Conserved Protein Domain Family
PLPDE_III_yhfX_like

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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
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PSSM-Id: 143486
View PSSM: cd06811
Aligned: 16 rows
Threshold Bit Score: 532.621
Threshold Setting Gi: 169631716
Created: 12-Jun-2008
Updated: 2-Oct-2020
Structure
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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
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                                  # #                   
P45550         1 MFVEALKRQNPALISAALSLWQQGKIaPDSWVIDVDQILENGKRLIETARLYGIELYLMTKQFGRNPWLAEKLLALGYsG 80  Escherichia col...
YP_001661835   1 MFLNMVIERNPQLIIEAAKLHRDGVIePNTYVLDVDSIYENARLIKETADKYNISLYYMTKQFGRNPIISKIIEKAGIdK 80  Thermoanaerobac...
ZP_02995783    1 MFLDITKKRNPNLIKAAFHLHQKGLIqPDTYIIDLDNIVDNARKIKEEADKYGIELYFMTKQFGRNPIVCHELMKLGYkG 80  Clostridium spo...
YP_077949      1 MFLESTLKYNKKLIEAALSFHQQGIIsPNTYVLDLDTVKKNAKVLSEKARKQDIELFFMTKQFGRNPLVAQAIAESGIgK 80  Bacillus lichen...
ZP_02185120    1 MFMDVVSKRNPKLIQEAITLHQSEKIlPDTYVLDLDIIRENAKKLIETAKKNDIELFFMLKQIGRNPAIAKMLVELGMkN 80  Carnobacterium ...
YP_074382      1 MFLEVTARRNPRLIDAALRFHAEGRLpPNTYVLDLDAIRNNARTLAEAARREGIQLYFMSKQLNRNPQVIAAVAEAGIpR 80  Symbiobacterium...
YP_805682      1 MFLKQLEKLNPELIQYAFELHHSGKIlPDTYVIDLDMIHQNTTHVVAEAKKNHVELLYMTKQVGRNPVIAQEVVNAGIpE 80  Lactobacillus c...
NP_241457      1 MFLPMTLKRNEGLIRAAVKLHQEGNIpANTYVVDLDSFESNVKVIQQTAKRYDVSLYYMTKQLGRSGFIGQIIEQQGIeK 80  Bacillus halodu...
YP_174177      1 MFTSMIAKRNPKLVEAAVCLHQSGALaPNTHLIDLDALERNAAILAKTAEEYGMTLYYMTKQIGRSGFVGKHIEKSGIhK 80  Bacillus clausi...
YP_001828412   3 VFLDTVLTRNPELVDAAAALHRRGEIpPDTYVMDLDAVEANAALLAAEAERLGIGLWFVVKQIGRNPELIRAVARHIP-R 81  Streptomyces gr...
Feature 1         #                        #                                            #        
P45550        81 IVAVDYKEARVMRRAGLPVAHQGHLVQIPchQVADAVEQG-TDVITVFTLDKAREVSAAAvKAGRIQSVLLKVYsdDDFL 159 Escherichia col...
YP_001661835  81 AVAVDFDEARVLFDNGLKIGHIGHLVQVPknDIKLSLLMK-PEVITCFSYEKAKEISDNAkELGIMQDILLRVIdeNDVI 159 Thermoanaerobac...
ZP_02995783   81 AVTVDFKEAITLKENNISLGHVGHLVQIPthSMEDIIEAK-PEVITVYSVEKAVEVSKVAqKLGLVQNIMIRVLddEDTL 159 Clostridium spo...
YP_077949     81 AVAVDPWEAITLSQNGIKIGHVGHLVQIPihMIPAILELH-PDYVTVFSLENAQNINRVAkKMGRKQKVFLRIAnkEDYI 159 Bacillus lichen...
ZP_02185120   81 AVVVDFREAKIMMENNIPLGNVGHLVQIPqmLLKDIMIYG-SKYLTVYSLEKLQAINVLAkEIGIKQKILLRVVseEDEL 159 Carnobacterium ...
YP_074382     81 GVAVDIDDARAFREAGVALGHVGHLVQIPraFLPQVLSWR-PEVMTVFGLAQARAVSDAAvGLGLRQDVLLRVA--SGCL 157 Symbiobacterium...
