5tqo - Revision history

OCA at 13:08, 4 October 2023

OCA — Wed, 04 Oct 2023 13:08:23 GMT

←Older revision		Revision as of 13:08, 4 October 2023
Line 3:		Line 3:
	<StructureSection load='5tqo' size='340' side='right'caption='[[5tqo]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='5tqo' size='340' side='right'caption='[[5tqo]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5tqo]] 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=5TQO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5TQO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5tqo]] 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=5TQO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TQO 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]] 1.7Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5tqp\|5tqp]]~~, [[~~5tqn~~\|~~5tqn]], [[5tr0\|5tr0~~]]</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='~~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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5tqo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tqo OCA], [https://pdbe.org/5tqo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5tqo RCSB], [https://www.ebi.ac.uk/pdbsum/5tqo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5tqo ProSAT]</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=5tqo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tqo OCA], [~~http~~://pdbe.org/5tqo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5tqo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5tqo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5tqo 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: Gee C]]
-	[[Category: Gee, C]]	+	[[Category: Poss EM]]
-	[[Category: Poss~~, E M]]~~	+
-	~~[[Category: Hydrogen tunneling]]~~	+
-	~~[[Category: Lipoxygenase~~]]	+

OCA at 08:06, 21 May 2019

OCA — Tue, 21 May 2019 08:06:26 GMT

←Older revision		Revision as of 08:06, 21 May 2019
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	==Lipoxygenase-1 (soybean) L546A/L754A mutant at 300K==		==Lipoxygenase-1 (soybean) L546A/L754A mutant at 300K==
-	<StructureSection load='5tqo' size='340' side='right' caption='[[5tqo]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='5tqo' size='340' side='right'caption='[[5tqo]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5tqo]] 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=5TQO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TQO FirstGlance]. <br>		<table><tr><td colspan='2'>[[5tqo]] 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=5TQO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TQO FirstGlance]. <br>
Line 12:		Line 12:
	== 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 ==
		+	Soybean lipoxygenase (SLO) has served as a prototype for understanding the molecular origin of enzymatic rate accelerations. The double mutant (DM) L546A/L754A is considered a dramatic outlier, due to the unprecedented size and near temperature-independence of its primary kinetic isotope effect, low catalytic efficiency, and elevated enthalpy of activation. To uncover the physical basis of these features, we herein apply three structural probes: hydrogen-deuterium exchange mass spectrometry, room-temperature X-ray crystallography and EPR spectroscopy on four SLO variants (wild-type (WT) enzyme, DM, and the two parental single mutants, L546A and L754A). DM is found to incorporate features of each parent, with the perturbation at position 546 predominantly influencing thermally activated motions that connect the active site to a protein-solvent interface, while mutation at position 754 disrupts the ligand field and solvation near the cofactor iron. However, the expanded active site in DM leads to more active site water molecules and their associated hydrogen bond network, and the individual features from L546A and L754A alone cannot explain the aggregate kinetic properties for DM. Using recently published QM/MM-derived ground-state SLO-substrate complexes for WT and DM, together with the thorough structural analyses presented herein, we propose that the impairment of DM is the combined result of a repositioning of the reactive carbon of linoleic acid substrate with regard to both the iron cofactor and a catalytically linked dynamic region of protein.
		+
		+	Biophysical Characterization of a Disabled Double Mutant of Soybean Lipoxygenase: The "Undoing" of Precise Substrate Positioning Relative to Metal Cofactor and an Identified Dynamical Network.,Hu S, Offenbacher AR, Thompson EM, Gee CL, Wilcoxen J, Carr CAM, Prigozhin DM, Yang V, Alber T, Britt RD, Fraser JS, Klinman JP J Am Chem Soc. 2019 Jan 30;141(4):1555-1567. doi: 10.1021/jacs.8b10992. Epub 2019, Jan 15. PMID:30645119<ref>PMID:30645119</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5tqo" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 17:		Line 26:
	</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 06:31, 18 April 2018

