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 I 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 I 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: 107256
View PSSM: cd01543
Aligned: 34 rows
Threshold Bit Score: 302.189
Threshold Setting Gi: 153890166
Created: 1-Jul-2004
Updated: 17-Jan-2013
Structure
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Aligned Rows:
 
putative ligandputative
Feature 1:putative ligand binding site [chemical binding site]
Evidence:
  • Comment:based on sequence similarity to other members of the LacI family.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                   ##  #                                               #                
gi 32471427   41 RIALLVevsraYGRELLRGIALYArtk-gdWSLLHEEmti-----dsvVPDWISRTRVDGVIARldhhsi--dplrrlRV 112
gi 87309612   38 KITLAVvpssdNQVRMIRGVMQYAtet-grIQITKRAaip------yvPIELLDKLAADGIIAYaesqeri-nflqslGI 109
gi 153890166  19 SILLALa---wYSPAVHRGIIRHAre--agWILDAAVe---------rYKNHFPLWREDGIISYlhadsalyefikktDK 84
gi 52215914    3 RLILLTdftesFSYNLLKGVLAYSkkh-epWVVCRMPpsykltygiegVLKWAKAWQADAIIGRfdnddnv-elfrknGI 80
gi 149198822   6 EIILALd---wYDYRIHQGVVNVAre--ngWSLLFLQns-------frSSAVPAAWRGDGAITLihsaety-qffqthKI 72
gi 29340924    3 KILLLIdysseFDRKLLRGLVQYSken-gpWLFYRLPsyysgmygekgILKWAKEWKADAIIGQwnndtv--nllkelNI 79
gi 87310003   18 HVLLALg---wYYSEIHRGVARFArd--hhWHVTFDF-----------DDLVPRDWQGDGVITLlgaqqqiwrslqqfDV 81
gi 149198758   5 RIALAFpmgssHWEKTAYGIRSYCnqerdkWKLITNPeth------dlKISEINLDAIDGIIAVvrnktdl-dhlkkhSV 77
gi 153889633  64 RVALLVetsttWARSILDGINNYLrkg-hnWQIFLEPhgs------neSIRMPAGWVGEGVIAEikdlgma-rhfaslNI 135
gi 87310075   13 RIALLVlnesqWSRSILEGVSRFAaeh-ggWDFWLHPram------ktQALMPADWKGEGIIARiadehvr-aslerhDM 84
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1             #             #                                   #                        
gi 32471427  113 PIVDVRgnrkf-pgvpQVEADNEQVAEMAFEHLWERGFRRFAFCGFrfa-tySDARLIAFRKLVEKagcpftehqspgap 190
gi 87309612  110 PFVNLTlqsepeagvpVVHSDNLQIGRRLAEHLLSLGLRNFAFVGHfaw-yhNRMRQTGFLQRLAEsgfdaas--idisf 186
gi 153890166  85 PVVNIGngkq--pgvpTVKPDVRKIGVMAADYFFERGFRDMAFFLKsha-paARERWRAFRARAEElgarahl---mnwl 158
gi 52215914   81 IAIAQDyksrf-snipNITGDYHKTGRMAAEFFLSKGFRNFAFYGYrdt-vwSQERCEGFYECIAEhgfgn------nfy 152
gi 149198822  73 PVVDLGlnkhg-laipRVVTDNVELGRMAAEHFLERGFTHFYALSTnni-qmFQERYQAFKETLMKkgydc------eii 144
gi 29340924   80 PIVLQNyhhrs-ttysNLTGDYKGTGRMAAQFFAKRMFHNFAYFGIngv-vwSDERCEGFRQEVKRigg----------- 146
