1UTB,1UTH,1UTB,2UYF,2UYE,1UTH


Conserved Protein Domain Family
PBP2_DntR_NahR_LinR_like

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cd08459: PBP2_DntR_NahR_LinR_like 
Click on image for an interactive view with Cn3D
The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold.
This CD includes LysR-like bacterial transcriptional regulators, 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. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate of the oxidative degradation of the aromatic ring in soil bacteria. LinR positively regulates expression of the genes (linD and linE) encoding enzymes for gamma-hexachlorocyclohexane (a haloorganic insecticide) degradation. Expression of linD and linE are induced by their substrates, 2,5-dichlorohydroquinone (2,5-DCHQ) and chlorohydroquinone (CHQ). The structural topology of this substrate-binding domain is most similar to that of 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: 176148
View PSSM: cd08459
Aligned: 65 rows
Threshold Bit Score: 175.843
Threshold Setting Gi: 13242048
Created: 29-Sep-2009
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
substratedimerization
Conserved site includes 7 residues -Click on image for an interactive view with Cn3D
Feature 1:substrate binding pocket [chemical binding site]
Evidence:
  • Structure:1UTB; Burkholderia sp. DntR binds acetic acid, contacts at 4 A.
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1              # ##   #                                                          #       
1UTB_A       106 TFNLAMTDIGEMYFMPPLMEALAQRAPhIQISTLRpnagnlkEDMESGaVDLALGLLpel-qtgFFQRRLFRHRYVCMFR 184 Burkholderia sp.
YP_726247     42 TFTLALSDVGEAAFLPRLLARLMKEAPhVDVRTVSarhtdimDQLERGrIDLAIGYYpdlggsdVFQQRLFRHGFVCLAR 121 Ralstonia eutro...
YP_001480843  98 TLTLCMPDIGEQYFLPPLINHLAQVAPgMAVVSHElapaqleEALESGrVDLAIGYFpdlrravFYQQRLFYSGFCCAVR 177 Serratia protea...
YP_001861040 103 TFTIALSDVGEMVSLPRLLQRVTSLAPsVNVTTVSfapkqllSSLQRSeVDLAIGYFpdldgvdVFQQHLVRHSFVCLVR 182 Burkholderia ph...
YP_001355260  98 TFSFYMTEIGEILLLPKLLKHIQVAAPnACVRVRRipeqgakEAMANGeIDLAVGLFpyl-kagFYQQRLYTDKFACIVR 176 Janthinobacteri...
YP_002889975 119 NLTVALSDVGELVFLPRILDSVRRLAPlAMLDSVTlapgelmRAMEDGeVDLAIGYYpdldaagFYREKLLDHRFVCLLR 198 Thauera sp. MZ1T
NP_520364    100 LFSIALSDVGEMVFLPRIVEAMARQAPhASVQSVTlppaqieRALETGaLDLAVGYFpdlkknnFFQQRLFTHYFTCIVR 179 Ralstonia solan...
NP_744094     98 LFTISTSDIGALIFVPPILRRLGEDAPnTDLRCVSlphqqleQALEQGsVDLAVGYFpdlqgeqVKTQALFEHNFTCIVR 177 Pseudomonas put...
