2ASY

Solution Structure of ydhR protein from Escherichia coli

Summary for 2ASY

• Entry DOI: 10.2210/pdb2asy/pdb
• Related: 1WD6
• NMR Information: BMRB: 6868
• Descriptor: Protein ydhR precursor (1 entity in total)
• Functional Keywords: dimeric apha+beta barrel, homodimer, structural genomics, ontario centre for structural proteomics, ocsp, unknown function
• Biological source: Escherichia coli
• Total number of polymer chains: 2
• Total formula weight: 27767.13

Authors

Revington, M.,Semesi, A.,Yee, A.,Shaw, G.S.,Ontario Centre for Structural Proteomics (OCSP) (deposition date: 2005-08-24, release date: 2005-11-15, Last modification date: 2024-05-22)

Primary citation

Revington, M.,Semesi, A.,Yee, A.,Shaw, G.S.
Solution structure of the Escherichia coli protein ydhR: A putative mono-oxygenase.
Protein Sci., 14:3115-3120, 2005

PubMed 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.

PubMed: 16260765
DOI: 10.1110/ps.051809305

Experimental method

SOLUTION NMR