4kvk - Revision history

OCA at 12:15, 1 March 2024

OCA — Fri, 01 Mar 2024 12:15:44 GMT

←Older revision		Revision as of 12:15, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4kvk]] 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=4KVK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KVK FirstGlance]. <br>		<table><tr><td colspan='2'>[[4kvk]] 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=4KVK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KVK FirstGlance]. <br>
-	</td></tr><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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DMU:DECYL-BETA-D-MALTOPYRANOSIDE'>DMU</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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]] 1.98Å</td></tr>
		+	<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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DMU:DECYL-BETA-D-MALTOPYRANOSIDE'>DMU</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=4kvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kvk OCA], [https://pdbe.org/4kvk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kvk RCSB], [https://www.ebi.ac.uk/pdbsum/4kvk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kvk 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=4kvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kvk OCA], [https://pdbe.org/4kvk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kvk RCSB], [https://www.ebi.ac.uk/pdbsum/4kvk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kvk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[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>		[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>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	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.
-
-	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>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4kvk" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:17, 7 December 2022

OCA — Wed, 07 Dec 2022 09:17:12 GMT

←Older revision		Revision as of 09:17, 7 December 2022
Line 3:		Line 3:
	<StructureSection load='4kvk' size='340' side='right'caption='[[4kvk]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='4kvk' size='340' side='right'caption='[[4kvk]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4kvk]] 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=4KVK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4KVK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4kvk]] 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=4KVK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KVK FirstGlance]. <br>
-	</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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DMU:DECYL-BETA-D-MALTOPYRANOSIDE'>DMU</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>~~</td></tr>~~	+	</td></tr><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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DMU:DECYL-BETA-D-MALTOPYRANOSIDE'>DMU</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4kvj\|4kvj]], [[4kvl\|4kvl]]~~</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=4kvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kvk OCA], [https://pdbe.org/4kvk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kvk RCSB], [https://www.ebi.ac.uk/pdbsum/4kvk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kvk ProSAT]</span></td></tr>
-	<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=4kvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kvk OCA], [~~http~~://pdbe.org/4kvk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4kvk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4kvk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4kvk ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[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>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Orysa~~]]	+	[[Category: Oryza sativa]]
-	[[Category: Koszelak-Rosenblum, M]]	+	[[Category: Koszelak-Rosenblum M]]
-	[[Category: Malkowski~~, M G~~]]	+	[[Category: Malkowski MG]]
-	[[Category: Zhu, G]]	+	[[Category: Zhu G]]
-	~~[[Category: Calcium binding]]~~	+
-	~~[[Category: Cox-like protein]]~~	+
-	~~[[Category: Fatty acid alpha-dioxygenase]]~~	+
-	~~[[Category: Heme binding]]~~	+
-	~~[[Category: Monotopic membrane protein]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Piox~~]]	+

OCA at 05:33, 13 February 2020

OCA — Thu, 13 Feb 2020 05:33:11 GMT

←Older revision		Revision as of 05:33, 13 February 2020
Line 1:		Line 1:

	==Crystal structure of Oryza sativa fatty acid alpha-dioxygenase==		==Crystal structure of Oryza sativa fatty acid alpha-dioxygenase==
-	<StructureSection load='4kvk' size='340' side='right' caption='[[4kvk]], [[Resolution\|resolution]] 1.98Å' scene=''>	+	<StructureSection load='4kvk' size='340' side='right'caption='[[4kvk]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4kvk]] 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=4KVK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KVK FirstGlance]. <br>		<table><tr><td colspan='2'>[[4kvk]] 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=4KVK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KVK FirstGlance]. <br>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Orysa]]		[[Category: Orysa]]
	[[Category: Koszelak-Rosenblum, M]]		[[Category: Koszelak-Rosenblum, M]]

OCA at 18:56, 4 August 2016

OCA — Thu, 04 Aug 2016 18:56:57 GMT

←Older revision		Revision as of 18:56, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of Oryza sativa fatty acid alpha-dioxygenase==		==Crystal structure of Oryza sativa fatty acid alpha-dioxygenase==
	<StructureSection load='4kvk' size='340' side='right' caption='[[4kvk]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='4kvk' size='340' side='right' caption='[[4kvk]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4kvk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Oryza_sativa Oryza sativa~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KVK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KVK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4kvk]] 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=4KVK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KVK FirstGlance]. <br>
	</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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DMU:DECYL-BETA-D-MALTOPYRANOSIDE'>DMU</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>		</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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DMU:DECYL-BETA-D-MALTOPYRANOSIDE'>DMU</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4kvj\|4kvj]], [[4kvl\|4kvl]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4kvj\|4kvj]], [[4kvl\|4kvl]]</td></tr>
-	<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=4kvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kvk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kvk RCSB], [http://www.ebi.ac.uk/pdbsum/4kvk PDBsum]</span></td></tr>	+	<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=4kvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kvk OCA], [http://pdbe.org/4kvk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4kvk RCSB], [http://www.ebi.ac.uk/pdbsum/4kvk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4kvk ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4kvk" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Oryza sativa~~]]	+	[[Category: Orysa]]
	[[Category: Koszelak-Rosenblum, M]]		[[Category: Koszelak-Rosenblum, M]]
	[[Category: Malkowski, M G]]		[[Category: Malkowski, M G]]

