5CYV

Crystal structure of CouR from Rhodococcus jostii RHA1 bound to p-coumaroyl-CoA

Summary for 5CYV

• Entry DOI: 10.2210/pdb5cyv/pdb
• Related: 3FM5
• Descriptor: Transcriptional regulator, MAGNESIUM ION, ACETATE ION, ... (6 entities in total)
• Functional Keywords: transcription regulator, p-hydroxycinnamate metabolism, mcsg, pf04017, psi-biology, marr, structural genomics, protein structure initiative, midwest center for structural genomics, transcriptional regulator
• Biological source: Rhodococcus jostii (strain RHA1)
• Total number of polymer chains: 2
• Total formula weight: 33723.62

Authors

Stogios, P.J.,Xu, X.,Dong, A.,Savchenko, A.,Joachimiak, A.,Midwest Center for Structural Genomics (MCSG) (deposition date: 2015-07-30, release date: 2015-08-12, Last modification date: 2024-03-13)

Primary citation

Otani, H.,Stogios, P.J.,Xu, X.,Nocek, B.,Li, S.N.,Savchenko, A.,Eltis, L.D.
The activity of CouR, a MarR family transcriptional regulator, is modulated through a novel molecular mechanism.
Nucleic Acids Res., 44:595-607, 2016

PubMed 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.

PubMed: 26400178
DOI: 10.1093/nar/gkv955

Experimental method

X-RAY DIFFRACTION (1.52 Å)