1nu3: Difference between revisions
New page: left|200px<br /><applet load="1nu3" size="450" color="white" frame="true" align="right" spinBox="true" caption="1nu3, resolution 1.75Å" /> '''Limonene-1,2-epoxide... |
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[[Image:1nu3.gif|left|200px]]<br /><applet load="1nu3" size=" | [[Image:1nu3.gif|left|200px]]<br /><applet load="1nu3" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="1nu3, resolution 1.75Å" /> | caption="1nu3, resolution 1.75Å" /> | ||
'''Limonene-1,2-epoxide hydrolase in complex with valpromide'''<br /> | '''Limonene-1,2-epoxide hydrolase in complex with valpromide'''<br /> | ||
==Overview== | ==Overview== | ||
Epoxide hydrolases are essential for the processing of epoxide-containing | Epoxide hydrolases are essential for the processing of epoxide-containing compounds in detoxification or metabolism. The classic epoxide hydrolases have an alpha/beta hydrolase fold and act via a two-step reaction mechanism including an enzyme-substrate intermediate. We report here the structure of the limonene-1,2-epoxide hydrolase from Rhodococcus erythropolis, solved using single-wavelength anomalous dispersion from a selenomethionine-substituted protein and refined at 1.2 A resolution. This enzyme represents a completely different structure and a novel one-step mechanism. The fold features a highly curved six-stranded mixed beta-sheet, with four alpha-helices packed onto it to create a deep pocket. Although most residues lining this pocket are hydrophobic, a cluster of polar groups, including an Asp-Arg-Asp triad, interact at its deepest point. Site-directed mutagenesis supports the conclusion that this is the active site. Further, a 1.7 A resolution structure shows the inhibitor valpromide bound at this position, with its polar atoms interacting directly with the residues of the triad. We suggest that several bacterial proteins of currently unknown function will share this structure and, in some cases, catalytic properties. | ||
==About this Structure== | ==About this Structure== | ||
1NU3 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rhodococcus_erythropolis Rhodococcus erythropolis] with MES and VPR as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Limonene-1,2-epoxide_hydrolase Limonene-1,2-epoxide hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.3.2.8 3.3.2.8] Full crystallographic information is available from [http:// | 1NU3 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rhodococcus_erythropolis Rhodococcus erythropolis] with <scene name='pdbligand=MES:'>MES</scene> and <scene name='pdbligand=VPR:'>VPR</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Limonene-1,2-epoxide_hydrolase Limonene-1,2-epoxide hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.3.2.8 3.3.2.8] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NU3 OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: Arand, M.]] | [[Category: Arand, M.]] | ||
[[Category: Bergfors, T.]] | [[Category: Bergfors, T.]] | ||
[[Category: Bont, J | [[Category: Bont, J A.M de.]] | ||
[[Category: Hallberg, B | [[Category: Hallberg, B M.]] | ||
[[Category: Jones, T | [[Category: Jones, T A.]] | ||
[[Category: Mowbray, S | [[Category: Mowbray, S L.]] | ||
[[Category: Oesch, F.]] | [[Category: Oesch, F.]] | ||
[[Category: Werf, M | [[Category: Werf, M J.van der.]] | ||
[[Category: Zou, J.]] | [[Category: Zou, J.]] | ||
[[Category: MES]] | [[Category: MES]] | ||
| Line 27: | Line 27: | ||
[[Category: protein-ligand complex]] | [[Category: protein-ligand complex]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:10:03 2008'' | ||
Revision as of 15:10, 21 February 2008
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Limonene-1,2-epoxide hydrolase in complex with valpromide
OverviewOverview
Epoxide hydrolases are essential for the processing of epoxide-containing compounds in detoxification or metabolism. The classic epoxide hydrolases have an alpha/beta hydrolase fold and act via a two-step reaction mechanism including an enzyme-substrate intermediate. We report here the structure of the limonene-1,2-epoxide hydrolase from Rhodococcus erythropolis, solved using single-wavelength anomalous dispersion from a selenomethionine-substituted protein and refined at 1.2 A resolution. This enzyme represents a completely different structure and a novel one-step mechanism. The fold features a highly curved six-stranded mixed beta-sheet, with four alpha-helices packed onto it to create a deep pocket. Although most residues lining this pocket are hydrophobic, a cluster of polar groups, including an Asp-Arg-Asp triad, interact at its deepest point. Site-directed mutagenesis supports the conclusion that this is the active site. Further, a 1.7 A resolution structure shows the inhibitor valpromide bound at this position, with its polar atoms interacting directly with the residues of the triad. We suggest that several bacterial proteins of currently unknown function will share this structure and, in some cases, catalytic properties.
About this StructureAbout this Structure
1NU3 is a Single protein structure of sequence from Rhodococcus erythropolis with and as ligands. Active as Limonene-1,2-epoxide hydrolase, with EC number 3.3.2.8 Full crystallographic information is available from OCA.
ReferenceReference
Structure of Rhodococcus erythropolis limonene-1,2-epoxide hydrolase reveals a novel active site., Arand M, Hallberg BM, Zou J, Bergfors T, Oesch F, van der Werf MJ, de Bont JA, Jones TA, Mowbray SL, EMBO J. 2003 Jun 2;22(11):2583-92. PMID:12773375
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