4kvl

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==Crystal structure of Oryza sativa fatty acid alpha-dioxygenase Y379F with palmitic acid==
==Crystal structure of Oryza sativa fatty acid alpha-dioxygenase Y379F with palmitic acid==
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<StructureSection load='4kvl' size='340' side='right' caption='[[4kvl]], [[Resolution|resolution]] 1.96&Aring;' scene=''>
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<StructureSection load='4kvl' size='340' side='right'caption='[[4kvl]], [[Resolution|resolution]] 1.96&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4kvl]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Orysa Orysa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KVL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KVL FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4kvl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryza_sativa Oryza sativa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KVL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KVL FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.96&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4kvj|4kvj]], [[4kvk|4kvk]]</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4kvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kvl OCA], [http://pdbe.org/4kvl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4kvl RCSB], [http://www.ebi.ac.uk/pdbsum/4kvl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4kvl ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4kvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kvl OCA], [https://pdbe.org/4kvl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kvl RCSB], [https://www.ebi.ac.uk/pdbsum/4kvl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kvl ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/PIOX_ORYSJ PIOX_ORYSJ] Alpha-dioxygenase that catalyzes the primary oxygenation step of a variety of 14-20 carbon fatty acids, containing up to three unsaturated bonds, into their corresponding 2R-hydroperoxides (PubMed:11909851, PubMed:18596034). Involved in the production of oxylipins that function in cell signaling, wound healing, and protection from infection (PubMed:11909851, PubMed:18596034).<ref>PMID:11909851</ref> <ref>PMID:18596034</ref>
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alpha-dioxygenases (alpha-DOX) are heme-containing enzymes found predominantly in plants and fungi, where they generate oxylipins in response to pathogen attack. alpha-DOX oxygenate a variety of 14-20 carbon fatty acids containing up to three unsaturated bonds through stereoselective removal of the pro-R hydrogen from the alpha-carbon by a tyrosyl radical generated via the oxidation of the heme moiety by hydrogen peroxide (H2 O2 ). We determined the X-ray crystal structures of wild type alpha-DOX from Oryza sativa, the wild type enzyme in complex with H2 O2 , and the catalytically inactive Y379F mutant in complex with the fatty acid palmitic acid (PA). PA binds within the active site cleft of alpha-DOX such that the carboxylate forms ionic interactions with His-311 and Arg-559. Thr-316 aids in the positioning of carbon-2 for hydrogen abstraction. Twenty-five of the twenty eight contacts made between PA and residues lining the active site occur within the carboxylate and first eight carbons, indicating that interactions within this region of the substrate are responsible for governing selectivity. Comparison of the wild type and H2 O2 structures provides insight into enzyme activation. The binding of H2 O2 at the distal face of the heme displaces residues His-157, Asp-158, and Trp-159 ~2.5A from their positions in the wild type structure. As a result, the Odelta2 atom of Asp-158 interacts with the Ca atom in the calcium binding loop, the side chains of Trp-159 and Trp-213 reorient, and the guanidinium group of Arg-559 is repositioned near Tyr-379, poised to interact with the carboxylate group of the substrate.
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Crystal Structures of alpha-Dioxygenase from Oryza sativa: Insights into Substrate Binding and Activation by Hydrogen Peroxide.,Zhu G, Koszelak-Rosenblum M, Malkowski MG Protein Sci. 2013 Aug 12. doi: 10.1002/pro.2327. PMID:23934749<ref>PMID:23934749</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 4kvl" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Orysa]]
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[[Category: Large Structures]]
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[[Category: Koszelak-Rosenblum, M]]
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[[Category: Oryza sativa]]
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[[Category: Malkowski, M G]]
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[[Category: Koszelak-Rosenblum M]]
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[[Category: Zhu, G]]
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[[Category: Malkowski MG]]
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[[Category: Calcium binding]]
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[[Category: Zhu G]]
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[[Category: Cox-like protein]]
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[[Category: Fatty acid alpha-dioxygenase]]
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[[Category: Heme binding]]
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[[Category: Monotopic membrane protein]]
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[[Category: Oxidoreductase]]
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[[Category: Piox]]
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Current revision

Crystal structure of Oryza sativa fatty acid alpha-dioxygenase Y379F with palmitic acid

PDB ID 4kvl

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