Solution structure of theEscherichia coliprotein ydhR: A putative mono-oxygenase
| Autor: | Gary S. Shaw, Adelinda Yee, Matthew Revington, Anthony Semesi |
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| Rok vydání: | 2005 |
| Předmět: |
Models
Molecular Molecular Sequence Data Sequence alignment Biology medicine.disease_cause Biochemistry Mixed Function Oxygenases Structural genomics Protein structure Escherichia coli medicine Amino Acid Sequence Protein Structure Quaternary Nuclear Magnetic Resonance Biomolecular Molecular Biology Protein secondary structure Peptide sequence Binding Sites Sequence Homology Amino Acid Escherichia coli Proteins Nuclear magnetic resonance spectroscopy Protein Structure Tertiary Crystallography Beta barrel Protein Structure Report Sequence Alignment |
| Zdroj: | Protein Science. 14:3115-3120 |
| ISSN: | 1469-896X 0961-8368 |
| DOI: | 10.1110/ps.051809305 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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