Conserved Protein Domain Family
PBP2_DntR_like_1

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cd08460: PBP2_DntR_like_1 
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold.
This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.
Statistics
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PSSM-Id: 176149
View PSSM: cd08460
Aligned: 36 rows
Threshold Bit Score: 205.517
Threshold Setting Gi: 54025696
Created: 29-Sep-2009
Updated: 2-Oct-2020
Structure
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Aligned Rows:
 
putativeputative
Feature 1:putative substrate binding pocket [chemical binding site]
Evidence:
  • Comment:based on the sequence-structure comparison with Burkholderia sp. DntR structure (1UTH_A)

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1              # ##   #                                                        #         
YP_001438141  97 TFTLRANDGFVEAFGPALIAAAARCAPgVRLRFAPkpvksdRPLREGeADLEIGVPgemgPEIKQQRLFRDRFVGVVRSD 176 Enterobacter sa...
NP_821904    103 TFTLQAADLVGAALAPGLLHLAQQEAPgVSFRLRAeeleagTALRDGrIDLEIGSIdhvdPETQVEELVSLRMMAAVRPG 182 Streptomyces av...
YP_003115610  93 GFTLRCHDALVAALAPALIEAVAETAPnVSIRFLAepsadaADLARGqTDLEVGAAapqrPEIAAHTIGTDRMVAVMRPD 172 Catenulispora a...
YP_715754    140 TFTILSSDMLVATIGVGLLDRLARQAPrVRLRLLPeptpsaDPLRDGtADLEIGQIdstaPEIRVETLGADSAIAVVRAG 219 Frankia alni AC...
ZP_05000756  100 TFTVLANEAFTAVSGATLFTRIAREAPgVRLRFLSeshvdvPALREGmADLELGVVdtrsPEVRVEHLSDELMVGVVRPG 179 Streptomyces sp...
YP_001108771  93 SFTLQTSDMLGAALTPVLLARVGAEAPeVTLRFAAeaaegtPALREGrVDVEIGVIehvdPETRSEALTSARLVAAVRPG 172 Saccharopolyspo...
ZP_04997043   95 VFTVRWHDTLTAACGTALTAAVHRQAPgVRLRLAAepgtddPGLRRGeVDLESSSSqpalPDIRHRLVGRDRLIVAVRPG 174 Streptomyces sp...
YP_002768193  97 TFVIRINEGTAASLTPALVRRFAAEAPnAVIRCVGegnedvDSLRNGsIDLDIGADplpsSDVCSEILYREGHVGLVSKS 176 Rhodococcus ery...
YP_889252     97 TFSVQLGDGLFSHCGPRLLARVHAEALnVTLKFVGeshedtHSLREGsVDIEIGQVrrtePETIIEPLVEENWVGVARAG 176 Mycobacterium s...
YP_003101919  95 VFCLRWHDAVTELVGPEVLAAVRERAPgVRLRFLGesdsdgREALEG-VDLGTSAGpapsPDVHHEVVRRDLPSVVLRED 173 Actinosynnema m...
Feature 1                                    #                                                   
YP_001438141 177 HPLagrdv-tpedYLAWGHVAASRRGVLTGPVDDALAQRGlsRNIAAVVPGFPAALAVARGtDLVALVPASFLINlpg-- 253 Enterobacter sa...
NP_821904    183 HPLtegpl-tparLAAAEHVAVSRRGRFSGPLDTALAEQNlhRRVSFVLPSHLAAMTLATRsDVVCLVPAAPPGAapspl 261 Streptomyces av...
YP_003115610 173 HPLatgpl-tpqrFAEADHLTISRRGRLTGPIDEALADLGlhRRVRAALPTTSTALELTARtTLITTVAEQVCRPawt-- 249 Catenulispora a...
YP_715754    220 HPLtegpl-tpqrLAAARHVVASRRGRLSGPIDEALAALGlrRTVVASVSSHTVALSLVAHsDLVGVAPRRLGRDrla-- 296 Frankia alni AC...
ZP_05000756  180 HPLlkgrl-tarrFAAADHLIASRRGRLEGPVDTALAELGltRRVVGSVGTFPASLFVLREsDLVGLLTTQAAPLaa--- 255 Streptomyces sp...
YP_001108771 173 HPLirgrv-tpdrFSAAAHISVSRRGRAWGPIDERLDAIGlrRRVAVVLPSHTAAMFLARDtDLVCLTPAISGNGtae-- 249 Saccharopolyspo...
ZP_04997043  175 HPLtegal-sperYAAAEHLTVSRRGNLHDPLDGALGALGleRRVVASGPTAAFALQLALGsDLVVTIPDAVTRAard-- 251 Streptomyces sp...
YP_002768193 177 SPLartaqptlaqLCEHPHVSTSRRGRTHGPIDDALSAVGmrRRVIAVVASPVAAALMAADsDLVALVPERLARYfaa-- 254 Rhodococcus ery...
YP_889252    177 HELtgkrv-tlkrFADAEHVVFSRRGRLRGPVDDLLAEHGlrRRVVACAPSPAGGLFLIQNsDLVGMLPAGIGAQaia-- 253 Mycobacterium s...
YP_003101919 174 HELargel-taerYAAAGHVVVSRRGALADRVDGLLAELGltRSVVAAVPTGVAALRLARRcGLVATLPSSVAGPlar-- 250 Actinosynnema m...
Feature 1                              #                         
YP_001438141 254 -----dtGLTWFELPVATRPITVSQMWHPrlDADPAHRWLRQFVLAEC 296 Enterobacter sakazakii ATCC BAA-894
NP_821904    262 tddaialGLFLLDIPLELPPLTIGMAWHPrhTADGAHHWLRNAIRRTL 309 Streptomyces avermitilis MA-4680
YP_003115610 250 -----nlGLRARPLPFTLPAVPVIVAWHHryDTDPAHSWLRTHLLAVL 292 Catenulispora acidiphila DSM 44928
YP_715754    297 -----alGLVPLDLGLDLPSLSLCLAWHPryDADAPHRWLRAQVRDVI 339 Frankia alni ACN14a
ZP_05000756  256 -----glGLETFRIPLDLPALPFGMAWHPrhDADPAHAWLRGCARELL 298 Streptomyces sp. Mg1
YP_001108771 250 -----alGLHTFEVPLELPPVEVGMAWHPrnDADPAHRWLRDHIREAV 292 Saccharopolyspora erythraea NRRL 2338
ZP_04997043  252 -----qlGLVTLPLPISLPDVSLYLLWHQryDDDRAHTWLRDLATETI 294 Streptomyces sp. Mg1
YP_002768193 255 -----rlDVAWFAVPTELPAVTIHQQWHGrlDHDPAHKWLREQVREAS 297 Rhodococcus erythropolis PR4
YP_889252    254 -----tfALQTFTIPLELPPLVIGMAWHPrfDADGAHRWLRDCVRSAV 296 Mycobacterium smegmatis str. MC2 155
YP_003101919 251 -----ehGLAHRPLPLDALEIALHLTWHRrhDGDPAHRWLRELCLVEL 293 Actinosynnema mirum DSM 43827

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