Database accession: MF7000622
Name: Transcriptional repressor, CouR
PDB ID: 6c9t
Experimental method: X-ray (2.07 Å)
Assembly: Homodimer
Source organism: Rhodopseudomonas palustris
Primary publication of the structure:
Cogan DP, Baraquet C, Harwood CS, Nair SK
Structural basis of transcriptional regulation by CouR, a repressor of coumarate catabolism, in .
(2018) J. Biol. Chem. 293: 11727-11735
PMID: 29794028
Abstract:
The MarR family transcriptional regulator CouR, from the soil bacterium Rhodopseudomonas palustris CGA009, has recently been shown to negatively regulate a p-coumarate catabolic operon. Unlike most characterized MarR repressors that respond to small metabolites at concentrations in the millimolar range, repression by CouR is alleviated by the 800-Da ligand p-coumaroyl-CoA with high affinity and specificity. Here we report the crystal structures of ligand-free CouR as well as the complex with p-coumaroyl-CoA, each to 2.1-Å resolution, and the 2.85-Å resolution cocrystal structure of CouR bound to an oligonucleotide bearing the cognate DNA operator sequence. In combination with binding experiments that uncover specific residues important for ligand and DNA recognition, these structures provide glimpses of a MarR family repressor in all possible states, providing an understanding of the molecular basis of DNA binding and the conformation alterations that accompany ligand-induced dissociation for activation of the operon.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
DNA-binding transcription factor activity DNA-binding transcription factor activity
Biological process:
response to stress response to stress
Cellular component: not assigned
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: A, B
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: Transcriptional regulator, MarR family
Source organism: Rhodopseudomonas palustris
Length: 183 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMTSSNRITSPAMTASKTAAVAKPTRAGRKAPAVETAPEASELKMGELSELLGYALKRAQLRVFEDFLHCVAPVQLTPAQFSVLLLLDANPGRNQTEIATTLGILRPNFVAMLDALEGRGLCVRTRSPSDRRSHILMLTDKGRATLARAKKLVATRHEDRLTELLGRDNRDALLSMLATIAREF
UniProtKB AC: Q6N8V9 (positions: 42-183)
Coverage: 77%
Name: Transcriptional regulator, MarR family
Source organism: Rhodopseudomonas palustris
Length: 183 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMTSSNRITSPAMTASKTAAVAKPTRAGRKAPAVETAPEASELKMGELSELLGYALKRAQLRVFEDFLHCVAPVQLTPAQFSVLLLLDANPGRNQTEIATTLGILRPNFVAMLDALEGRGLCVRTRSPSDRRSHILMLTDKGRATLARAKKLVATRHEDRLTELLGRDNRDALLSMLATIAREF
UniProtKB AC: Q6N8V9 (positions: 42-183)
Coverage: 77%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: Winged helix DNA-binding domain (MarR type I) transcriptional regulator
Evidence level: Direct evidence
Evidence coverage: Only some parts of the structure participates in mutual synergistic folding.
Complex Evidence:
The MarR-type family transcriptional regulator, NadR is dimeric in solution (SE-HPLC/MALLS) as other MarR faimily proteins (PMID:18272181). Compared to ligand-stabilized holo-NadR, apo-NadR displayed an intrinsic flexibility focused in the DNA-binding region (PMID:27105075). The structural features of several family members have been described, they all have two subdomains: there is a helix-turn-helix (HTH) DNA-binding domain plus dimerization helices that form an interlocked dimerization domain. Dimerization is mediated by helices α1, α5, and α6 from each monomer resulting in an interlocked, tight dimer burying a large, hydrophobic solvent-accessible surface area. The structure of the dimerization region reveals domain swapping, where α1 of one subunit is inserted between α5′ and α6′ of the other subunit and forms a coiled coil with helix α6′ (PMID:19586910). The DNA-binding elements contain helices α3-α4 and strands β1-β2 from each monomer (PMID:29794028, PMID:35367827).
Chain A:
N/A
Chain B:
N/A
Surface and contacts features:
Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap). Download the CIF file (.cif)
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