6jgb - Revision history

OCA at 08:04, 17 October 2024

2024-10-17T08:04:15Z

← Older revision		Revision as of 08:04, 17 October 2024
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	<StructureSection load='6jgb' size='340' side='right'caption='[[6jgb]], [[Resolution\|resolution]] 1.47Å' scene=''>		<StructureSection load='6jgb' size='340' side='right'caption='[[6jgb]], [[Resolution\|resolution]] 1.47Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>~~[[6jgb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Hordeum_vulgare_subsp._vulgare Hordeum vulgare subsp. vulgare].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JGB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JGB FirstGlance]. <br>		<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JGB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JGB FirstGlance]. <br>
	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.47Å</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]] 1.47Å</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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PRD_900098:METHYL+6-THIO-BETA-GENTIOBIOSIDE'>PRD_900098</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=U1Y:methyl+6-thio-beta-D-glucopyranoside'>U1Y</scene></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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PRD_900098:METHYL+6-THIO-BETA-GENTIOBIOSIDE'>PRD_900098</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=U1Y:methyl+6-thio-beta-D-glucopyranoside'>U1Y</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=6jgb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jgb OCA], [https://pdbe.org/6jgb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jgb RCSB], [https://www.ebi.ac.uk/pdbsum/6jgb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jgb 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=6jgb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jgb OCA], [https://pdbe.org/6jgb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jgb RCSB], [https://www.ebi.ac.uk/pdbsum/6jgb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jgb ProSAT]</span></td></tr>
	</table>		</table>
	~~== Function ==~~
	~~[https://www.uniprot.org/uniprot/Q9XEI3_HORVV Q9XEI3_HORVV]~~
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	In the barley beta-D-glucan glucohydrolase, a glycoside hydrolase family 3 (GH3) enzyme, the Trp286/Trp434 clamp ensures beta-D-glucosides binding, which is fundamental for substrate hydrolysis during plant growth and development. We employ mutagenesis, high-resolution X-ray crystallography, and multi-scale molecular modelling methods to examine the binding and conformational behaviour of isomeric beta-D-glucosides during substrate-product assisted processive catalysis that operates in GH3 hydrolases. Enzyme kinetics reveals that the W434H mutant retains broad specificity, while W434A behaves as a strict (1,3)-beta-D-glucosidase. Investigations of reactant movements on the nanoscale reveal that processivity is sensitive to mutation-specific alterations of the tryptophan clamp. While wild-type and W434H utilise a lateral cavity for glucose displacement and sliding of (1,3)-linked hydrolytic products through the catalytic site without dissociation, consistent with their high hydrolytic rates, W434A does not adopt processive catalysis. Phylogenomic analyses of GH3 hydrolases disclose the evolutionary advantage of the tryptophan clamp that confers broad specificity, high catalytic efficiency, and processivity.

	The evolutionary advantage of an aromatic clamp in plant family 3 glycoside exo-hydrolases.,Luang S, Fernandez-Luengo X, Nin-Hill A, Streltsov VA, Schwerdt JG, Alonso-Gil S, Ketudat Cairns JR, Pradeau S, Fort S, Marechal JD, Masgrau L, Rovira C, Hrmova M Nat Commun. 2022 Sep 23;13(1):5577. doi: 10.1038/s41467-022-33180-5. PMID:36151080<ref>PMID:36151080</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 6jgb" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Hordeum vulgare subsp. vulgare]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Hrmova M]]		[[Category: Hrmova M]]
	[[Category: Luang S]]		[[Category: Luang S]]
	[[Category: Streltsov VA]]		[[Category: Streltsov VA]]

