5t5v - Revision history

OCA at 12:55, 4 October 2023

2023-10-04T12:55:02Z

←Older revision		Revision as of 12:55, 4 October 2023
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	<StructureSection load='5t5v' size='340' side='right'caption='[[5t5v]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='5t5v' size='340' side='right'caption='[[5t5v]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5t5v]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Glycine_hispida~~ Glycine ~~hispida~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T5V OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5T5V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5t5v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T5V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5T5V FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=FE:FE+(III)+ION'>FE</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]] 1.8Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">LOX1.~~1~~, LOX1 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=3847 Glycine hispida])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[http://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.12 1.13.11.12]~~ </~~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=5t5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t5v OCA], [https://pdbe.org/5t5v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5t5v RCSB], [https://www.ebi.ac.uk/pdbsum/5t5v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5t5v 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=5t5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t5v OCA], [~~http~~://pdbe.org/5t5v PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5t5v RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5t5v PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5t5v ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/LOX1_SOYBN LOX1_SOYBN]] Plant lipoxygenase may be involved in a number of diverse aspects of plant physiology including growth and development, pest resistance, and senescence or responses to wounding. With linoleate as substrate, L-1 shows a preference for carbon 13 as the site for hydroperoxidation (in contrast to L-2 and L-3, which utilize either carbon 9 or 13). At pH above 8.5, only (9Z,11E,13S)-13-hydroperoxyoctadeca-9,11-dienoate is produced, but as the pH decreases, the proportion of (9S)-hydroperoxide increases linearly until at pH 6.0 it represents about 25 % of the products.<ref>PMID:16157595</ref>	+	[https://www.uniprot.org/uniprot/LOX1_SOYBN LOX1_SOYBN] Plant lipoxygenase may be involved in a number of diverse aspects of plant physiology including growth and development, pest resistance, and senescence or responses to wounding. With linoleate as substrate, L-1 shows a preference for carbon 13 as the site for hydroperoxidation (in contrast to L-2 and L-3, which utilize either carbon 9 or 13). At pH above 8.5, only (9Z,11E,13S)-13-hydroperoxyoctadeca-9,11-dienoate is produced, but as the pH decreases, the proportion of (9S)-hydroperoxide increases linearly until at pH 6.0 it represents about 25 % of the products.<ref>PMID:16157595</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Glycine ~~hispida~~]]	+	[[Category: Glycine max]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Oxidoreductase]]~~	+	[[Category: Fraser JS]]
-	[[Category: Fraser~~, J S~~]]	+	[[Category: Poss EM]]
-	[[Category: Poss~~, E M]]~~	+
-	~~[[Category: Hydrogen tunneling]]~~	+
-	~~[[Category: Lipoxygenase~~]]	+

OCA at 12:28, 25 December 2019

2019-12-25T12:28:38Z

←Older revision		Revision as of 12:28, 25 December 2019
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	==LIPOXYGENASE-1 (SOYBEAN) AT 293K==		==LIPOXYGENASE-1 (SOYBEAN) AT 293K==
-	<StructureSection load='5t5v' size='340' side='right' caption='[[5t5v]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='5t5v' size='340' side='right'caption='[[5t5v]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5t5v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Glycine_hispida Glycine hispida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T5V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T5V FirstGlance]. <br>		<table><tr><td colspan='2'>[[5t5v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Glycine_hispida Glycine hispida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T5V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T5V FirstGlance]. <br>
Line 25:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Glycine hispida]]		[[Category: Glycine hispida]]
		+	[[Category: Large Structures]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Fraser, J S]]		[[Category: Fraser, J S]]

OCA at 20:47, 24 January 2018

2018-01-24T20:47:12Z

←Older revision		Revision as of 20:47, 24 January 2018
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/LOX1_SOYBN LOX1_SOYBN]] Plant lipoxygenase may be involved in a number of diverse aspects of plant physiology including growth and development, pest resistance, and senescence or responses to wounding. With linoleate as substrate, L-1 shows a preference for carbon 13 as the site for hydroperoxidation (in contrast to L-2 and L-3, which utilize either carbon 9 or 13). At pH above 8.5, only (9Z,11E,13S)-13-hydroperoxyoctadeca-9,11-dienoate is produced, but as the pH decreases, the proportion of (9S)-hydroperoxide increases linearly until at pH 6.0 it represents about 25 % of the products.<ref>PMID:16157595</ref>		[[http://www.uniprot.org/uniprot/LOX1_SOYBN LOX1_SOYBN]] Plant lipoxygenase may be involved in a number of diverse aspects of plant physiology including growth and development, pest resistance, and senescence or responses to wounding. With linoleate as substrate, L-1 shows a preference for carbon 13 as the site for hydroperoxidation (in contrast to L-2 and L-3, which utilize either carbon 9 or 13). At pH above 8.5, only (9Z,11E,13S)-13-hydroperoxyoctadeca-9,11-dienoate is produced, but as the pH decreases, the proportion of (9S)-hydroperoxide increases linearly until at pH 6.0 it represents about 25 % of the products.<ref>PMID:16157595</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Defining specific pathways for efficient heat transfer from protein-solvent interfaces to their active sites represents one of the compelling and timely challenges in our quest for a physical description of the origins of enzyme catalysis. Enzymatic hydrogen tunneling reactions constitute excellent systems in which to validate experimental approaches to this important question, given the inherent temperature independence of quantum mechanical wave function overlap. Herein, we present the application of hydrogen-deuterium exchange coupled to mass spectrometry toward the spatial resolution of protein motions that can be related to an enzyme's catalytic parameters. Employing the proton-coupled electron transfer reaction of soybean lipoxygenase as proof of principle, we first corroborate the impact of active site mutations on increased local flexibility and, second, uncover a solvent-exposed loop, 15-34 A from the reactive ferric center whose temperature-dependent motions are demonstrated to mirror the enthalpic barrier for catalytic C-H bond cleavage. A network that connects this surface loop to the active site is structurally identified and supported by changes in kinetic parameters that result from site-specific mutations.
		+
		+	Hydrogen-Deuterium Exchange of Lipoxygenase Uncovers a Relationship between Distal, Solvent Exposed Protein Motions and the Thermal Activation Barrier for Catalytic Proton-Coupled Electron Tunneling.,Offenbacher AR, Hu S, Poss EM, Carr CAM, Scouras AD, Prigozhin DM, Iavarone AT, Palla A, Alber T, Fraser JS, Klinman JP ACS Cent Sci. 2017 Jun 28;3(6):570-579. doi: 10.1021/acscentsci.7b00142. Epub, 2017 Jun 9. PMID:28691068<ref>PMID:28691068</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5t5v" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 14:21, 6 November 2017

