1nu3: Difference between revisions
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==Limonene-1,2-epoxide hydrolase in complex with valpromide== | ==Limonene-1,2-epoxide hydrolase in complex with valpromide== | ||
<StructureSection load='1nu3' size='340' side='right' caption='[[1nu3]], [[Resolution|resolution]] 1.75Å' scene=''> | <StructureSection load='1nu3' size='340' side='right'caption='[[1nu3]], [[Resolution|resolution]] 1.75Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1nu3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"mycobacterium_erythropolis"_gray_and_thornton_1928 "mycobacterium erythropolis" gray and thornton 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NU3 OCA]. For a <b>guided tour on the structure components</b> use [http:// | <table><tr><td colspan='2'>[[1nu3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"mycobacterium_erythropolis"_gray_and_thornton_1928 "mycobacterium erythropolis" gray and thornton 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NU3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1NU3 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=VPR:2-PROPYLPENTANAMIDE'>VPR</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=VPR:2-PROPYLPENTANAMIDE'>VPR</scene></td></tr> | ||
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">limA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1833 "Mycobacterium erythropolis" Gray and Thornton 1928])</td></tr> | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">limA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1833 "Mycobacterium erythropolis" Gray and Thornton 1928])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http:// | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1nu3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nu3 OCA], [http://pdbe.org/1nu3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nu3 RCSB], [http://www.ebi.ac.uk/pdbsum/1nu3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nu3 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
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==See Also== | ==See Also== | ||
*[[Epoxide hydrolase|Epoxide hydrolase]] | *[[Epoxide hydrolase 3D structures|Epoxide hydrolase 3D structures]] | ||
*[[Limonene-1%2C2-epoxide hydrolase|Limonene-1%2C2-epoxide hydrolase]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
| Line 39: | Line 40: | ||
</StructureSection> | </StructureSection> | ||
[[Category: Mycobacterium erythropolis gray and thornton 1928]] | [[Category: Mycobacterium erythropolis gray and thornton 1928]] | ||
[[Category: Large Structures]] | |||
[[Category: Limonene-1,2-epoxide hydrolase]] | [[Category: Limonene-1,2-epoxide hydrolase]] | ||
[[Category: Arand, M]] | [[Category: Arand, M]] | ||
Revision as of 11:56, 2 December 2020
Limonene-1,2-epoxide hydrolase in complex with valpromideLimonene-1,2-epoxide hydrolase in complex with valpromide
Structural highlights
Function[LIMA_RHOER] Catalyzes the conversion of limonene-1,2-epoxide to limonene-1,2-diol. Can use both the (-) and (+) isomers of limonene-1,2-epoxide as substrates and also has some activity with 1-methylcyclohexene oxide, cyclohexene oxide and indene oxide as substrates. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedEpoxide 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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