YP_551510     98 HWRLSLSDLGEMLFLPALAGALRSQAPgARLSNISvaandvaAALEAReIDLAIGILqpr-qrgIRTELLFRENYVAVAS 176 Polaromonas sp....
BAE93937      99 HFVIATSDLGDMYFGPKLISHIRDISQdITIEFVGnsrphifESLENGeVDILLGFRpdl-itnMFVFRLFYQGWRILAR 177 Sphingomonas sp...
Feature 1                                          #                                             
1UTB_A       185 KDHPsaksp----mslkqFSELEHVGVval-ntGHGEVDGLLeragikrrMRLVVPHFIAIGPILHStDLIATVPQRFAV 259 Burkholderia sp.
YP_726247    122 KNHPvargr----mtaqqFREPPHAMIqne-srSQELVEAYLrqhgiarrEMLRSPHFLSIPLVIASsDLVVTVPLPVGE 196 Ralstonia eutro...
YP_001480843 178 QGHPqigkt----lslpqFLQAEHVTArlr-irSQEIAEQAMreqgivrnVKLQTSHFLSLTQIIAQtDLLATVTYEAAQ 252 Serratia protea...
YP_001861040 183 QNHPavqgr----ltkklFCELPHAVVqve-grRQEIVEQFLkengirrrEVLHTPHFLSIPMTIAMtDLVVTVSSDVGE 257 Burkholderia ph...
YP_001355260 177 QGHPtvhds----ltpqqYVDTPHVIVmsantgHDAAIEKILltehlrrkIVMTSQNFLVLPMIIEQtDAIATIPFRMAQ 252 Janthinobacteri...
YP_002889975 199 ADHPvqdrq----lslerFLSLEHAAVrak-grSQEIFEKYLerlriqrrIVLRTPHFMSLPGIIGRsDLVVTLPHAIGH 273 Thauera sp. MZ1T
NP_520364    180 ADHPvtrggnt-rlsmqqFLEYGHAVVrae-grSQELYERFLerkrirrkPALLTPHFMSIPFILARtDLIATVPHAVGL 257 Ralstonia solan...
NP_744094    178 RNHPsigdt----lsleqFLAADHLVVnqe-grSQEIFEQRLrelklqrrVHLEVPHFMSVPQLIAStNMVATVPLSLGV 252 Pseudomonas put...
YP_551510    177 PQWRpasgrsgrtlttqqLAEAAFVVAspt-atFHGSVEQMLvrmklqdrIVLRARHFGALPDLALAtDLLSIVPEMYAR 255 Polaromonas sp....
BAE93937     178 KDHPifssk----apredLLACRWIGVrse-gsGSASVNAELlkvgmdrnIVVWTSNFGTLAPLLAVgDLAACVPEIYTT 252 Sphingomonas sp...
Feature 1                              #                         
1UTB_A       260 Rcev-pfGLTTSPHPAKLPDIAINLFWHAkyNRDPGNMWLRQLFVELF 306 Burkholderia sp.
YP_726247    197 Lfar-iaDVQVLEPPFPIPAFDLRQHWHRcqHDDPGNRWLRAITQELF 243 Ralstonia eutropha H16
YP_001480843 253 Llqa-agKVHIYPVPFPIPQFPVMQYWHEraHHDRGNQWLRGEIRGLF 299 Serratia proteamaculans 568
YP_001861040 258 Ifar-iaELEILDPPYKMPRFDVNQYWHRsqHDDPGNRWMRGLVRELF 304 Burkholderia phymatum STM815
YP_001355260 253 KiasystGIKILESPIPFPNVDIKQHWHErfHYDPANKWMRDLMVTLF 300 Janthinobacterium sp. Marseille
YP_002889975 274 YftrvgeKVRMAEPPLAIPHIELYQHWHRgfHHDPRNRWLRTLVAGLF 321 Thauera sp. MZ1T
NP_520364    258 SfmqshaNIRVMEPPLALPSFDLKQHWHRkfHNDARSQWLRALVSSLF 305 Ralstonia solanacearum GMI1000
NP_744094    253 Wfa--seQIKMLTPPIEVEKFELKLHWHRqmEDDPAVSWFRNAVFEEL 298 Pseudomonas putida KT2440
YP_551510    256 Nlr--qrYDFRVWGIPGAPSYEVRLVWHSstDNDPAHQWMRALVQQLF 301 Polaromonas sp. JS666
BAE93937     253 Vide-afGLKSMPFPVDLPKHSISSVWHSkaHNDPANQWLRQQVSILF 299 Sphingomonas sp. A4

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