2017-11-06T14:21:23Z

←Older revision		Revision as of 14:21, 6 November 2017
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	<StructureSection load='5t5v' size='340' side='right' caption='[[5t5v]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='5t5v' size='340' side='right' caption='[[5t5v]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5t5v]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T5V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T5V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5t5v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Glycine_hispida Glycine hispida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T5V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T5V FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LOX1.1, LOX1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3847 Glycine hispida])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.12 1.13.11.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.12 1.13.11.12] </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=5t5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t5v OCA], [http://pdbe.org/5t5v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t5v RCSB], [http://www.ebi.ac.uk/pdbsum/5t5v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t5v 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=5t5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t5v OCA], [http://pdbe.org/5t5v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t5v RCSB], [http://www.ebi.ac.uk/pdbsum/5t5v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t5v ProSAT]</span></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Glycine hispida]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Fraser, J S]]		[[Category: Fraser, J S]]

OCA at 09:44, 13 September 2017

2017-09-13T09:44:43Z

←Older revision		Revision as of 09:44, 13 September 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5t5v is ~~ON HOLD until Paper Publication~~	+	==LIPOXYGENASE-1 (SOYBEAN) AT 293K==
-		+	<StructureSection load='5t5v' size='340' side='right' caption='[[5t5v]], [[Resolution\|resolution]] 1.80Å' scene=''>
-	~~Authors~~: ~~Poss~~, E.M., ~~Fraser~~, J.S.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5t5v]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T5V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T5V FirstGlance]. <br>
-	~~Description~~: ~~LIPOXYGENASE~~-1 (~~SOYBEAN~~) ~~AT 293K~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.12 1.13.11.12] </span></td></tr>
-	[[Category: Fraser, J.S]]	+	<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=5t5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t5v OCA], [http://pdbe.org/5t5v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t5v RCSB], [http://www.ebi.ac.uk/pdbsum/5t5v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t5v ProSAT]</span></td></tr>
-	[[Category: Poss, E.M]]	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/LOX1_SOYBN LOX1_SOYBN]] Plant lipoxygenase may be involved in a number of diverse aspects of plant physiology including growth and development, pest resistance, and senescence or responses to wounding. With linoleate as substrate, L-1 shows a preference for carbon 13 as the site for hydroperoxidation (in contrast to L-2 and L-3, which utilize either carbon 9 or 13). At pH above 8.5, only (9Z,11E,13S)-13-hydroperoxyoctadeca-9,11-dienoate is produced, but as the pH decreases, the proportion of (9S)-hydroperoxide increases linearly until at pH 6.0 it represents about 25 % of the products.<ref>PMID:16157595</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Oxidoreductase]]
		+	[[Category: Fraser, J S]]
		+	[[Category: Poss, E M]]
		+	[[Category: Hydrogen tunneling]]
		+	[[Category: Lipoxygenase]]

OCA at 13:22, 9 March 2017

2017-03-09T13:22:30Z

←Older revision		Revision as of 13:22, 9 March 2017
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	Description: LIPOXYGENASE-1 (SOYBEAN) AT 293K		Description: LIPOXYGENASE-1 (SOYBEAN) AT 293K
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Poss, E.M]]
	[[Category: Fraser, J.S]]		[[Category: Fraser, J.S]]
		+	[[Category: Poss, E.M]]

OCA at 16:25, 2 November 2016

2016-11-02T16:25:04Z

←Older revision		Revision as of 16:25, 2 November 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5t5v is ON HOLD	+	The entry 5t5v is ON HOLD until Paper Publication

	Authors: Poss, E.M., Fraser, J.S.		Authors: Poss, E.M., Fraser, J.S.

OCA: Protected "5t5v" [edit=sysop:move=sysop]

2016-09-09T15:45:25Z

Protected "5t5v" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:45, 9 September 2016

OCA: New page: '''Unreleased structure''' The entry 5t5v is ON HOLD Authors: Poss, E.M., Fraser, J.S. Description: LIPOXYGENASE-1 (SOYBEAN) AT 293K Category: Unreleased Structures [[Category: Pos...

2016-09-09T15:45:24Z

New page: '''Unreleased structure''' The entry 5t5v is ON HOLD Authors: Poss, E.M., Fraser, J.S. Description: LIPOXYGENASE-1 (SOYBEAN) AT 293K Category: Unreleased Structures [[Category: Pos...

New page

'''Unreleased structure'''

The entry 5t5v is ON HOLD

Authors: Poss, E.M., Fraser, J.S.

Description: LIPOXYGENASE-1 (SOYBEAN) AT 293K
[[Category: Unreleased Structures]]
[[Category: Poss, E.M]]
[[Category: Fraser, J.S]]