Conserved Protein Domain Family
PLPDE_III_yhfX_like

?
cd06811: PLPDE_III_yhfX_like 
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme yhfX
This subfamily is composed of the uncharacterized protein yhfX from Escherichia coli K-12 and similar bacterial proteins. These proteins are homologous to bacterial alanine racemases (AR), which are fold type III PLP-dependent enzymes containing an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists 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. It catalyzes the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. Members of this subfamily may act as PLP-dependent enzymes.
Statistics
?
PSSM-Id: 143486
View PSSM: cd06811
Aligned: 16 rows
Threshold Bit Score: 532.621
Threshold Setting Gi: 169631716
Created: 12-Jun-2008
Updated: 17-Jan-2013
Structure
?
Aligned Rows:
Conserved Features/SitesClick to see Conserved Features Help
 
Feature 1:active site [active site]
Evidence:
  • Comment:Based on the binding of the PLP cofactor and substrate analogs 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
?
Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                  # #                   
gi 1176261     1 MFVEALKRQNPALISAALSLWQQGKIaPDSWVIDVDQILENGKRLIETARLYGIELYLMTKQFGRNPWLAEKLLALGYsG 80
gi 167038850   1 MFLNMVIERNPQLIIEAAKLHRDGVIePNTYVLDVDSIYENARLIKETADKYNISLYYMTKQFGRNPIISKIIEKAGIdK 80
gi 187779310   1 MFLDITKKRNPNLIKAAFHLHQKGLIqPDTYIIDLDNIVDNARKIKEEADKYGIELYFMTKQFGRNPIVCHELMKLGYkG 80
gi 52079158    1 MFLESTLKYNKKLIEAALSFHQQGIIsPNTYVLDLDTVKKNAKVLSEKARKQDIELFFMTKQFGRNPLVAQAIAESGIgK 80
gi 163790693   1 MFMDVVSKRNPKLIQEAITLHQSEKIlPDTYVLDLDIIRENAKKLIETAKKNDIELFFMLKQIGRNPAIAKMLVELGMkN 80
gi 51891691    1 MFLEVTARRNPRLIDAALRFHAEGRLpPNTYVLDLDAIRNNARTLAEAARREGIQLYFMSKQLNRNPQVIAAVAEAGIpR 80
gi 116493948   1 MFLKQLEKLNPELIQYAFELHHSGKIlPDTYVIDLDMIHQNTTHVVAEAKKNHVELLYMTKQVGRNPVIAQEVVNAGIpE 80
gi 15613154    1 MFLPMTLKRNEGLIRAAVKLHQEGNIpANTYVVDLDSFESNVKVIQQTAKRYDVSLYYMTKQLGRSGFIGQIIEQQGIeK 80
gi 56962451    1 MFTSMIAKRNPKLVEAAVCLHQSGALaPNTHLIDLDALERNAAILAKTAEEYGMTLYYMTKQIGRSGFVGKHIEKSGIhK 80
gi 182440693   3 VFLDTVLTRNPELVDAAAALHRRGEIpPDTYVMDLDAVEANAALLAAEAERLGIGLWFVVKQIGRNPELIRAVARHIP-R 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1         #                        #                                            #        