OCA at 15:37, 21 December 2014

OCA — Sun, 21 Dec 2014 15:37:09 GMT

←Older revision		Revision as of 15:37, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4kvk\| PDB=4kvk \| SCENE= }}~~	+	==Crystal structure of Oryza sativa fatty acid alpha-dioxygenase==
-	===Crystal structure of Oryza sativa fatty acid alpha-dioxygenase===	+	<StructureSection load='4kvk' size='340' side='right' caption='[[4kvk]], [[Resolution\|resolution]] 1.98Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23934749}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4kvk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Oryza_sativa Oryza sativa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KVK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KVK FirstGlance]. <br>
		+	</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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DMU:DECYL-BETA-D-MALTOPYRANOSIDE'>DMU</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4kvj\|4kvj]], [[4kvl\|4kvl]]</td></tr>
		+	<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=4kvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kvk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kvk RCSB], [http://www.ebi.ac.uk/pdbsum/4kvk PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	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.

-	~~==About this Structure==~~	+	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>
-	~~[[4kvk]] is a 1 chain structure with sequence~~ from ~~[http~~:~~//en~~.~~wikipedia~~.~~org/wiki/Oryza_sativa Oryza sativa]~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=4KVK OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:023934749</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Oryza sativa]]		[[Category: Oryza sativa]]
-	[[Category: Koszelak-Rosenblum, M.]]	+	[[Category: Koszelak-Rosenblum, M]]
-	[[Category: Malkowski, M G.]]	+	[[Category: Malkowski, M G]]
-	[[Category: Zhu, G.]]	+	[[Category: Zhu, G]]
	[[Category: Calcium binding]]		[[Category: Calcium binding]]
	[[Category: Cox-like protein]]		[[Category: Cox-like protein]]

OCA at 05:58, 28 August 2013

OCA — Wed, 28 Aug 2013 05:58:32 GMT

←Older revision		Revision as of 05:58, 28 August 2013
Line 1:		Line 1:
	{{STRUCTURE_4kvk\| PDB=4kvk \| SCENE= }}		{{STRUCTURE_4kvk\| PDB=4kvk \| SCENE= }}
	===Crystal structure of Oryza sativa fatty acid alpha-dioxygenase===		===Crystal structure of Oryza sativa fatty acid alpha-dioxygenase===
		+	{{ABSTRACT_PUBMED_23934749}}

	==About this Structure==		==About this Structure==
	[[4kvk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Oryza_sativa Oryza sativa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KVK OCA].		[[4kvk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Oryza_sativa Oryza sativa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KVK OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:023934749</ref><references group="xtra"/><references/>
	[[Category: Oryza sativa]]		[[Category: Oryza sativa]]
	[[Category: Koszelak-Rosenblum, M.]]		[[Category: Koszelak-Rosenblum, M.]]

OCA at 08:35, 21 August 2013

OCA — Wed, 21 Aug 2013 08:35:55 GMT

←Older revision		Revision as of 08:35, 21 August 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4kvk\| PDB=4kvk \| SCENE= }}
		+	===Crystal structure of Oryza sativa fatty acid alpha-dioxygenase===

-	~~The entry~~ 4kvk is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
-		+	[[4kvk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Oryza_sativa Oryza sativa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KVK OCA].
-	~~Authors~~: ~~Zhu, G.,~~ Koszelak-Rosenblum, M., Malkowski, M.G.	+	[[Category: Oryza sativa]]
-		+	[[Category: Koszelak-Rosenblum, M.]]
-	~~Description~~: ~~Crystal structure of Oryza sativa fatty~~ acid alpha-dioxygenase	+	[[Category: Malkowski, M G.]]
		+	[[Category: Zhu, G.]]
		+	[[Category: Calcium binding]]
		+	[[Category: Cox-like protein]]
		+	[[Category: Fatty acid alpha-dioxygenase]]
		+	[[Category: Heme binding]]
		+	[[Category: Monotopic membrane protein]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Piox]]

OCA at 20:01, 7 August 2013

OCA — Wed, 07 Aug 2013 20:01:54 GMT

←Older revision		Revision as of 20:01, 7 August 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4kvk is ON HOLD	+	The entry 4kvk is ON HOLD until Paper Publication

	Authors: Zhu, G., Koszelak-Rosenblum, M., Malkowski, M.G.		Authors: Zhu, G., Koszelak-Rosenblum, M., Malkowski, M.G.

	Description: Crystal structure of Oryza sativa fatty acid alpha-dioxygenase		Description: Crystal structure of Oryza sativa fatty acid alpha-dioxygenase

OCA: Protected "4kvk" [edit=sysop:move=sysop]

OCA — Wed, 19 Jun 2013 12:06:09 GMT

Protected "4kvk" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:06, 19 June 2013

OCA: New page: '''Unreleased structure''' The entry 4kvk is ON HOLD Authors: Zhu, G., Koszelak-Rosenblum, M., Malkowski, M.G. Description: Crystal structure of Oryza sativa fatty acid alpha-dioxygena...

OCA — Wed, 19 Jun 2013 12:06:07 GMT

New page: '''Unreleased structure''' The entry 4kvk is ON HOLD Authors: Zhu, G., Koszelak-Rosenblum, M., Malkowski, M.G. Description: Crystal structure of Oryza sativa fatty acid alpha-dioxygena...

New page

'''Unreleased structure'''

The entry 4kvk is ON HOLD

Authors: Zhu, G., Koszelak-Rosenblum, M., Malkowski, M.G.

Description: Crystal structure of Oryza sativa fatty acid alpha-dioxygenase