Solution structure of the Escherichia coli protein ydhR: A putative mono‐oxygenase

Abstract

YdhR is a 101‐residue conserved protein from Escherichia coli . Sequence searches reveal that the protein has >50% identity to proteins found in a variety of other bacterial genomes. Using size exclusion chromatography and fluorescence spectroscopy, we determined that ydhR exists in a dimeric state with a dissociation constant of ∼40 nM. The three‐dimensional structure of dimeric ydhR was determined using NMR spectroscopy. A total of 3400 unambiguous NOEs, both manually and automatically assigned, were used for the structure calculation that was refined using an explicit hydration shell. A family of 20 structures was obtained with a backbone RMSD of 0.48 Å for elements of secondary structure. The structure reveals a dimeric α,β fold characteristic of the alpha+beta barrel superfamily of proteins. Bioinformatic approaches were used to show that ydhR likely belongs to a recently identified group of mono‐oxygenase proteins that includes ActVA‐Orf6 and YgiN and are involved in the oxygenation of polyaromatic ring compounds.