2dio: Difference between revisions
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<StructureSection load='2dio' size='340' side='right'caption='[[2dio]], [[Resolution|resolution]] 1.70Å' scene=''> | <StructureSection load='2dio' size='340' side='right'caption='[[2dio]], [[Resolution|resolution]] 1.70Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2dio]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[2dio]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DIO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DIO FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EOD:11-[(2R,3S)-3-PENTYLOXIRAN-2-YL]UNDECANOIC+ACID'>EOD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=2dio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dio OCA], [https://pdbe.org/2dio PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dio RCSB], [https://www.ebi.ac.uk/pdbsum/2dio PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dio 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=2dio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dio OCA], [https://pdbe.org/2dio PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dio RCSB], [https://www.ebi.ac.uk/pdbsum/2dio PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dio ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[https://www.uniprot.org/uniprot/AOC2_ARATH AOC2_ARATH] Involved in the production of 12-oxo-phytodienoic acid (OPDA), a precursor of jasmonic acid. | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/di/2dio_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/di/2dio_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/ | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </jmolCheckbox> | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Arabidopsis thaliana]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Hofmann | [[Category: Hofmann E]] | ||
[[Category: Schaller | [[Category: Schaller F]] | ||
[[Category: Zerbe | [[Category: Zerbe P]] | ||
Latest revision as of 03:52, 21 November 2024
Crystal Structure of the Allene Oxide Cyclase 2 with bound inhibitor vernolic acidCrystal Structure of the Allene Oxide Cyclase 2 with bound inhibitor vernolic acid
Structural highlights
FunctionAOC2_ARATH Involved in the production of 12-oxo-phytodienoic acid (OPDA), a precursor of jasmonic acid. 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 PubMedWe describe the crystallization and structure elucidation of Arabidopsis thaliana allene oxide cyclase 2 (AOC2), a key enzyme in the biosynthesis of jasmonates. In a coupled reaction with allene oxide synthase, AOC2 releases the first cyclic and biologically active metabolite, 12-oxo-phytodienoic acid (OPDA). AOC2 (AT3G25770) folds into an eight-stranded antiparallel beta-barrel with a C-terminal partial helical extension. The protein forms a hydrophobic binding cavity with two distinct polar patches. AOC2 is trimeric in crystals, in vitro and in planta. Based on the observed folding pattern, we assigned AOC2 as a low molecular weight member of the lipocalin family with enzymatic activity in plants. We determined the binding position of the competitive inhibitor vernolic acid (a substrate analog) in the binding pocket. Based on models for bound substrate 12,13-epoxy-9,11,15-octadecatrienoic acid and product OPDA, we propose a reaction scheme that explains the influence of the C15 double bond on reactivity. Reaction is promoted by anchimeric assistance through a conserved Glu residue. The transition state with a pentadienyl carbocation and an oxyanion is stabilized by a strongly bound water molecule and favorable pi-pi interactions with aromatic residues in the cavity. Stereoselectivity results from steric restrictions to the necessary substrate isomerizations imposed by the protein. The crystal structure of Arabidopsis thaliana allene oxide cyclase: insights into the oxylipin cyclization reaction.,Hofmann E, Zerbe P, Schaller F Plant Cell. 2006 Nov;18(11):3201-17. Epub 2006 Nov 3. PMID:17085685[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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