EAN90745       4 STYVEVCLRNIAYNVECIRRIAg-kAELIPMVKGNAYGHGMGKVSEYLHNvcgVHTFGVASLGEALELIESQpsiaekaq 82  Trypanosoma cruzi
ZP_02088525    9 SCWLEISLDNVRDNFFAFKKMVgpdVKVMPAVKANAYGHGIVPCGKELEAc-gADYLGMGSISEAIKLRENGvk------ 81  Clostridium bol...
YP_001264617  20 GNAFQLDERAFHANVEQVRRLLppgTKIYQCAKGDGYGVGVERIVCLGVRa-gVDGFCLGTPEEALRAKCVAag------ 92  Sphingomonas wi...
EDY37343     459 PRRLLVDLDAIRDNITRFRALCgpeVAILAVLKAWAYGTELPRLAAALQDs-gIDWIGVSAADEGAVIRRAGvh------ 531 Cyanobium sp. P...
ZP_01733546  417 ETILEINLDAISHNLNFYKSKLkhdTKIMVMVKAFGYGNGGYEIAKLLEHh-kVDYLGVAFADEGIELRKAGit------ 489 Flavobacteria b...
NP_905309    462 ETALRINLSAIIHNLNFYRNLVpsgTKTICMVKAQGYGVGSYELVKTLQEh-rVDYIAVAVADEGKELRERGig------ 534 Porphyromonas g...
ACD54585      23 SSIMRIDLNAMRCNLEQFCSVVastTKMMMIVKASAYGVGIKKIGKWAEKtrlIDYLAVVYTAEGVELRKANih------ 96  Adineta vaga
Feature 1             #                                                           #      #       
1L6G_A        80 aPILVLGAsr------paDAALAAQq--rIALTVFRs----DWLEEASalys----gpfpIHFHLXMDtGMGRLGVKdee 143 Geobacillus ste...
1RCQ_A        73 qPILLLEGffe-----asELELIVAh--dFWCVVHCa----WQLEAIErasl-----arpLNVWLXMDsGMHRVGFFpe- 135 Pseudomonas aer...
YP_897976     75 kDIIFLSGiy------aeCFDFKIPk--nVIPILGNellikDYIKYEDdk---------sKQVMLDFDcGMGRFGFYkd- 136 Francisella tul...
EAN90745      83 nEIFVFSDtevlnegcqsYYQPCGRwavrLTPILGTl----PQLKAFCasna-----fnnTKLCLKLEtGMNRLGLRfd- 152 Trypanosoma cruzi
ZP_02088525   82 mPLLVFASnti-----eeVAELYIQy--hLIPTILSe----REAKAISdaa------sspVPVFVKIDtGRGRLGVNae- 143 Clostridium bol...
YP_001264617  93 rPVLLFAGcd------paALGEMVEa--gIIVSISSv----EGCEALLrsg-------atGDVFFKLDcGFRRYGLNep- 152 Sphingomonas wi...
EDY37343     532 rPVLVMLMdp-------dEVDKAVRw--rVTPLIYSl----PFAQALVrtlqs---mgahLEVHLEIEtGMGRLGVApe- 594 Cyanobium sp. P...
ZP_01733546  490 tPIMVLNPen-------sSFRAMIAy--nLEPEIYSi----TGLQAFLkiaqe--qnisnYPIHIKLDtGMHRLGFEmp- 553 Flavobacteria b...
NP_905309    535 mPIVVMNPqr-------nAFQTLIDy--gLEPEIYSf----ALLASFSetvvr--nglvgYPVHIKIDtGMHRLGFLps- 598 Porphyromonas g...
ACD54585      97 lPIMIINIdk-------eDFKICQEy--nLELVIYSi----SLLQQLMiwlekntqicsfPSIHVKINtGMNRLGLDid- 162 Adineta vaga
Feature 1                                #                                           ##          
1L6G_A       144 eTKRIVALIErh--pHFVLEGLYTHFATADEvn----tDYFSYQYTRFLHMLEwlp---srPPLVHCANSAASLRFPdrt 214 Geobacillus ste...