gi 1176261    81 IVAVDYKEARVMRRAGLPVAHQGHLVQIPchQVADAVEQG-TDVITVFTLDKAREVSAAAvKAGRIQSVLLKVYsdDDFL 159
gi 167038850  81 AVAVDFDEARVLFDNGLKIGHIGHLVQVPknDIKLSLLMK-PEVITCFSYEKAKEISDNAkELGIMQDILLRVIdeNDVI 159
gi 187779310  81 AVTVDFKEAITLKENNISLGHVGHLVQIPthSMEDIIEAK-PEVITVYSVEKAVEVSKVAqKLGLVQNIMIRVLddEDTL 159
gi 52079158   81 AVAVDPWEAITLSQNGIKIGHVGHLVQIPihMIPAILELH-PDYVTVFSLENAQNINRVAkKMGRKQKVFLRIAnkEDYI 159
gi 163790693  81 AVVVDFREAKIMMENNIPLGNVGHLVQIPqmLLKDIMIYG-SKYLTVYSLEKLQAINVLAkEIGIKQKILLRVVseEDEL 159
gi 51891691   81 GVAVDIDDARAFREAGVALGHVGHLVQIPraFLPQVLSWR-PEVMTVFGLAQARAVSDAAvGLGLRQDVLLRVA--SGCL 157
gi 116493948  81 AVVVDFREAETFMENGLALGNVGHLVQPPkhFLTRLLKYG-TKYVTMYSLENTQALNEAAkEVGIKQKVLLKVVgnGDDI 159
gi 15613154   81 AVAVDIDEAIQLKERSCQIGNIGHIVQPSrsQWKFVLTKLnPEVVTIFSYERAKQLSEAAvNVGKVQDVILRIVysHDAV 160
gi 56962451   81 AVAVDIDEAIQLKDGGCAIGNLGHLVQPGknQWPFVLTDMkPEVVTLFSLERAKQLNEAAvQAGVVQDVIVRVIskGDCV 160
gi 182440693  82 SAAIDPAEARALHAAGARPGNLGHLVQIPrrALPGMLAWR-PENVTVFDLANARAVSDAArEQGFVQDVLIRLEgaEGTV 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1           #                             #                                          ##  
gi 1176261   160 YPGQESGFaLKVLPEIVAEIQnlPGLHLAGLTHFPCLLWDEAvgkvLPTPNLHTLIQARDQLAKSGi-ALEQLNAPSATS 238
gi 167038850 160 YPGQEGGIyLGKLKETVHHILklKNIKIAGITSFPCFLYDYEkkeiTPTHNVYTLLKAKEILNEMGl-EIWQVNGPSATC 238
gi 187779310 160 YPAQYGGFyLKDLIEKAKEIKklPNINIYGITSFPCFLYDEKegdiKATNNVQTLKKAQKLLENHLkiKIEQLNMPSATC 239
gi 52079158  160 YKGQEGGFtFEQIVKDIESIEqlEGLEIAGLTSFPCILIQDGl--pAVTPNVASMQTVKSFLMERGy-KKLEMNMPSATS 236
gi 163790693 160 YPGQYGGFmLEELPSLISLFNelKHIEISGLTSFPCFLYDAEketlEPTHNIETVKAAKKLLENEGi-DIQELNMPSATS 238
gi 51891691  158 YPGQEGGIpLGELPAVALAISrlPGVRVAGVTAFPCLVAEDGr--pVATPNLEAVTRAAALLRDELgmEIAQVNAPSLTC 235
gi 116493948 160 YPGQTGGFtLAELDKQLKQLKtlSNIALVGITTFPAILYNESqedfAATANVKTIDEAKSIFSKHGl-KAQVVSLPSATS 238
gi 15613154  161 FPGQYGGFlIEELEGQLQKLQrlKGISVVGITSFPIFELNPDnndyQFTPNMTSLLQGKKLLEASGi-QVKQVNAPSATS 239
gi 56962451  161 FPGQYGGFlLEELPAAIKELTalTGIRLIGVTSFPVLAYTAGdnsyHYASNAQTIVKAVGLLQQAGv-EVKHVNTPSATS 239
gi 182440693 161 YPGQEGGVpLERLDVFAEAAEalGGIRIAGVTAFPCVLCDPEsgrpAATATFDLALKARELLAARGh-QDLRLSAPSATS 239
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                       ####                                          #                  
gi 1176261   239 CTSLPLLAQYGVTHAEPGHALTGTIPANQq-gDQPERIAMLWLSEISHHFR-GDSYCYGGGYYRRGHAQH-------ALV 309