gi 87310003   82 PMVDLSesrpd-vplpRVTMDNVAIGQMAAQHFLDRGFRHFAFVHRwel-gvSQRRRDAFTAELAQydrrce----ilsw 155
gi 149198758  78 PCVNISgtlqk-sdlpRVCPDFYQMGQLAAQHFFERGFQNFAYFGLset-vfSERMYQGFHKELSKktkt---------c 146
gi 153889633 136 PVVNLSqvtfrdiafpTVTSDIAACARMAGRYYFERGYQNFAYLRLern-alDAQHSANFGEFVTQaggsff-----slg 209
gi 87310075   85 PTINVSwhseqsrrfpKVIADPQGSGELAGNFFVQRGFQHFGYIGPplcynyRDPVQPAAERVIEEagysl------rsf 158
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                #                                                     #                 
gi 32471427  191 giTLRELERAGVVEQEALVEWLSTLERPtGLFVcnDIRGQQVLNACRFANIAVPDDVGVIGVDDDdTICSICdPSLSSVR 270
gi 87309612  187 dsELSLETSDRQVHQGELQQAIAGLPEPcGVASchDEFAHEIVEACKVIGRSIPHSVSVIGVNDYrLICETTmPGLSSVA 266
gi 153890166 159 rhSGGRVQYSEAALVEWLGESVTALPKPlAIMAehDEHAIEVIHACIQFSIPIPEQVAVLGVNNDpLRCEFApVPLSSID 238
gi 52215914  153 syQEQSLDDLWFYEAPPLLTWLKSLPQPtALMAcdDNQGNRITEICKVNNIRVPDKIAILGVDNDeIICNLSdPPLSSIS 232
gi 149198822 145 evPNLYDTHLLDLSQAILKQKLSKFKNPaALFAyeDSWAAQWIYLAESMGLKVPNDLAILGADNNpLIARSLsTPLSSVE 224
gi 29340924  147 nfYCFESDKHEDEIRIEVSQWLQELPKPiALFCcdDSHALFISETCKISNIHIPEEISLLGVDNDdLICNISdPPISSIE 226
gi 87310003  156 qtQRGRQADTRQQRHRWLAQRLSELPKPlAIFAprDIEAVEIIEAAMAISALVPDEISVLGVDNTeTICDCLqTPLSSID 235
gi 149198758 147 ekLEVTFGANFLEQDELIHEFLKSLKLPcAILAahDPRAQILLEACEEMALRVPEDIAILGSNNDtVSCEFSsPPLSSIE 226
gi 153889633 210 vkNRAWGVADWNMSIKALADWLAGLPKPvGIFS--WAIGREVVQACHLAGLRMPEEVALVMLSDDeIFLEMShIPISGIM 287
gi 87310075  159 spDPASPSSDYDYQRSRLVQWVRSLPKPiGVIAfsTVVAREIMLTCSAEGINVPNDVAVLAVEHDpLISQLSpMPISYIQ 238
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
Feature 1        #                                                        
gi 32471427  271 PNAELAGYRAAEI----------------LQQMLNGWVPDkeVERIPPISVTERLST 311
gi 87309612  267 QNSERIGYLAAQL----------------VDQLIEGAERPakPILVPPGQLIVRRSS 307
gi 153890166 239 SNHEVMGYEAAVL----------------LDRILHGETPPaePVLIPPAGVVTRLST 279
gi 52215914  233 QNIVRGGFEAAEL----------------IEHLLNDEECSyqDVVLQPVNIVNRLST 273
gi 149198822 225 TNQEGLGQQAALV----------------LKDLMEGKGIGdhLYKLQPTSVVTRAST 265
gi 29340924  227 LEVERGGYSIGRL----------------IHQQIKKEHEGtfNIVINPIRIELRQST 267
gi 87310003  236 NNLEQVGYEGAAL----------------LSRLMAGEQSPteTFYIAPSRVVERRST 276
gi 149198758 227 RDDQKIGFEAAKA----------------LDMLMRQEACQh-ELIIPPLKVKTRKST 266
gi 153889633 288 HPGEQIGHEAAQMldelmtaakskkhaatFSGKSQPAASPppVRLIQPLGVKTRQSS 344
gi 87310075  239 QRPELVGYEAARE----------------LRRLISGGTPRdePIAIAPEGIIEKPST 279

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