OCA at 14:34, 29 November 2023

2023-11-29T14:34:20Z

← Older revision		Revision as of 14:34, 29 November 2023
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	==Crystal structure of barley exohydrolaseI W286F mutant in complex with methyl 6-thio-beta-gentiobioside==		==Crystal structure of barley exohydrolaseI W286F mutant in complex with methyl 6-thio-beta-gentiobioside==
	<StructureSection load='6jgb' size='340' side='right'caption='[[6jgb]]' scene=''>		<StructureSection load='6jgb' size='340' side='right'caption='[[6jgb]], [[Resolution\|resolution]] 1.47Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JGB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6JGB FirstGlance]. <br>		<table><tr><td colspan='2'>[[6jgb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Hordeum_vulgare_subsp._vulgare Hordeum vulgare subsp. vulgare]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JGB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JGB FirstGlance]. <br>
	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6jgb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jgb OCA], [~~http~~://pdbe.org/6jgb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6jgb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6jgb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6jgb ProSAT]</span></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]] 1.47Å</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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PRD_900098:METHYL+6-THIO-BETA-GENTIOBIOSIDE'>PRD_900098</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=U1Y:methyl+6-thio-beta-D-glucopyranoside'>U1Y</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=6jgb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jgb OCA], [https://pdbe.org/6jgb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jgb RCSB], [https://www.ebi.ac.uk/pdbsum/6jgb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jgb ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/Q9XEI3_HORVV Q9XEI3_HORVV]
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			In the barley beta-D-glucan glucohydrolase, a glycoside hydrolase family 3 (GH3) enzyme, the Trp286/Trp434 clamp ensures beta-D-glucosides binding, which is fundamental for substrate hydrolysis during plant growth and development. We employ mutagenesis, high-resolution X-ray crystallography, and multi-scale molecular modelling methods to examine the binding and conformational behaviour of isomeric beta-D-glucosides during substrate-product assisted processive catalysis that operates in GH3 hydrolases. Enzyme kinetics reveals that the W434H mutant retains broad specificity, while W434A behaves as a strict (1,3)-beta-D-glucosidase. Investigations of reactant movements on the nanoscale reveal that processivity is sensitive to mutation-specific alterations of the tryptophan clamp. While wild-type and W434H utilise a lateral cavity for glucose displacement and sliding of (1,3)-linked hydrolytic products through the catalytic site without dissociation, consistent with their high hydrolytic rates, W434A does not adopt processive catalysis. Phylogenomic analyses of GH3 hydrolases disclose the evolutionary advantage of the tryptophan clamp that confers broad specificity, high catalytic efficiency, and processivity.

			The evolutionary advantage of an aromatic clamp in plant family 3 glycoside exo-hydrolases.,Luang S, Fernandez-Luengo X, Nin-Hill A, Streltsov VA, Schwerdt JG, Alonso-Gil S, Ketudat Cairns JR, Pradeau S, Fort S, Marechal JD, Masgrau L, Rovira C, Hrmova M Nat Commun. 2022 Sep 23;13(1):5577. doi: 10.1038/s41467-022-33180-5. PMID:36151080<ref>PMID:36151080</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 6jgb" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Hordeum vulgare subsp. vulgare]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Hrmova M]]		[[Category: Hrmova M]]
	[[Category: Luang S]]		[[Category: Luang S]]
	[[Category: Streltsov VA]]		[[Category: Streltsov VA]]

OCA at 06:16, 19 August 2020

2020-08-19T06:16:52Z

← Older revision		Revision as of 06:16, 19 August 2020
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	~~'''Unreleased structure'''~~

	~~The entry~~ 6jgb is ~~ON HOLD until Paper Publication~~		==Crystal structure of barley exohydrolaseI W286F mutant in complex with methyl 6-thio-beta-gentiobioside==
			<StructureSection load='6jgb' size='340' side='right'caption='[[6jgb]]' scene=''>
	~~Authors~~:		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JGB OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6JGB FirstGlance]. <br>
	~~Description~~:		</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6jgb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jgb OCA], [http://pdbe.org/6jgb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jgb RCSB], [http://www.ebi.ac.uk/pdbsum/6jgb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jgb ProSAT]</span></td></tr>
	[[Category: ~~Unreleased Structures~~]]		</table>
			__TOC__
			</StructureSection>
			[[Category: Large Structures]]
			[[Category: Hrmova M]]
			[[Category: Luang S]]
			[[Category: Streltsov VA]]

OCA at 04:07, 22 April 2020

2020-04-22T04:07:29Z

← Older revision		Revision as of 04:07, 22 April 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 6jgb is ON HOLD until ~~Aug 14 2021~~		The entry 6jgb is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 02:26, 13 February 2020

2020-02-13T02:26:48Z

← Older revision		Revision as of 02:26, 13 February 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 6jgb is ON HOLD until ~~Paper Publication~~		The entry 6jgb is ON HOLD until Aug 14 2021

	Authors:		Authors:

OCA at 06:26, 2 October 2019

2019-10-02T06:26:32Z

← Older revision		Revision as of 06:26, 2 October 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 6jgb is ON HOLD		The entry 6jgb is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6jgb" [edit=sysop:move=sysop]

2019-02-21T05:00:25Z

Protected "6jgb" [edit=sysop:move=sysop]

← Older revision	Revision as of 05:00, 21 February 2019
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6jgb is ON HOLD Authors: Description: Category: Unreleased Structures

2019-02-21T05:00:24Z

New page: '''Unreleased structure''' The entry 6jgb is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6jgb is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]