1RCQ_A       136 dFRAAHERLRas--gKVAKIVMMSHFSRADEld----cPRTEEQLAAFSAASQg------lEGEISLRNSPAVLGWPkvp 203 Pseudomonas aer...
YP_897976    137 dFIKHLYKLKn---aGFSNITLFSHIPTGYNg-----fDKSKKYIDKILSLATq------tKLKYTFSNSPVSLFSYdfq 202 Francisella tul...
EAN90745     153 eLEEAVPILKq----RGGVDLLLQHFGIAGSve---rlAETLNHYEAFKNAKKflhdsgveVRATSVSNSGAVEQRIgle 225 Trypanosoma cruzi
ZP_02088525  144 eFPDFYRKITal--pNLYVEGVYSHMAAVNWpdv--saEYGLWQYERFSAAIEvlgeegkkIPFCQLANTPGGIALPeir 219 Clostridium bol...
YP_001264617 153 dLRTVLARVRrq--sSVRCIGAYSHFGSRADeivdgglPLFDRLTRLIEDAVQr-------PIETMVASSTLILQRPglg 223 Sphingomonas wi...
EDY37343     595 eALAAARLLRds--gVVTVTGVMTHLAGADDpa---adDETRAQLERFDAVMArlhqelgtPLLVHAAATSGAVRFPqsr 669 Cyanobium sp. P...
ZP_01733546  554 qMDELVSLLKnn--nFIKIKSVFSHLAASDDkk---lnEFTQLQFQRFDEMYNaiaavlsyIPIRHILNTSGIFNYPekq 628 Flavobacteria b...
NP_905309    599 dMTRLGEILAkd--aGLSIRSVFTHLAGADDpd---ldDFTRSQLLSFDAAFAslssllgyIPLRHVLNTAGVERFAdyh 673 Porphyromonas g...
ACD54585     163 eIPVFLNILFkytrcRLMVKSIYTHVAASDDpq---edQYTADQTRAYLSSVHiletglgyTVLKHMCNSMGILRHPnlh 239 Adineta vaga
Feature 1            ####                                            #                   #       
1L6G_A       215 FNMVRFGIAMYGLAPspgikpllpypLKEAFSLHSRLVHVKKLQPG--EKVSYGATYt-AQTEEWIGTIPIGYADGWLRr 291 Geobacillus ste...
1RCQ_A       204 SDWVRPGILLYGATPferah-pladrLRPVMTLESKVISVRDLPAG--EPVGYGARYs-TERRQRIGVVAMGYADGYPRh 279 Pseudomonas aer...
YP_897976    203 QEYIRPCSAILGYDQep-------qeIKFSLALKACIISIRDIPKG--QYISYANEYf-CDRDTTVAILNIGYADGLGCk 272 Francisella tul...
EAN90745     226 ETYIRPGIMLYGPRSvtsk---nlwnGKFASCFYTKVLHHFPLRKG--EGVGYDLTP--VKADSVIVMLPIGYADGFLCt 298 Trypanosoma cruzi
ZP_02088525  220 MTGVCPGRAIWGYSPldrre-ghpqlKHPITAWKSRLIHINQVCGGk-FGENYKAVK--LDSPKRIGIMAGGLGDGISPk 295 Clostridium bol...
YP_001264617 224 HSAVDPGRLLYGMMAagpe---mppfQPIVPRISSRLLQVTPFDEArlLTVGYADKTa-IPAGGATGVFPLGWIDGLSAh 299 Sphingomonas wi...
EDY37343     670 YGMVRLGLGLFGLHPspava--eaieLELAVAFISRLVQVREYGRG--QRIGYNGTYvvSAERQRIGIVAAGYNDGVPWr 745 Cyanobium sp. P...
ZP_01733546  629 MEMARLGIGLYGIGNseqe----lqtLENVSTLKTIISQIREVLPG--ESIGYSRKYs-VTKKMKVATIPIGYADGIKRa 701 Flavobacteria b...
