PMID:16260765
| Citation |
Revington, M, Semesi, A, Yee, A and Shaw, GS (2005) Solution structure of the Escherichia coli protein ydhR: a putative mono-oxygenase. Protein Sci. 14:3115-20 |
|---|---|
| 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 approximately 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 A for elements of secondary structure. The structure reveals a dimeric alpha,beta 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. |
| Links |
PubMed PMC2253234 Online version:10.1110/ps.051809305 |
| Keywords |
Amino Acid Sequence; Binding Sites; Escherichia coli/enzymology; Escherichia coli Proteins/chemistry; Escherichia coli Proteins/metabolism; Mixed Function Oxygenases/chemistry; Mixed Function Oxygenases/metabolism; Models, Molecular; Molecular Sequence Data; Nuclear Magnetic Resonance, Biomolecular; Protein Structure, Quaternary; Protein Structure, Tertiary; Sequence Alignment; Sequence Homology, Amino Acid |
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