6md6 - Revision history

OCA at 06:28, 11 October 2023

OCA — Wed, 11 Oct 2023 06:28:49 GMT

←Older revision		Revision as of 06:28, 11 October 2023
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	<StructureSection load='6md6' size='340' side='right'caption='[[6md6]], [[Resolution\|resolution]] 1.68Å' scene=''>		<StructureSection load='6md6' size='340' side='right'caption='[[6md6]], [[Resolution\|resolution]] 1.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6md6]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Domesticated_barley Domesticated barley~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MD6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6MD6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6md6]] 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=6MD6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MD6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=~~JSV~~:~~methyl+2~~-~~S-beta~~-D-~~glucopyranosyl-2-thio-beta-D-glucopyranoside~~'>~~JSV~~</scene>, <scene name='pdbligand=~~NAG~~:N-~~ACETYL~~-D-~~GLUCOSAMINE~~'>~~NAG~~</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.68Å</td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td><td class="sblockDat">[[1ex1\|1ex1]], [[1ieq\|1ieq]], [[1iev\|1iev]], [[1iew\|1iew]], [[1iex\|1iex]], [[1j8v\|1j8v]], [[3wlh\|3wlh]], [[3wli\|3wli]], [[3wlj\|3wlj]], [[3wlk\|3wlk]], [[3wll\|3wll]], [[3wlm\|3wlm]], [[3wln\|3wln]], [[3wlo\|3wlo]], [[3wlp\|3wlp]], [[3wlq\|3wlq]], [[3wlr\|3wlr]], [[3wlt\|3wlt]]</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=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_900099:METHYL+2-THIO-BETA-SOPHOROSIDE'>PRD_900099</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=U2A:methyl+2-thio-beta-D-glucopyranoside'>U2A</scene></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=6md6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6md6 OCA], [~~http~~://pdbe.org/6md6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6md6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6md6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6md6 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=6md6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6md6 OCA], [https://pdbe.org/6md6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6md6 RCSB], [https://www.ebi.ac.uk/pdbsum/6md6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6md6 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9XEI3_HORVV Q9XEI3_HORVV]
	<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: ~~Domesticated barley~~]]	+	[[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~~, V A]]~~	+	[[Category: Streltsov VA]]
-	~~[[Category: Beta barrel]]~~	+
-	~~[[Category: Grain development]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: N-glycosylation]]~~	+
-	~~[[Category: Plant apoplast]]~~	+
-	~~[[Category: Tim barrel/beta sheet~~]]	+

