4FE7,4FE4


Conserved Protein Domain Family
PBP1_XylR

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cd01543: PBP1_XylR 
ligand-binding domain of DNA transcription repressor specific for xylose (XylR)
Ligand-binding domain of DNA transcription repressor specific for xylose (XylR), a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of XylR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type 1 periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type 1 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Statistics
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PSSM-Id: 380485
Aligned: 104 rows
Threshold Bit Score: 243.262
Created: 1-Jul-2004
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
ligand bindingdimer interface
Conserved site includes 6 residues -Click on image for an interactive view with Cn3D
Feature 1:ligand binding site [chemical binding site]
Evidence:
  • Structure:4FE7; Escherichia coli transcription activator and regulator of diauxie, XylR, in complex with xylose, contacts at 4A
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                #                                                #                   
4FE7_A     27 RITLLFnankaYDRQVVEGVGEYLqasqseWDIFIEEdf--raRIDKIKDWLGDGVIADFDdKQIEQala----dvDVPI 100 Escherichia coli
OGV69250   10 QVAVLLptsvkVSRDMRRGILQYVyrh-gpWGLHIIEgrngeqKLVRMKEWGCTGIIGRLYtPELVRiag----raDVPQ 84  Lentisphaerae bact...
OGV71085   10 RVVVILetcvqPDRQKLDGILKYVrfy-gpWHLHIIQnrvgeqKLAHFERWNANGIIVGQSmFDMEPila----rvKVPL 84  Lentisphaerae bact...
OGV66380   12 NVLILTe---wYDHHVRQGIGLYAce--hnWHLTAEE------RVTIPRGWKGDGVLTVFShRRDIMayv---krlAIPV 77  Lentisphaerae bact...
OAM87512   21 RVHIAFtqcfsFVESARHGILDYAktc-grWKLSFTPeal-gpSIAWLRHARIDGAIAHVVsTADKRivn----slPFPV 94  Verrucomicrobia sp...
ACB76509   11 KVLVAAa---iAPPECIRGITRHAra--hdWHLVMDMl----fTGALPRGWNGSGVLALGAhQPELLahl---qasGLPC 78  Opitutus terrae PB...
ADE53480    9 NVLLLIs---gLKTSTHQGIARAAke--fgWYLNLSFi----eQALAPENWHGDGILCALSsHPTIEqlv---lraTQPV 76  Coraliomargarita a...
AKJ65155    7 HRRVLLvmgerYNMRVHRGVAQYAsg--nrWHLTNLFg----tDPGPIRRRGCDGIVAVLDpDDPLTgav---lrrRVPK 77  bacterium L21-Fru-AB
OGV62869   10 KVIIALlmsgkGGQDKLNGIFRYLedh-rhWDCTIIRtsd-slTTKLIESMPCNGVRGLIFsLPSHEavlkrivlsNTPT 87  Lentisphaerae bact...
KPJ72504   28 NVALLLaagweSAERFRRGVIDYVrrk-arWTITTMPetf-gpSIRSLAGWDGDGVIANIRrKRDVHaag----klGIPV 101 Planctomycetes bac...
Feature 1                                                              #   #                  
4FE7_A    101 VGVGgsyhlae---syppvhYIATDNyALVESAFLHLKEkGVNRFAFYGLpessgkrWATEREYAFRQLVAEeky----- 172 Escherichia coli
OGV69250   85 VLVDpekvfqhsghqlalhsIVRSDTvAVGRMAAEYFLNrKFIHYAYVGEvrg--fgWSVKRGEAFAAVVRKagf----- 157 Lentisphaerae bact...
OGV71085   85 VLVDplpchlkpsspfyrrsYVQNDAvSVGVMAADFFINkGFRNFAYVGEvln--rmWSRGRGQGFSSRLRKagf----- 157 Lentisphaerae bact...
OGV66380   78 VGMGlyrmd-------ipvpRVVGDHaKIGGMAAEHFADrGFRCTAWFSTtf---spVHELRFDGFRSACAGlrld---- 143 Lentisphaerae bact...
OAM87512   95 VNLAalidp-------kgmlSVIGNQqQIGKLAACHLLErGFRRLAYYGTsn---mwYSRQRLIGFSETIRQtgat---- 160 Verrucomicrobia sp...