NP_905309    674 ADMIRLGIGLYGVTAsgv------qgLRPVATLMTTILQIKDISSS--DTVGYGRKGr-VQQPSRIAIIPIGYADGLDRr 744 Porphyromonas g...
ACD54585     240 FDMVRVGGGLYGAAEcflp---ymstLLPAISMISTVTQVRHVKKD--STIGYNRRGr-VNRDSFIGILRLGYADGLRRq 313 Adineta vaga
Feature 1                                 ##                                                     
1L6G_A       292 l--qhFHVLVdgQKAPIVGRi----CMDQCMIrlpg------------plpvGTKVTLIGrqgd-evisIDDVARHLETI 352 Geobacillus ste...
1RCQ_A       280 aa-dgTLVFIdgKPGRLVGRv----SMDMLTVdltdh----------pqaglGSRVELWGpn-----vpVGALAAQFGSI 339 Pseudomonas aer...
YP_897976    273 ih-kdSYLIIkdTKCPILAI-----NMDYLYIdisaik---------hqlkiLDMIELFGpns----lsLEQHASMYNIT 333 Francisella tul...
EAN90745     299 ykgmpIKVTPedAAEPIIGTvhgriNMDMAAVvvypeevgknignimaavkkESRIHVWGd-------dIEEKAVSVGAI 371 Trypanosoma cruzi
ZP_02088525  296 l--agGYVLLhgRKAKVASTi----SLEHTIIdladf----------pdakvGDEIVILGrqgdeeitmEQRMEEWGRGV 359 Clostridium bol...
YP_001264617 300 r--gfGEVLIrgTRLSVVAR-----TLQHSIVnlsgl----------sdvrvGDEVVLVGaqgd-eqigLEAMASAQGMS 361 Sphingomonas wi...
EDY37343     746 fs-nrGEVMIqgRRLAVLGRv----SMDSMAVdldpl----------peatvGDEVLIFGayeg-qvlrPEQAALQAGTI 809 Cyanobium sp. P...
ZP_01733546  702 wgnekGYVIInnEKATILGSi----CMDMMMVdvtni-----------scntGDEVIVFGkn-----pkVTEMASVIGTI 761 Flavobacteria b...
NP_905309    745 lscgvGEVLVrgHRCPIVGNv----CMDICMIdvtgm-----------paeeGDPVVVFGee-----lpIEEVARKMNTI 804 Porphyromonas g...
ACD54585     314 lgnghGHVWIhdCRVSFIGSi----CMDFAMIdltdvpi------dnkyeleNESVEIFGsh-----nnIEEIARCSDTI 378 Adineta vaga
Feature 1             #                
1L6G_A       353 n----YEVPCTISy-RVPRIFF 369 Geobacillus stearothermophilus
1RCQ_A       340 p----YQLLCNLK--RVPRVYS 355 Pseudomonas aeruginosa
YP_897976    334 k----DEALTKLNalRVKKIVC 351 Francisella tularensis subsp. novicida U112
EAN90745     372 p----HQLTCGLSi-RVPRIYM 388 Trypanosoma cruzi
ZP_02088525  360 -----PSFWIEISs-HTARCYY 375 Clostridium bolteae ATCC BAA-613
YP_001264617 362 vteahFRLLAAIAa-GVPNGRQ 382 Sphingomonas wittichii RW1
EDY37343     810 p----YDLLVQVDgrRVQRIFR 827 Cyanobium sp. PCC 7001
ZP_01733546  762 p----YEILTGISq-RVKRIFY 778 Flavobacteria bacterium BAL38
NP_905309    805 p----YEVLTGISp-RVRRVYF 821 Porphyromonas gingivalis W83
ACD54585     379 v----FDFISTIGk-RVKRVYI 395 Adineta vaga

| Disclaimer | Privacy statement | Accessibility |
NCBI Home NCBI Search NCBI SiteMap