Conserved Protein Domain Family
PBP1_AglR_RafR_like

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cd06271: PBP1_AglR_RafR_like 
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Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators
Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. 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 sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. 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: 107266
View PSSM: cd06271
Aligned: 46 rows
Threshold Bit Score: 217.063
Threshold Setting Gi: 116672304
Created: 17-Jul-2006
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
ligand binding
Conserved site includes 11 residues -Click on image for an interactive view with Cn3D
Feature 1:ligand binding site [chemical binding site]
Evidence:
  • Comment:based on structural 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                           #   #                                                        
3BBL_A         6 XIGYSWtqtep---gqvnhILDQFLSSXVREAgavnYFVLPFPfsedrsqiDIYRDLIRSgNVDGFVLSsinynDPRVQF 82
gi 13476262   61 TLTAVLpmetrd--ylsdlAKLPLIEGMTLAArqagYSLSIYSttpdddpvESVQRLLQAhSADGLIITrmvsgDPRVRL 138
gi 16264840   63 QVAAIMtapgpkenewegvEYAQLLSGISWALeespYRVSLYAvrdfeesqETISQIVSMkKADGIIISgtradDPRIRL 142
gi 16264850   70 QAAVLMpvtaardyewdgvEYTQILSGISQALegsdYRMSVHVvrnvedgcEVARRIIDEgLADGLIFSgiradDPRIDL 149
gi 86359300   81 VVAILLdshe-----evvgFSTSIMYGIAKALketsYHLVVAPnflsttnvEAAEYIIRNhLADGLIFTrteplDARVRL 155
gi 87122471   63 NICAILpvtkpg-divgdvGSLALIEGLTAALkgtpYHLTVLPmapdedpmEPVRYAFENnLCGGMIFNltktqDERVAY 141
gi 89056427   73 VVTLLLnteh-----eflgFTHEFLSGMTEALrgtgYSVNVVPdhvgedrlEPVRNILRNhLADGVLFTrteafDPRVRL 147
gi 89068763   68 QIAAVMtaprpeedewegvEYAQLLSGISLALegspYRVMLYAvddhaeatQVIRQLVDGgEADGVILSgtrprDERVAL 147
gi 118591968  79 VISLLLntrh-----eflsFTSEFLGGMSEGLagtgYAITITAdgladdrlEVIRNIRRHsLADAIVFTrtecfDDRVRY 153
gi 163740131  77 VISLVMsaer-----emmtQTARLLTSLGLALrethYHLNVSPvfpdddplRAVRYIVENqTADCVIFNqvepeDKRAEY 151
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                 ##          ####                                   #                   
3BBL_A        83 LLKQKFPFVAFGRsnpdwdfaWVDIDGTAGTRQAVEYLIgrGHRRIAILAWpedsrVGNDRLQGYLEAXQTAQlpi-etg 161
gi 13476262  139 LLDQGIPFVAFGRtdlgiaypYVDIDNEQIAYEATRRLMdkGCRRIALQLLvqkdqASATRLAGYRRAMAEAGipi-dqs 217
gi 16264840  143 MQEAEFPFVTYGMsihnaphaYVDADNEQMIRLSVARLIerGHRRIALLNPkeqfaYGVVRLESYRKALEKAGlpy-dpa 221
gi 16264850  150 LDESRFPFVSLGRcrkpldyaHVDIDNEWAAHAATARLIagGHRRIALVNPlrhlsYAEDRVDGFLRAFREANlsp-sdd 228
