OCA at 14:36, 29 November 2023

OCA — Wed, 29 Nov 2023 14:36:16 GMT

←Older revision		Revision as of 14:36, 29 November 2023
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	==Crystal structure of barley exohydrolaseI W434A mutant in complex with methyl 6-thio-beta-gentiobioside==		==Crystal structure of barley exohydrolaseI W434A mutant in complex with methyl 6-thio-beta-gentiobioside==
-	<StructureSection load='6k6v' size='340' side='right'caption='[[6k6v]]' scene=''>	+	<StructureSection load='6k6v' size='340' side='right'caption='[[6k6v]], [[Resolution\|resolution]] 1.98Å' 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=6K6V OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6K6V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6k6v]] 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=6K6V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6K6V 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=6k6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k6v OCA], [~~http~~://pdbe.org/6k6v PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6k6v RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6k6v PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6k6v 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]] 1.98Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=6k6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k6v OCA], [https://pdbe.org/6k6v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6k6v RCSB], [https://www.ebi.ac.uk/pdbsum/6k6v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6k6v 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 6k6v" 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 06:17, 19 August 2020

OCA — Wed, 19 Aug 2020 06:17:16 GMT

←Older revision		Revision as of 06:17, 19 August 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6k6v is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of barley exohydrolaseI W434A mutant in complex with methyl 6-thio-beta-gentiobioside==
-		+	<StructureSection load='6k6v' size='340' side='right'caption='[[6k6v]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K6V OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6K6V 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=6k6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k6v OCA], [http://pdbe.org/6k6v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k6v RCSB], [http://www.ebi.ac.uk/pdbsum/6k6v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k6v ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Hrmova M]]
		+	[[Category: Luang S]]
		+	[[Category: Streltsov VA]]

OCA at 04:04, 7 August 2019

OCA — Wed, 07 Aug 2019 04:04:58 GMT

←Older revision		Revision as of 04:04, 7 August 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6k6v is ON HOLD	+	The entry 6k6v is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6k6v" [edit=sysop:move=sysop]

OCA — Wed, 12 Jun 2019 03:55:32 GMT

Protected "6k6v" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:55, 12 June 2019

OCA: New page: '''Unreleased structure''' The entry 6k6v is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 12 Jun 2019 03:55:31 GMT

New page: '''Unreleased structure''' The entry 6k6v is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6k6v is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

6k6v - Revision history

OCA at 14:36, 29 November 2023

OCA at 06:17, 19 August 2020

OCA at 04:04, 7 August 2019

OCA: Protected "6k6v" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 6k6v is ON HOLD Authors: Description: Category: Unreleased Structures