YP_805682     81 AVVVDFREAETFMENGLALGNVGHLVQPPkhFLTRLLKYG-TKYVTMYSLENTQALNEAAkEVGIKQKVLLKVVgnGDDI 159 Lactobacillus c...
NP_241457     81 AVAVDIDEAIQLKERSCQIGNIGHIVQPSrsQWKFVLTKLnPEVVTIFSYERAKQLSEAAvNVGKVQDVILRIVysHDAV 160 Bacillus halodu...
YP_174177     81 AVAVDIDEAIQLKDGGCAIGNLGHLVQPGknQWPFVLTDMkPEVVTLFSLERAKQLNEAAvQAGVVQDVIVRVIskGDCV 160 Bacillus clausi...
YP_001828412  82 SAAIDPAEARALHAAGARPGNLGHLVQIPrrALPGMLAWR-PENVTVFDLANARAVSDAArEQGFVQDVLIRLEgaEGTV 160 Streptomyces gr...
Feature 1           #                             #                                          ##  
P45550       160 YPGQESGFaLKVLPEIVAEIQnlPGLHLAGLTHFPCLLWDEAvgkvLPTPNLHTLIQARDQLAKSGi-ALEQLNAPSATS 238 Escherichia col...
YP_001661835 160 YPGQEGGIyLGKLKETVHHILklKNIKIAGITSFPCFLYDYEkkeiTPTHNVYTLLKAKEILNEMGl-EIWQVNGPSATC 238 Thermoanaerobac...
ZP_02995783  160 YPAQYGGFyLKDLIEKAKEIKklPNINIYGITSFPCFLYDEKegdiKATNNVQTLKKAQKLLENHLkiKIEQLNMPSATC 239 Clostridium spo...
YP_077949    160 YKGQEGGFtFEQIVKDIESIEqlEGLEIAGLTSFPCILIQDGl--pAVTPNVASMQTVKSFLMERGy-KKLEMNMPSATS 236 Bacillus lichen...
ZP_02185120  160 YPGQYGGFmLEELPSLISLFNelKHIEISGLTSFPCFLYDAEketlEPTHNIETVKAAKKLLENEGi-DIQELNMPSATS 238 Carnobacterium ...
YP_074382    158 YPGQEGGIpLGELPAVALAISrlPGVRVAGVTAFPCLVAEDGr--pVATPNLEAVTRAAALLRDELgmEIAQVNAPSLTC 235 Symbiobacterium...
YP_805682    160 YPGQTGGFtLAELDKQLKQLKtlSNIALVGITTFPAILYNESqedfAATANVKTIDEAKSIFSKHGl-KAQVVSLPSATS 238 Lactobacillus c...
NP_241457    161 FPGQYGGFlIEELEGQLQKLQrlKGISVVGITSFPIFELNPDnndyQFTPNMTSLLQGKKLLEASGi-QVKQVNAPSATS 239 Bacillus halodu...
YP_174177    161 FPGQYGGFlLEELPAAIKELTalTGIRLIGVTSFPVLAYTAGdnsyHYASNAQTIVKAVGLLQQAGv-EVKHVNTPSATS 239 Bacillus clausi...
YP_001828412 161 YPGQEGGVpLERLDVFAEAAEalGGIRIAGVTAFPCVLCDPEsgrpAATATFDLALKARELLAARGh-QDLRLSAPSATS 239 Streptomyces gr...
Feature 1                       ####                                          #                  
P45550       239 CTSLPLLAQYGVTHAEPGHALTGTIPANQq-gDQPERIAMLWLSEISHHFR-GDSYCYGGGYYRRGHAQH-------ALV 309 Escherichia col...
YP_001661835 239 CSSIPLLNKYGITHGEPGHALLGTTPLHAy-tKQPEKPSIVYVSEISHINN-EKAYCYGGGFYPRSNVKY-------ALV 309 Thermoanaerobac...
ZP_02995783  240 VSNMKNIAENGGTHGEPGHGLTGTTPYHAe-hEGAEIPCLVYVSEISHNLK-EESFCYGGGNYRRSHMSK-------ALV 310 Clostridium spo...
YP_077949    237 CATMKLLKENGATQGEPGHALIGTTPIHAt-kQLAERPAMVYVTEVSHISN-HHAYVFGGGFYPRSHMKA-------ALV 307 Bacillus lichen...