gi 86359300  156 LLETRFPFICHGRtefstphpYVDYDNFTFAYEATRRLIakGRTKVAVILPpkrltFCQHILHGFMTAVREAGiay-eip 234
gi 87122471  142 LHNNEIPFVTFGQtemsiehpYVDIDNHDMAYRAARQLYeqGRKNIRLLSSshdytYAWHKYYGARRAAREFGydf-eie 220
gi 89056427  148 LLEADFPFVSHGRtefttphpYVDFDNEAFARTAVQRLVakGRKRLSLILPedrftFTQHLRYGFLSAVREAGveyeivs 227
gi 89068763  148 LQARDVPFVTLGTtehhaphaFVDTDNAAIMEVALRRLAgrGHERIALINPpaemsYARTREAVYRRMLDELGlav-dea 226
gi 118591968 154 LLEHDFPFATHGRtdfttphpYVDFDNEVFARMAVERLVekGRRHICMVMPnerytFGQHLRFGARQAAMAHGvql-tip 232
gi 163740131 152 LIERNFPFATHGRtkwadqhpYYDFDNFAFSELSLAELAarGRRNIVLLAPplaqnYANDMVNGARHAAKALGiql-hva 230
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                          #                           #                 
3BBL_A       162 YILRGEGTfEVGRAXTLHLLDlsperrptAIXTLNDTXAIGAXAAARERgltigtdLAIIGFDDApxvqylfPPLSSVRQ 241
gi 13476262  218 LIGDGTFTmESSAAWFDRLLAssd--rptGLACANELGLLGALHALGRRglvpgrdVHIVTRDNTrlarflpANIGVHSV 295
gi 16264840  222 LVAHGRLTpAFGRENVVTMSAlad--pptAYICANEATALGAFSGFHARglvhgrdAVINATDDLnvsqyfaPPITSYYL 299
gi 16264850  229 LIAEGDLStHFGRESALGLLDaar--pptAFVCSNESTTLGVLSGLGSRgrrigvdVDVVAYDDInvsayftPPITTFYQ 306
gi 86359300  235 ETVDLDTPaDVLRDFVRARAAapd--apnSFICPGEVSALAVISGMSDAgrtlaadYDIVAKETSrlltqlqPKVDTIHE 312
gi 87122471  221 KNIILDSDvDDYRKLGNKMMLgdq--apdGLICGSEISACGLLAGIQDTgktigedIDVVLVETCdlpsffmPPISGYRQ 298
gi 89056427  228 GVTLDSSSaDIAQATRDSRNSptp---pdGYVCVGEVTALVTLSALSDSgavlgrdADIFAKRASpifdnirPRIDTVYE 304
gi 89068763  227 LILSGTLNpAFGRAAVARLSAlsa--pptAYICANEAAALGALSGFAEHglvhgrdAVINATDDLnvsayfvPPLTTFFL 304
gi 118591968 233 TGVDLDSDpDEIAATLRALHAgpn--apdGYVCVGEVMALVTLAYLNDMgltpgleVDVVAKRASpisnhfrPRIETIDE 310
gi 163740131 231 RQVQSNGLyKDLRNWAAEKHRedp--tidGFLCASTNATMSVVAGMESCgctvgqeFDVVAKEGLhmlkfvrPEIIVVQE 308
                        250       260       270
                 ....*....|....*....|....*....|....*
Feature 1                                           
3BBL_A       242 PIAEAGRKCIELlvaive-grepeqKHILLQPSLI 275
gi 13476262  296 DMADVGHKLIEVlesria-nplgpvATILLQGRFE 329
gi 16264840  300 PIGEPSALLGKFilrrme-geppdaLQTLLMPDLI 333
gi 16264850  307 PIEVLGRTLGEFllrrma-gedarsLKQVFRPRLI 340
gi 86359300  313 DLTAAGEDLGRMllqrin-npdaqdLHLLLPPQIN 346
gi 87122471  299 DFHQVGRKLIQHllrrin-getvkhLQTLQKTVYY 332
gi 89056427  305 DLRETGHKMAEMllrrmg-geaptgLTHLLAPDFE 338
gi 89068763  305 PISRPARLLGEYmlarla-gepvekLQTLLMPELI 338
gi 118591968 311 DLRATGRAMAKVllarig-gapmedMQILLKPEGA 344
gi 163740131 309 DIEATGVFLAKAalqaikspdlppqQFLEVPTEFV 343

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