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PROTEIN STRUCTURE REPORT

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

¹ Department of Biochemistry, The University of Western Ontario, London, Ontario, N6A 5C1, Canada
² Ontario Centre for Structural Proteomics, University Health Network, Toronto, Ontario, M5G 2C4, Canada

(RECEIVED August 26, 2005; FINAL REVISION August 26, 2005; ACCEPTED August 31, 2005)

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 , 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.

Keywords: alpha + beta barrel; automated refinement; NMR; structural genomics; water refinement

Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.051809305.

Reprint requests to: Gary S. Shaw, Department of Biochemistry, The University of Western Ontario, London, ON, N6A 5C1, Canada; e-mail: gshaw1{at}uwo.ca; fax: (519) 661-3175.

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