ZP_02185120  239 VYTLPFIKKIGGTQGEPGHALTGTTPMHAe-kELAEKPALVYVSEVSHNFK-GKGYLFGGGFYRRGHLKN-------VLI 309 Carnobacterium ...
YP_074382    236 AATLALLRQAGATHGEPGHAITGTTPLHAv-sDQPELPAMVYLTEVSHTYG-GRAYVYGGGSYPRGHMQN-------ALV 306 Symbiobacterium...
YP_805682    239 TTSLPLIKQLGGNEGEPGHALTGTTPLHAv-kEQPEKPAYCYVSEVSHTFG-PHSYIFGGGWYRRGHLKN-------ALI 309 Lactobacillus c...
NP_241457    240 CRTIPMLSEIGVTHGEPGHALTGTTPLHAyqeDLPEVPCMVYVSEISHMDD-THAYTIAGGFYSRSGMEG-------ALF 311 Bacillus halodu...
YP_174177    240 VNTIPMLKQLGATHAEPGHALTGTTPLHAyreDLAELPAMVYVSEISHQDQ-THAYTIAGGFYPRSNMAY-------AFY 311 Bacillus clausi...
YP_001828412 240 MASLPLLAERGATHGEPGHALTGTTPLHAldpAQPEKPAYVYVSEVAHTLGdGRPALFGGGFYARSHIRHallprtgARL 319 Streptomyces gr...
Feature 1                                                                                        
P45550       310 FTPENQkitetn-lktvddSSIDYTLPLAge-----fPVSSAVVLCFRTQIFVTRSDVVLVSGIHRGe--PEIVGRYDSL 381 Escherichia col...
YP_001661835 310 SNNPEDildrifdveelppESIDYYGTILlnn--rkvNVGDTVIYSFRTQIFVTRAKVALLEGLSSGk--PKLTYIFDSK 385 Thermoanaerobac...
ZP_02995783  311 GKSIEDsikvkt--slpplESIDYYITLKsn-----aNVGDTVVMSYRTQIFVTRSSVAVVKGIKEGk--PKLLGIYDSQ 381 Clostridium spo...
YP_077949    308 GTNKDHlkkvqa--iemtpDHIDYYGSLNtv----eaKVGDTAIFAFRTQVFVTNAHIAILKNVAED---PELIGVYDSK 378 Bacillus lichen...
ZP_02185120  310 DNHGKQteahi---nalsdENIDYYLEIDkk-----ePVGATAIMAFRTQIFVTRSEVALVSGIQEGk--PKIEGIYDSQ 379 Carnobacterium ...
YP_074382    307 GTALRRaplh-----rpaaENIDYYLTLDdp----laREGEPVVAAFRTQAFTARANLALVEGVQQGa--PRLAGLYDRA 375 Symbiobacterium...
YP_805682    310 QDGDQYthahv---lplenSNIDYYLELDqq-----fKSGLPVIMAFRTQIFVTRSTVALVRGLHTAdktPELVGLYDSQ 381 Lactobacillus c...
NP_241457    312 GAHADAavaqrakvdlvspTNIDYYGALDrck---emNVGDSVIYAFRTQIFVTRAHVAFVRNIKQK---PEVVYFQKRG 385 Bacillus halodu...
YP_174177    312 GDSPKTifnkae-vdlvspGNIDYYGALKreq---gmQTGDTVVYAYRSQVFVTRSHVAFVRGVANGk--PVIVHQQKRG 385 Bacillus clausi...
YP_001828412 320 GVQGAPa------------ENIDYYRLLDapppgsdvRLGDTALLAFRTQIFVTRSTVAVVSGLASGr--PRLNGLYDAH 385 Streptomyces gr...
Feature 1         
P45550       382 G 382 Escherichia coli K12
YP_001661835 386 G 386 Thermoanaerobacter sp. X514
ZP_02995783  382 G 382 Clostridium sporogenes ATCC 15579
YP_077949    379 G 379 Bacillus licheniformis ATCC 14580
ZP_02185120  380 G 380 Carnobacterium sp. AT7
YP_074382    376 N 376 Symbiobacterium thermophilum IAM 14863
YP_805682    382 G 382 Lactobacillus casei ATCC 334
NP_241457    386 M 386 Bacillus halodurans C-125
YP_174177    386 M 386 Bacillus clausii KSM-K16
YP_001828412 386 G 386 Streptomyces griseus subsp. griseus NBRC 13350

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