4kvj - Revision history

OCA at 12:15, 1 March 2024

2024-03-01T12:15:40Z

←Older revision		Revision as of 12:15, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4kvj]] 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=4KVJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KVJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[4kvj]] 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=4KVJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KVJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=P33:3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL'>P33</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</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]] 2.12Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=P33:3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL'>P33</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</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=4kvj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kvj OCA], [https://pdbe.org/4kvj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kvj RCSB], [https://www.ebi.ac.uk/pdbsum/4kvj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kvj 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=4kvj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kvj OCA], [https://pdbe.org/4kvj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kvj RCSB], [https://www.ebi.ac.uk/pdbsum/4kvj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kvj 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 4kvj" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:17, 7 December 2022

2022-12-07T09:17:02Z

←Older revision		Revision as of 09:17, 7 December 2022
Line 3:		Line 3:
	<StructureSection load='4kvj' size='340' side='right'caption='[[4kvj]], [[Resolution\|resolution]] 2.12Å' scene=''>		<StructureSection load='4kvj' size='340' side='right'caption='[[4kvj]], [[Resolution\|resolution]] 2.12Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4kvj]] 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=4KVJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4KVJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4kvj]] 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=4KVJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KVJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=P33:3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL'>P33</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</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=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=P33:3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL'>P33</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</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">[[4kvk\|4kvk]], [[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=4kvj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kvj OCA], [https://pdbe.org/4kvj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kvj RCSB], [https://www.ebi.ac.uk/pdbsum/4kvj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kvj 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=4kvj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kvj OCA], [~~http~~://pdbe.org/4kvj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4kvj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4kvj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4kvj 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 05:02, 13 February 2020

2020-02-13T05:02:37Z

←Older revision		Revision as of 05:02, 13 February 2020
Line 1:		Line 1:

	==Crystal structure of Oryza sativa fatty acid alpha-dioxygenase with hydrogen peroxide==		==Crystal structure of Oryza sativa fatty acid alpha-dioxygenase with hydrogen peroxide==
-	<StructureSection load='4kvj' size='340' side='right' caption='[[4kvj]], [[Resolution\|resolution]] 2.12Å' scene=''>	+	<StructureSection load='4kvj' size='340' side='right'caption='[[4kvj]], [[Resolution\|resolution]] 2.12Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4kvj]] 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=4KVJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KVJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[4kvj]] 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=4KVJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KVJ 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 05:29, 5 August 2016

2016-08-05T05:29:20Z

←Older revision		Revision as of 05:29, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of Oryza sativa fatty acid alpha-dioxygenase with hydrogen peroxide==		==Crystal structure of Oryza sativa fatty acid alpha-dioxygenase with hydrogen peroxide==
	<StructureSection load='4kvj' size='340' side='right' caption='[[4kvj]], [[Resolution\|resolution]] 2.12Å' scene=''>		<StructureSection load='4kvj' size='340' side='right' caption='[[4kvj]], [[Resolution\|resolution]] 2.12Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4kvj]] 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=4KVJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KVJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4kvj]] 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=4KVJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KVJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=P33:3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL'>P33</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</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=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=P33:3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL'>P33</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</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">[[4kvk\|4kvk]], [[4kvl\|4kvl]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4kvk\|4kvk]], [[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=4kvj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kvj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kvj RCSB], [http://www.ebi.ac.uk/pdbsum/4kvj 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=4kvj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kvj OCA], [http://pdbe.org/4kvj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4kvj RCSB], [http://www.ebi.ac.uk/pdbsum/4kvj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4kvj 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 4kvj" 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 14:35, 21 December 2014

2014-12-21T14:35:48Z

←Older revision		Revision as of 14:35, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4kvj\| PDB=4kvj \| SCENE= }}~~	+	==Crystal structure of Oryza sativa fatty acid alpha-dioxygenase with hydrogen peroxide==
-	===Crystal structure of Oryza sativa fatty acid alpha-dioxygenase with hydrogen peroxide===	+	<StructureSection load='4kvj' size='340' side='right' caption='[[4kvj]], [[Resolution\|resolution]] 2.12Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23934749}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4kvj]] 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=4KVJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KVJ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=P33:3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL'>P33</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</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">[[4kvk\|4kvk]], [[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=4kvj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kvj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kvj RCSB], [http://www.ebi.ac.uk/pdbsum/4kvj 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>
-	~~[[4kvj]] 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=4KVJ 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 05:18, 28 August 2013

2013-08-28T05:18:57Z

←Older revision		Revision as of 05:18, 28 August 2013
Line 1:		Line 1:
	{{STRUCTURE_4kvj\| PDB=4kvj \| SCENE= }}		{{STRUCTURE_4kvj\| PDB=4kvj \| SCENE= }}
	===Crystal structure of Oryza sativa fatty acid alpha-dioxygenase with hydrogen peroxide===		===Crystal structure of Oryza sativa fatty acid alpha-dioxygenase with hydrogen peroxide===
		+	{{ABSTRACT_PUBMED_23934749}}

	==About this Structure==		==About this Structure==
	[[4kvj]] 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=4KVJ OCA].		[[4kvj]] 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=4KVJ 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

2013-08-21T08:35:52Z

←Older revision		Revision as of 08:35, 21 August 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4kvj\| PDB=4kvj \| SCENE= }}
		+	===Crystal structure of Oryza sativa fatty acid alpha-dioxygenase with hydrogen peroxide===

-	~~The entry~~ 4kvj is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
-		+	[[4kvj]] 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=4KVJ 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 ~~with hydrogen peroxide~~	+	[[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: Protected "4kvj" [edit=sysop:move=sysop]

2013-06-19T12:06:05Z

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

←Older revision

Revision as of 12:06, 19 June 2013

OCA: New page: '''Unreleased structure''' The entry 4kvj is ON HOLD until Paper Publication Authors: Zhu, G., Koszelak-Rosenblum, M., Malkowski, M.G. Description: Crystal structure of Oryza sativa fa...

2013-06-19T12:06:03Z

New page: '''Unreleased structure''' The entry 4kvj is ON HOLD until Paper Publication Authors: Zhu, G., Koszelak-Rosenblum, M., Malkowski, M.G. Description: Crystal structure of Oryza sativa fa...

New page

'''Unreleased structure'''

The entry 4kvj is ON HOLD until Paper Publication

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

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