Conserved Protein Domain Family
PBP1_TreR_like

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cd01542: PBP1_TreR_like 
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Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators
Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of TreR 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: 107255
View PSSM: cd01542
Aligned: 31 rows
Threshold Bit Score: 244.787
Threshold Setting Gi: 89076506
Created: 1-Jul-2004
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
ligand bindingdimerization
Conserved site includes 7 residues -Click on image for an interactive view with Cn3D
Feature 1:ligand binding site [chemical binding site]
Evidence:

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                    ##                                               #                  
1BYK_A         4 VVAIIVTRlDSLSENLAVQTMLPAFyeqGYDPIMMEsqfspqlVAEHLGVLKRRNIDGVVLFgftgite--emlahwQSS 81
gi 116617416  63 TIGVIVPRlDSSAQVEMLRGLDDANe--NDTFLIVNtyqstkrELAAIEKLRTQNVGGLIVLtanlndelrnaltefDAP 140
gi 16123837   64 VVGIIVSRlDSPSENQAVRTMLPLFyqqGYDPILMEsqfdttlVSEHLHILQQRHVDGVILFgfsglta--emlapwQEK 141
gi 9655365    64 VVGIIISRlDSPSENKAVSTMLQAFyahGYDVVIMEsqfsrekTNAHLKVLAKRQVDGVIVFgftdidh--dallswQHR 141
gi 46912844   64 VVGVIISRlDSPSENKAVSGILDVIytaGYDAVIMEsqfsaekTNEHLSVLQKRNVDGVILFgfsgcdl--siveslNHK 141
gi 145297562  64 VVGIIVSRlDSSSENQAVRGMLETLyqrGYDAVLMEskfspakVQEHLAVLERRGVDGIILFafndldy--damaplKDK 141
gi 37527169   64 IIALIVSRlGSFSENLSISAMLPLFyqhGYDPIIMEsnfdpqlLQEHLRQLALRHADGIILFgftglse--eslfpwRDK 141
gi 52307345   62 VVGVIVSKlDSGSESQTLRAILQALqaeHITPLIVEsrfeaeqVRHHFQLFRERQVNAVILFgffplpl--eivrewQGS 139
gi 15601412   61 LIGVIVPRvSSHATAQGVDGLTAIFeqaGKHVLLANthqvhakEIEYIQIFNQKRVEGIVFYathldqplvhaiqhsAVP 140
gi 119944732  61 LIGVIVPRmYSNATAKGLDGLSSIIdqaGKYVLLANsqqnhaqEIEYIKRFNQKRVEGILLYathldsalvdaikqsKAP 140
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                               #                        
1BYK_A        82 LVLLArdak--gfaSVCYDDEGAIKILMQRLYd-qGHRNISYLGVPHSDVTTGKRRHEAYLAFCKAhkl--hpVAALPGL 156
gi 116617416 141 VVIQGqeep--nfhRVVMNDLQAGTVVGEFAAslhPQNTLLLKIDETMDWAIGHDRFLNIRKKLSTsk----vTVVDSKF 214
gi 16123837  142 MVVLAreyr--gfsSVCYDDEGAIYLLMDKLRq-aGHRHISYIGVQSSDATTGMRRYQAYLDYSQQhgl--tpMVALGEL 216
gi 9655365   142 CVLLAmhsd--eisSINYDNAGVIERALQHLAq-kQLRDIAFIGVDPRDKTTGEQRLNAYLNWCVEhei--vaNYQTGQL 216
