1nu3: Difference between revisions

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<StructureSection load='1nu3' size='340' side='right'caption='[[1nu3]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
<StructureSection load='1nu3' size='340' side='right'caption='[[1nu3]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1nu3]] is a 2 chain structure with sequence from [https://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 [https://proteopedia.org/fgij/fg.htm?mol=1NU3 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1nu3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_erythropolis Rhodococcus erythropolis]. 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 [https://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" id="ligandDat"><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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75&#8491;</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='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=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=VPR:2-PROPYLPENTANAMIDE'>VPR</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">limA ([https://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'>[https://en.wikipedia.org/wiki/Limonene-1,2-epoxide_hydrolase Limonene-1,2-epoxide hydrolase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=1nu3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nu3 OCA], [https://pdbe.org/1nu3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nu3 RCSB], [https://www.ebi.ac.uk/pdbsum/1nu3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nu3 ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1nu3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nu3 OCA], [https://pdbe.org/1nu3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nu3 RCSB], [https://www.ebi.ac.uk/pdbsum/1nu3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nu3 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/LIMA_RHOER 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.  
[https://www.uniprot.org/uniprot/LIMA_RHOER 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 ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1nu3 ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1nu3 ConSurf].
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<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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<ref>PMID:12773375</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1nu3" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Epoxide hydrolase 3D structures|Epoxide hydrolase 3D structures]]
*[[Epoxide hydrolase 3D structures|Epoxide hydrolase 3D structures]]
*[[Limonene-1%2C2-epoxide hydrolase|Limonene-1%2C2-epoxide hydrolase]]
*[[Limonene-1%2C2-epoxide hydrolase|Limonene-1%2C2-epoxide hydrolase]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Mycobacterium erythropolis gray and thornton 1928]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Limonene-1,2-epoxide hydrolase]]
[[Category: Rhodococcus erythropolis]]
[[Category: Arand, M]]
[[Category: Arand M]]
[[Category: Bergfors, T]]
[[Category: Bergfors T]]
[[Category: Bont, J A.M de]]
[[Category: Hallberg BM]]
[[Category: Hallberg, B M]]
[[Category: Jones TA]]
[[Category: Jones, T A]]
[[Category: Mowbray SL]]
[[Category: Mowbray, S L]]
[[Category: Oesch F]]
[[Category: Oesch, F]]
[[Category: Zou J]]
[[Category: Werf, M J.van der]]
[[Category: De Bont JAM]]
[[Category: Zou, J]]
[[Category: Van der Werf MJ]]
[[Category: Hydrolase]]
[[Category: Protein-ligand complex]]
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