Database accession: MF7000757
Name: CouR with p-coumaroyl-CoA (Rhodococcus jostii RHA1)
PDB ID: 5cyv
Experimental method: X-ray (1.52 Å)
Assembly: Homodimer
Source organism: Rhodococcus jostii
Primary publication of the structure:
Otani H, Stogios PJ, Xu X, Nocek B, Li SN, Savchenko A, Eltis LD
The activity of CouR, a MarR family transcriptional regulator, is modulated through a novel molecular mechanism.
(2016) Nucleic Acids Res. 44: 595-607
PMID: 26400178
Abstract:
CouR, a MarR-type transcriptional repressor, regulates the cou genes, encoding p-hydroxycinnamate catabolism in the soil bacterium Rhodococcus jostii RHA1. The CouR dimer bound two molecules of the catabolite p-coumaroyl-CoA (Kd = 11 ± 1 μM). The presence of p-coumaroyl-CoA, but neither p-coumarate nor CoASH, abrogated CouR's binding to its operator DNA in vitro. The crystal structures of ligand-free CouR and its p-coumaroyl-CoA-bound form showed no significant conformational differences, in contrast to other MarR regulators. The CouR-p-coumaroyl-CoA structure revealed two ligand molecules bound to the CouR dimer with their phenolic moieties occupying equivalent hydrophobic pockets in each protomer and their CoA moieties adopting non-equivalent positions to mask the regulator's predicted DNA-binding surface. More specifically, the CoA phosphates formed salt bridges with predicted DNA-binding residues Arg36 and Arg38, changing the overall charge of the DNA-binding surface. The substitution of either arginine with alanine completely abrogated the ability of CouR to bind DNA. By contrast, the R36A/R38A double variant retained a relatively high affinity for p-coumaroyl-CoA (Kd = 89 ± 6 μM). Together, our data point to a novel mechanism of action in which the ligand abrogates the repressor's ability to bind DNA by steric occlusion of key DNA-binding residues and charge repulsion of the DNA backbone.
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
metal ion binding metal ion binding
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
Source organism: Rhodococcus jostii
Length: 146 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMAESQALSDDIGFLLSRVGGMVLGAVNKALVPTGLRVRSYSVLVLACEQAEGVNQRGVAATMGLDPSQIVGLVDELEERGLVVRTLDPSDRRNKLIAATEEGRRLRDDAKARVDAAHGRYFEGIPDTVVNQMRDTLQSIAFPTFVE
UniProtKB AC: Q0S6D0 (positions: 4-146)
Coverage: 97%
Name: Transcriptional regulator
Source organism: Rhodococcus jostii
Length: 146 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMAESQALSDDIGFLLSRVGGMVLGAVNKALVPTGLRVRSYSVLVLACEQAEGVNQRGVAATMGLDPSQIVGLVDELEERGLVVRTLDPSDRRNKLIAATEEGRRLRDDAKARVDAAHGRYFEGIPDTVVNQMRDTLQSIAFPTFVE
UniProtKB AC: Q0S6D0 (positions: 4-146)
Coverage: 97%
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 II) transcriptional regulator
Evidence level: Indirect evidence
Evidence coverage: Only some parts of the structure participates in mutual synergistic folding.
Complex Evidence:
Thermal unfolding measured with circular dichroism of the MarR family protein, HucR, suggested two-state model of unfolding (PMID:15448166). Also, a decrease in pH induced a molten globule-like state, where the protein remained in dimeric form (PMID:27282811). Helices 1, 2, 6 and 7 form the dimerization subdomain, they form an apparently stable dimer interface that preconfigures the DNA recognition HTH subdomain for DNA binding (PMID:16750221).
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)
Download this entry's XML file (.xml)
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