gi 167038850 239 CSSIPLLNKYGITHGEPGHALLGTTPLHAy-tKQPEKPSIVYVSEISHINN-EKAYCYGGGFYPRSNVKY-------ALV 309
gi 187779310 240 VSNMKNIAENGGTHGEPGHGLTGTTPYHAe-hEGAEIPCLVYVSEISHNLK-EESFCYGGGNYRRSHMSK-------ALV 310
gi 52079158  237 CATMKLLKENGATQGEPGHALIGTTPIHAt-kQLAERPAMVYVTEVSHISN-HHAYVFGGGFYPRSHMKA-------ALV 307
gi 163790693 239 VYTLPFIKKIGGTQGEPGHALTGTTPMHAe-kELAEKPALVYVSEVSHNFK-GKGYLFGGGFYRRGHLKN-------VLI 309
gi 51891691  236 AATLALLRQAGATHGEPGHAITGTTPLHAv-sDQPELPAMVYLTEVSHTYG-GRAYVYGGGSYPRGHMQN-------ALV 306
gi 116493948 239 TTSLPLIKQLGGNEGEPGHALTGTTPLHAv-kEQPEKPAYCYVSEVSHTFG-PHSYIFGGGWYRRGHLKN-------ALI 309
gi 15613154  240 CRTIPMLSEIGVTHGEPGHALTGTTPLHAyqeDLPEVPCMVYVSEISHMDD-THAYTIAGGFYSRSGMEG-------ALF 311
gi 56962451  240 VNTIPMLKQLGATHAEPGHALTGTTPLHAyreDLAELPAMVYVSEISHQDQ-THAYTIAGGFYPRSNMAY-------AFY 311
gi 182440693 240 MASLPLLAERGATHGEPGHALTGTTPLHAldpAQPEKPAYVYVSEVAHTLGdGRPALFGGGFYARSHIRHallprtgARL 319
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                        
gi 1176261   310 FTPENQkitetn-lktvddSSIDYTLPLAge-----fPVSSAVVLCFRTQIFVTRSDVVLVSGIHRGe--PEIVGRYDSL 381
gi 167038850 310 SNNPEDildrifdveelppESIDYYGTILlnn--rkvNVGDTVIYSFRTQIFVTRAKVALLEGLSSGk--PKLTYIFDSK 385
gi 187779310 311 GKSIEDsikvkt--slpplESIDYYITLKsn-----aNVGDTVVMSYRTQIFVTRSSVAVVKGIKEGk--PKLLGIYDSQ 381
gi 52079158  308 GTNKDHlkkvqa--iemtpDHIDYYGSLNtv----eaKVGDTAIFAFRTQVFVTNAHIAILKNVAED---PELIGVYDSK 378
gi 163790693 310 DNHGKQteahi---nalsdENIDYYLEIDkk-----ePVGATAIMAFRTQIFVTRSEVALVSGIQEGk--PKIEGIYDSQ 379
gi 51891691  307 GTALRRaplh-----rpaaENIDYYLTLDdp----laREGEPVVAAFRTQAFTARANLALVEGVQQGa--PRLAGLYDRA 375
gi 116493948 310 QDGDQYthahv---lplenSNIDYYLELDqq-----fKSGLPVIMAFRTQIFVTRSTVALVRGLHTAdktPELVGLYDSQ 381
gi 15613154  312 GAHADAavaqrakvdlvspTNIDYYGALDrck---emNVGDSVIYAFRTQIFVTRAHVAFVRNIKQK---PEVVYFQKRG 385
gi 56962451  312 GDSPKTifnkae-vdlvspGNIDYYGALKreq---gmQTGDTVVYAYRSQVFVTRSHVAFVRGVANGk--PVIVHQQKRG 385
gi 182440693 320 GVQGAPa------------ENIDYYRLLDapppgsdvRLGDTALLAFRTQIFVTRSTVAVVSGLASGr--PRLNGLYDAH 385

                 .
Feature 1         
gi 1176261   382 G 382
gi 167038850 386 G 386
gi 187779310 382 G 382
gi 52079158  379 G 379
gi 163790693 380 G 380
gi 51891691  376 N 376
gi 116493948 382 G 382
gi 15613154  386 M 386
gi 56962451  386 M 386
gi 182440693 386 G 386

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