OCA at 23:06, 5 June 2019

OCA — Wed, 05 Jun 2019 23:06:42 GMT

←Older revision		Revision as of 23:06, 5 June 2019
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	<StructureSection load='6md6' size='340' side='right'caption='[[6md6]], [[Resolution\|resolution]] 1.68Å' scene=''>		<StructureSection load='6md6' size='340' side='right'caption='[[6md6]], [[Resolution\|resolution]] 1.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6md6]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MD6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MD6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6md6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Domesticated_barley Domesticated barley]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MD6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MD6 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=JSV:methyl+2-S-beta-D-glucopyranosyl-2-thio-beta-D-glucopyranoside'>JSV</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=JSV:methyl+2-S-beta-D-glucopyranosyl-2-thio-beta-D-glucopyranoside'>JSV</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ex1\|1ex1]], [[1ieq\|1ieq]], [[1iev\|1iev]], [[1iew\|1iew]], [[1iex\|1iex]], [[1j8v\|1j8v]], [[3wlh\|3wlh]], [[3wli\|3wli]], [[3wlj\|3wlj]], [[3wlk\|3wlk]], [[3wll\|3wll]], [[3wlm\|3wlm]], [[3wln\|3wln]], [[3wlo\|3wlo]], [[3wlp\|3wlp]], [[3wlq\|3wlq]], [[3wlr\|3wlr]], [[3wlt\|3wlt]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ex1\|1ex1]], [[1ieq\|1ieq]], [[1iev\|1iev]], [[1iew\|1iew]], [[1iex\|1iex]], [[1j8v\|1j8v]], [[3wlh\|3wlh]], [[3wli\|3wli]], [[3wlj\|3wlj]], [[3wlk\|3wlk]], [[3wll\|3wll]], [[3wlm\|3wlm]], [[3wln\|3wln]], [[3wlo\|3wlo]], [[3wlp\|3wlp]], [[3wlq\|3wlq]], [[3wlr\|3wlr]], [[3wlt\|3wlt]]</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=6md6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6md6 OCA], [http://pdbe.org/6md6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6md6 RCSB], [http://www.ebi.ac.uk/pdbsum/6md6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6md6 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=6md6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6md6 OCA], [http://pdbe.org/6md6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6md6 RCSB], [http://www.ebi.ac.uk/pdbsum/6md6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6md6 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Substrates associate and products dissociate from enzyme catalytic sites rapidly, which hampers investigations of their trajectories. The high-resolution structure of the native Hordeum exo-hydrolase HvExoI isolated from seedlings reveals that non-covalently trapped glucose forms a stable enzyme-product complex. Here, we report that the alkyl beta-D-glucoside and methyl 6-thio-beta-gentiobioside substrate analogues perfused in crystalline HvExoI bind across the catalytic site after they displace glucose, while methyl 2-thio-beta-sophoroside attaches nearby. Structural analyses and multi-scale molecular modelling of nanoscale reactant movements in HvExoI reveal that upon productive binding of incoming substrates, the glucose product modifies its binding patterns and evokes the formation of a transient lateral cavity, which serves as a conduit for glucose departure to allow for the next catalytic round. This path enables substrate-product assisted processive catalysis through multiple hydrolytic events without HvExoI losing contact with oligo- or polymeric substrates. We anticipate that such enzyme plasticity could be prevalent among exo-hydrolases.
		+
		+	Discovery of processive catalysis by an exo-hydrolase with a pocket-shaped active site.,Streltsov VA, Luang S, Peisley A, Varghese JN, Ketudat Cairns JR, Fort S, Hijnen M, Tvaroska I, Arda A, Jimenez-Barbero J, Alfonso-Prieto M, Rovira C, Mendoza F, Tiessler-Sala L, Sanchez-Aparicio JE, Rodriguez-Guerra J, Lluch JM, Marechal JD, Masgrau L, Hrmova M Nat Commun. 2019 May 20;10(1):2222. doi: 10.1038/s41467-019-09691-z. PMID:31110237<ref>PMID:31110237</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6md6" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Domesticated barley]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Hrmova, M]]		[[Category: Hrmova, M]]

OCA at 06:13, 29 May 2019

OCA — Wed, 29 May 2019 06:13:16 GMT

←Older revision		Revision as of 06:13, 29 May 2019
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-	'''Unreleased structure'''