gi 46912844  142 AVVIAvdtg--risSVGYDNYGIIELAMANLQq-qGKQHISFIGVDPSDKTTGLMRLNAYIEYCESani--epIYQTGQL 216
gi 145297562 142 LVLVAreyp--gfsSVCFDDGGAVRTMLAELAi-rGLSDIAYLGVDTSDLTTGQRRLDAYLGYCAEqgl--taRSALGDL 216
gi 37527169  142 MVVFAreyt--gfsSVCYDDIGAVRLLMNEFYr-rGHREISFLGVDDCDTTTGFLRHQSYLACCEQqgl--rpLSVQCDL 216
gi 52307345  140 LVVIArtyp--nisSVYYDDEQAITRLMTELYr-qGHRRIAYLGIQDSDETTGKLRTQSYLQFCRShni--rpNSVSVEL 214
gi 15601412  141 VVLVGqdgslynipSIVHDDHRVGFEAGQRLVk-aGCKQIGFIGVQSDDIAVDVLRSQGLQQALGFhqq-tllFHARGNF 218
gi 119944732 141 VVLIGqdgslfnipSVIYDDLSVGFSAGQRLFg-aGASNIGFIGVNSQDIAVDQCRFEGLRQALQHtkqisplFHSRGAF 219
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                 # #                                            #       
1BYK_A       157 AMKQGYENVAKVITpe--ttALLCATDTLALGASKYLQEQRId---tLQLASVGNTPLMKFLHPEIVTVDPGYAEAGRQA 231
gi 116617416 215 SIAEAKIAAQQAMQsqn-fdLIIGATDRITIGALQAGLATGQn----AQYIGFGRSDLSTTVTPNLTSFEYDFYQTGKKI 289
gi 16123837  217 SYQSGFQLAPQVITpq--tsALVCASDTIAMGVSKYLQQQEReq-ppIQVCGIGNTPLLHFLFPDTLTIELGYGRAGVKA 293
gi 9655365   217 HHESAYLLVDKVLTeq--tqAIVCASDTLALGVIKRLQELQRd---dVVVTGVGGNELLSFLFPNIFSVDPGYREAGKLA 291
gi 46912844  217 SHESAYVLTDHVLKpe--teAIVCASDTLAMGVAKRLQELDRs---dVLVSGVGATDLLSFIFPNTFSIDPGYYAAGKAS 291
gi 145297562 217 SLQSGYRLAADLLTpt--tqALVCASDTLAIGAAKYLQEQGRs---eVLVTGLGNNPMLSFLFPNALSLDLGYKRAGEQA 291
gi 37527169  217 SYQSGFQHINKVLRek--ttALICATDSLALGAYKYLQQNSRe---dIQIGSIGNTPLLNFLYPNTVSIDLGYSEAGKYA 291
gi 52307345  215 SAESAYLHCAELFTrp--vdALVCATGRLALGAFKFSQQSGRv----FPIAYVGYNELLQYMMPNALSLDFGYCQAGLKA 288
gi 15601412  219 SIESGYQMAKQAYLdypqldGLFCATDRLAVGAIKALQELGVhvgqqVKLLGVGNDELAYVSNPPLSTFNYAFDKAGENA 298
gi 119944732 220 SIESGYQQTKQLLIdwpqldGLFCATDRIAIGAMKAISESGKvpgkeIKVLGVGNDELSQVSTPSLSTFSYAFDLTGEKS 299
                        250       260
                 ....*....|....*....|....*
Feature 1                                 
1BYK_A       232 ACQliaqv-tgrsePQQIIIPATLS 255
gi 116617416 290 YELfctvrdtnpsnTIRTVLDGELV 314
gi 16123837  294 AQQlldql-snsqpIQQIIIPGQLV 317
gi 9655365   292 ADLlieql-cgsdhGCVHLTQMPVS 315
gi 46912844  292 ASLlikql--agchEVTHLTQKAMI 314
gi 145297562 292 ARQllgqi-eqgrcPLATIAPCHTL 315
gi 37527169  292 SDQlisqi-nrqyfKQKVIIPSKLA 315
gi 52307345  289 VELlmrql-rgkssTEHYLVSTHQP 312
gi 15601412  299 AKMlleriagrgqeMSKVVLTFQNI 323
gi 119944732 300 ANMlldlienkqssVSKLVMSFEII 324

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