ACB76509   79 VVLTdgdpi-------vdlpRVEPDHrAIGRLAADHFLErAHRSFAWAPFln---daANRERLAGFQERLAEhgr----- 143 Opitutus terrae PB...
ADE53480   77 VDIAmqrse-------vhlpRVVADNeQIGREAAAHLLQqNHQHFAWFCFns---dpVAQARLAGFEDAIGK-------- 138 Coraliomargarita a...
AKJ65155   78 VDLSiirdr-------lampHLTGDNeAMGREAALHFLDrGFRSFLWFSArd---haPARKRCEGYTAELARhgfncrrl 147 bacterium L21-Fru-AB
OGV62869   88 VIMDildakilh-nrkehiaFVANDSdAIGTCAAEYLLGlTAFRSYAYVGpsq-nfeWSRIRREAFCRMLDEysr----- 160 Lentisphaerae bact...
KPJ72504  102 VVMSgalae-------gllpRVLTDNeAIGRLGAEHLLDcGFRRAAFYGRrg---ayDISLRRKGFVDRCSHaga----- 166 Planctomycetes bac...
Feature 1                                                                             #       
4FE7_A    173 -rgVVYQGLETap-----enWQHAQNRLADWLQTLPPQTGIIAvtDARARHILQVCEHLHIPVPEKLCVIGIDNEeLTRY 246 Escherichia coli
OGV69250  158 -dcHIYGALSReeq----kdAGRERDRLCAWLRGLPKPVALLAamDNRGRQIMDACAWAGIGVPRDIAVLGVDNDeDLCE 232 Lentisphaerae bact...
OGV71085  158 -acHTYPLLTRvem----ndWAVEQAKLAGWLAGLPKPVALFAamDIRARQILDTCLINGLKVPDDIAILGVDNDeQLCL 232 Lentisphaerae bact...
OGV66380  144 aplKWVWEKSCrdl---pedWMRLRIWLARQLKNAPRPLAVFAydDYDAAKVEDICRFAKIEVPEDIAILGVDNNeLICL 220 Lentisphaerae bact...
OAM87512  161 cesHVVDSKLHms-----agWHEQHRQLECWLRGLRLPVGVFActDARAAMIVDACESIGLRIPEDVAVIGVDNDpSICQ 235 Verrucomicrobia sp...
ACB76509  144 -tcRLLPPAHTrigpywqdnWDDYRRNLAAELLRLPRPTAIFAfnDCTAANVIDCCQDAALAVPEDVAVLGVGNS-LVCE 221 Opitutus terrae PB...
ADE53480  139 ---AALSLVPR---------RSNYRTAVLQKLHALPRPCGIFAktDADAAWILNLCIEEGFRIPDDFAIIGVDNNpLICD 206 Coraliomargarita a...
AKJ65155  148 vvdAQFGTRTPp--------WEKLEAWIHDELAVAALPCAAYVynDVQAADLLDACVSGGIQVPHEVAVLGTDNHpLICP 219 bacterium L21-Fru-AB
OGV62869  161 -kcSVYSDPVEpsk----nsMEVNQRRLAKWLQRLPKPAGILAshDYMGLQVLETCRSAGLKVPDEVSVLGVNNEeIVCE 235 Lentisphaerae bact...
KPJ72504  167 -acATFWAPSLfgr---wsnWSHAGQKLDGFLAGLRPPLGVMAcdDLRARMVLDSCRRVGYRVPDDVAILGVDNNeLICE 242 Planctomycetes bac...
Feature 1               #                                          
4FE7_A    247 LSrVALSSVAQGARQMGYQAAKL-LHRLLDKEEMPl-qRILVPPVRVIERRST 297 Escherichia coli
OGV69250  233 TTnPPMSSILLDAERASYEAAQY-LDDLMRHATRKr-kVIIYGPERVVSRRST 283 Lentisphaerae bacterium RIFOXYA12_FULL_48_11
OGV71085  233 GSsPTLSSLECDMGHCGFMAAQL-LDEQMRGKRKRk-iILKYGVKRTAVRQST 283 Lentisphaerae bacterium RIFOXYA12_FULL_48_11
OGV66380  221 NQpVPLSSIAHDLERVGYESAAL-LDRLIDGKAVPs-rPILIPPTNIVLRQST 271 Lentisphaerae bacterium RIFOXYA12_FULL_48_11
OAM87512  236 LSsISLTSIARNDWKIGWAAATV-LDHAMAGHALDn-eLTLIEPERVVARKST 286 Verrucomicrobia sp. TSB47
ACB76509  222 LSpVPLSSVDDDMTELGYRAALL-LESVLSGAGTAt-rTLRIPPRGIVTRLSS 272 Opitutus terrae PB90-1
ADE53480  207 FLpVPLSSVNHDLEQLGYQAACL-LEALMNGDAAPs-eTTLVKPTGVTVRGST 257 Coraliomargarita akajimensis DSM 45221
AKJ65155  220 TAaVPLSSINHDLEELGRRAAAE-LDRLMSGEPSAr-rIITIPHRGITVRQSS 270 bacterium L21-Fru-AB
OGV62869  236 HTiPTLSSVQPDFEQEGYIAASL-LDQIMQGIEVQrkkTVLCGVKQIVARRST 287 Lentisphaerae bacterium RIFOXYA12_FULL_48_11
KPJ72504  243 FAdPPLSSVARAILLSPPGLVRRrSTDVLAIEDPHvasAVTLIRERIGEPFGV 295 Planctomycetes bacterium DG_20

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