-	~~The entry 6md6 is ON HOLD until Paper Publication~~	+	==CRYSTAL STRUCTURE ANALYSIS OF PLANT EXOHYDROLASE IN COMPLEX WITH METHYL 2-THIO-BETA-SOPHOROSIDE==
-		+	<StructureSection load='6md6' size='340' side='right'caption='[[6md6]], [[Resolution\|resolution]] 1.68Å' scene=''>
-	~~Authors: Streltsov, V.A., Luang, S., Hrmova, M.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6md6]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MD6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MD6 FirstGlance]. <br>
-	~~Description:~~ CRYSTAL STRUCTURE ANALYSIS OF PLANT EXOHYDROLASE IN COMPLEX WITH METHYL 2-THIO-BETA-SOPHOROSIDE	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=JSV:methyl+2-S-beta-D-glucopyranosyl-2-thio-beta-D-glucopyranoside'>JSV</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ex1\|1ex1]], [[1ieq\|1ieq]], [[1iev\|1iev]], [[1iew\|1iew]], [[1iex\|1iex]], [[1j8v\|1j8v]], [[3wlh\|3wlh]], [[3wli\|3wli]], [[3wlj\|3wlj]], [[3wlk\|3wlk]], [[3wll\|3wll]], [[3wlm\|3wlm]], [[3wln\|3wln]], [[3wlo\|3wlo]], [[3wlp\|3wlp]], [[3wlq\|3wlq]], [[3wlr\|3wlr]], [[3wlt\|3wlt]]</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=6md6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6md6 OCA], [http://pdbe.org/6md6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6md6 RCSB], [http://www.ebi.ac.uk/pdbsum/6md6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6md6 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Hrmova, M]]		[[Category: Hrmova, M]]
-	[[Category: Streltsov, V.A]]
	[[Category: Luang, S]]		[[Category: Luang, S]]
		+	[[Category: Streltsov, V A]]
		+	[[Category: Beta barrel]]
		+	[[Category: Grain development]]
		+	[[Category: Hydrolase]]
		+	[[Category: N-glycosylation]]
		+	[[Category: Plant apoplast]]
		+	[[Category: Tim barrel/beta sheet]]

OCA at 06:23, 3 October 2018

OCA — Wed, 03 Oct 2018 06:23:43 GMT

←Older revision		Revision as of 06:23, 3 October 2018
Line 5:		Line 5:
	Authors: Streltsov, V.A., Luang, S., Hrmova, M.		Authors: Streltsov, V.A., Luang, S., Hrmova, M.

-	Description: CRYSTAL STRUCTURE ANALYSIS OF PLANT EXOHYDROLASE	+	Description: CRYSTAL STRUCTURE ANALYSIS OF PLANT EXOHYDROLASE IN COMPLEX WITH METHYL 2-THIO-BETA-SOPHOROSIDE
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Hrmova, M]]		[[Category: Hrmova, M]]
	[[Category: Streltsov, V.A]]		[[Category: Streltsov, V.A]]
	[[Category: Luang, S]]		[[Category: Luang, S]]

OCA at 06:26, 26 September 2018

OCA — Wed, 26 Sep 2018 06:26:26 GMT

←Older revision		Revision as of 06:26, 26 September 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6md6 is ON HOLD	+	The entry 6md6 is ON HOLD until Paper Publication

	Authors: Streltsov, V.A., Luang, S., Hrmova, M.		Authors: Streltsov, V.A., Luang, S., Hrmova, M.
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	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Hrmova, M]]		[[Category: Hrmova, M]]
-	[[Category: Luang, S]]
	[[Category: Streltsov, V.A]]		[[Category: Streltsov, V.A]]
		+	[[Category: Luang, S]]

OCA: Protected "6md6" [edit=sysop:move=sysop]

OCA — Wed, 12 Sep 2018 06:14:39 GMT

Protected "6md6" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:14, 12 September 2018

OCA: New page: '''Unreleased structure''' The entry 6md6 is ON HOLD Authors: Streltsov, V.A., Luang, S., Hrmova, M. Description: CRYSTAL STRUCTURE ANALYSIS OF PLANT EXOHYDROLASE [[Category: Unrelease...

OCA — Wed, 12 Sep 2018 06:14:37 GMT

New page: '''Unreleased structure''' The entry 6md6 is ON HOLD Authors: Streltsov, V.A., Luang, S., Hrmova, M. Description: CRYSTAL STRUCTURE ANALYSIS OF PLANT EXOHYDROLASE [[Category: Unrelease...

New page

'''Unreleased structure'''

The entry 6md6 is ON HOLD

Authors: Streltsov, V.A., Luang, S., Hrmova, M.

Description: CRYSTAL STRUCTURE ANALYSIS OF PLANT EXOHYDROLASE
[[Category: Unreleased Structures]]
[[Category: Hrmova, M]]
[[Category: Luang, S]]
[[Category: Streltsov, V.A]]