OCA — Wed, 18 Apr 2018 06:31:32 GMT

←Older revision		Revision as of 06:31, 18 April 2018
Line 3:		Line 3:
	<StructureSection load='5tqo' size='340' side='right' caption='[[5tqo]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='5tqo' size='340' side='right' caption='[[5tqo]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5tqo]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TQO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TQO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5tqo]] 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=5TQO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TQO 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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5tqp\|5tqp]], [[5tqn\|5tqn]], [[5tr0\|5tr0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5tqp\|5tqp]], [[5tqn\|5tqn]], [[5tr0\|5tr0]]</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=5tqo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tqo OCA], [http://pdbe.org/5tqo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tqo RCSB], [http://www.ebi.ac.uk/pdbsum/5tqo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tqo 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=5tqo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tqo OCA], [http://pdbe.org/5tqo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tqo RCSB], [http://www.ebi.ac.uk/pdbsum/5tqo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tqo 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 06:30, 1 November 2017

OCA — Wed, 01 Nov 2017 06:30:49 GMT

←Older revision		Revision as of 06:30, 1 November 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5tqo is ~~ON HOLD until Paper Publication~~	+	==Lipoxygenase-1 (soybean) L546A/L754A mutant at 300K==
-		+	<StructureSection load='5tqo' size='340' side='right' caption='[[5tqo]], [[Resolution\|resolution]] 1.70Å' scene=''>
-	~~Authors~~: ~~Poss~~, E.M., ~~Fraser~~, J.S.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5tqo]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TQO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TQO FirstGlance]. <br>
-	~~Description~~: ~~Lipoxygenase~~-1 (~~soybean~~) ~~L546A/L754A mutant~~ at ~~300K~~	+	</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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5tqp\|5tqp]], [[5tqn\|5tqn]], [[5tr0\|5tr0]]</td></tr>
-	[[Category: Poss, E.M]]	+	<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=5tqo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tqo OCA], [http://pdbe.org/5tqo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tqo RCSB], [http://www.ebi.ac.uk/pdbsum/5tqo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tqo ProSAT]</span></td></tr>
		+	</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: Gee, C]]
		+	[[Category: Poss, E M]]
		+	[[Category: Hydrogen tunneling]]
		+	[[Category: Lipoxygenase]]

OCA at 13:26, 27 September 2017

OCA — Wed, 27 Sep 2017 13:26:45 GMT

←Older revision		Revision as of 13:26, 27 September 2017
Line 7:		Line 7:
	Description: Lipoxygenase-1 (soybean) L546A/L754A mutant at 300K		Description: Lipoxygenase-1 (soybean) L546A/L754A mutant at 300K
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Fraser, J.S]]
	[[Category: Poss, E.M]]		[[Category: Poss, E.M]]
		+	[[Category: Fraser, J.S]]

OCA at 13:44, 9 March 2017

OCA — Thu, 09 Mar 2017 13:44:50 GMT

←Older revision		Revision as of 13:44, 9 March 2017
Line 7:		Line 7:
	Description: Lipoxygenase-1 (soybean) L546A/L754A mutant at 300K		Description: Lipoxygenase-1 (soybean) L546A/L754A mutant at 300K
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Poss, E.M]]
	[[Category: Fraser, J.S]]		[[Category: Fraser, J.S]]
		+	[[Category: Poss, E.M]]

OCA at 17:45, 9 December 2016

OCA — Fri, 09 Dec 2016 17:45:30 GMT

←Older revision		Revision as of 17:45, 9 December 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

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

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

OCA — Wed, 02 Nov 2016 17:02:59 GMT

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

←Older revision

Revision as of 17:02, 2 November 2016

OCA: New page: '''Unreleased structure''' The entry 5tqo is ON HOLD Authors: Poss, E.M., Fraser, J.S. Description: Lipoxygenase-1 (soybean) L546A/L754A mutant at 300K [[Category: Unreleased Structure...

OCA — Wed, 02 Nov 2016 17:02:58 GMT

New page: '''Unreleased structure''' The entry 5tqo is ON HOLD Authors: Poss, E.M., Fraser, J.S. Description: Lipoxygenase-1 (soybean) L546A/L754A mutant at 300K [[Category: Unreleased Structure...

New page

'''Unreleased structure'''

The entry 5tqo is ON HOLD

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

Description: Lipoxygenase-1 (soybean) L546A/L754A mutant at 300K
[[Category: Unreleased Structures]]
[[Category: Poss, E.M]]
[[Category: Fraser, J.S]]