2asy
From Proteopedia
(New page: 200px<br /><applet load="2asy" size="450" color="white" frame="true" align="right" spinBox="true" caption="2asy" /> '''Solution Structure of ydhR protein from Esch...) |
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| - | [[Image:2asy.gif|left|200px]]<br /><applet load="2asy" size=" | + | [[Image:2asy.gif|left|200px]]<br /><applet load="2asy" size="350" color="white" frame="true" align="right" spinBox="true" |
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'''Solution Structure of ydhR protein from Escherichia coli'''<br /> | '''Solution Structure of ydhR protein from Escherichia coli'''<br /> | ||
==Overview== | ==Overview== | ||
| - | YdhR is a 101-residue conserved protein from Escherichia coli. Sequence | + | 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. |
==About this Structure== | ==About this Structure== | ||
| - | 2ASY is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http:// | + | 2ASY is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ASY OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: OCSP, Ontario | + | [[Category: OCSP, Ontario Centre for Structural Proteomics.]] |
[[Category: Revington, M.]] | [[Category: Revington, M.]] | ||
[[Category: Semesi, A.]] | [[Category: Semesi, A.]] | ||
| - | [[Category: Shaw, G | + | [[Category: Shaw, G S.]] |
[[Category: Yee, A.]] | [[Category: Yee, A.]] | ||
[[Category: dimeric apha+beta barrel]] | [[Category: dimeric apha+beta barrel]] | ||
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[[Category: structural genomics]] | [[Category: structural genomics]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:30:43 2008'' |
Revision as of 14:30, 21 February 2008
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Solution Structure of ydhR protein from Escherichia coli
Overview
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.
About this Structure
2ASY is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
Reference
Solution structure of the Escherichia coli protein ydhR: a putative mono-oxygenase., Revington M, Semesi A, Yee A, Shaw GS, Protein Sci. 2005 Dec;14(12):3115-20. Epub 2005 Oct 31. PMID:16260765
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