Structural basis for regulation of a p-coumarate catabolic gene cluster by CouR, a MarR-family transcriptional regulator in Rhodopseudomonas palustris

Many soil-dwelling bacteria have evolved capabilities of using plant-derived phenylpropanoids as carbon sources by converting them to acetyl-CoA and benzaldehyde-derivatives that can be used in fatty-acid metabolism, polyketide biosynthesis, and aromatic ring degradation. The molecular mechanisms behind regulation of these carbon sources, however, have remained enigmatic in terms of the structure-function relationships between transcriptional regulators and their cognate binding partners. The MarR-family transcriptional regulator CouR, from the soil bacterium Rhodopseudomonas palustris, has recently been shown to negatively regulate a p-coumarate catabolic operon whose repression is alleviated by p-coumaroyl-CoA. Here we report the crystal structure of CouR in complex with p-coumaroyl-CoA at 2.2 Å, representing the first view of a MarR protein bound to an aryl-CoA thioester. In addition, we have solved the 2.9 Å crystal structure of CouR bound to its DNA promoter fragment, thus providing a molecular basis for ligand induced dissociation and activation of the operon. Preliminary results of a gel-shift assay also reveal important DNA binding residues selected on the basis of the crystal structure. These findings represent the first simultaneous account of a MarR-family regulator bound to both its physiologically relevant ligand and promoter fragment.