Conserved Protein Domain Family
PBP2_ClcR

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cd08485: PBP2_ClcR 
The C-terminal substrate binding domain of LysR-type transcriptional regulator ClcR involved in the chlorocatechol catabolism, contains type 2 periplasmic binding fold.
In soil bacterium Pseudomonas putida, the ortho-pathways of catechol and 3-chlorocatechol are central catabolic pathways that convert aromatic and chloroaromaric compounds to tricarboxylic acid (TCA) cycle intermediates. The 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR and an intermediate of the pathway, 2-chloromuconate, as an inducer for activation. The 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: 176174
View PSSM: cd08485
Aligned: 4 rows
Threshold Bit Score: 348.992
Threshold Setting Gi: 154367889
Created: 19-Oct-2009
Updated: 2-Oct-2020
Structure
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Aligned Rows:
 
putativeputative
Feature 1:putative dimerization interface [polypeptide binding site]
Evidence:
  • Comment:based on the sequence-structure comparison with Cupriavidus necator CbnR structure (1IZ1_A).

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1           #    ###  ##  #  #       ##             ##         #                     #
Q05840     91 GELRVAYFGTVVLHTLPLLLRQLLSVAPsATVSLTQmsKNRQIEALDAGtIDIGFGRFYPyqegVVVRNVTNeRLFLGAQ 170 Pseudomonas putida
ABQ23433   91 GELRVAYFGTVVLHTLPLLLRQLLSVAPsATVSLTQmsKNRQIEALDAGtIDIGFGRFYPyqegVVVRNVTNeRLFLGAQ 170 Alcaligenes sp. Ny...
ABS81345   91 GELRVAYFGTVVLHTLPLLLRQLLSVAPsATVSLTQmsKNRQIEALDAGtIDIGFGRFYPhqegVVVRNVTNeRLFLGAQ 170 Pandoraea pnomenusa
CAA06967   91 GELRVAYFGTVVLHTLPLLLRQLLSVAPsATVSLTQmsKNRQIEALDAGtIDIGFGRFYPyqegVVVRNVTNeRLFLGAQ 170 Ralstonia sp. JS705
Feature 1                                  #  ### #        ## # #  #      #  ##             ##
Q05840    171 KSRarSFGEQVHCsaLRNEPFILFPregrPSFADEVIGVFKnaRVEPKVVAIVEDVnAAMALALAGvGVTIVPETvamIS 250 Pseudomonas putida
ABQ23433  171 KSRarSFGEQVHCsaLRNEPLILFPregrPSFADEVIGVFKnaRVEPKVVAIVEDVnAAMALALAGvGVTIVPETvamIS 250 Alcaligenes sp. Ny...
ABS81345  171 NSRarSFGEQVHCsaLRNEPLILFPregrPSFADEVIGVFKraRVEPKVVAIVEDVnAAMALALAGvGVTIVPETvamIS 250 Pandoraea pnomenusa
CAA06967  171 KSRarSFGEQVHCsaLRNEPLILFPregrPSFADEVIGVFKnaRVEPKVVAIVEDVnAAMALALAGvGVTIVPETvamIS 250 Ralstonia sp. JS705
Feature 1     ##                    #               
Q05840    251 WPDFGFTELVGskaTVPVSCIYRHdhiaPILKTFLNLL 288 Pseudomonas putida
ABQ23433  251 WPDFGFTELVGskaTVPVSCIYRHdhiaPILKTFLNLL 288 Alcaligenes sp. NyZ215
ABS81345  251 RTDFGFTELVGtkaTVPVSCIYRHdhiaPILETFLSLL 288 Pandoraea pnomenusa
CAA06967  251 WPDFGFTELVGskaTVPVSCIYRHdhiaPILKTFLNLL 288 Ralstonia sp. JS705

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