5jt0 - Revision history

OCA at 19:05, 20 September 2023

OCA — Wed, 20 Sep 2023 19:05:12 GMT

←Older revision		Revision as of 19:05, 20 September 2023
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	==Crystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis in complex with Mn2+, uridine-diphosphate (UDP) and glucosyl-3-phosphoglycerate (GPG) - GpgSGPGUDP*Mn2+==		==Crystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis in complex with Mn2+, uridine-diphosphate (UDP) and glucosyl-3-phosphoglycerate (GPG) - GpgSGPGUDP*Mn2+==
-	<StructureSection load='5jt0' size='340' side='right' caption='[[5jt0]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='5jt0' size='340' side='right'caption='[[5jt0]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jt0]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Myctu Myctu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JT0 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JT0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jt0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JT0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JT0 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene>, <scene name='pdbligand=XDX:(2R)-2-(ALPHA-D-GLUCOPYRANOSYLOXY)-3-(PHOSPHONOOXY)PROPANOIC+ACID'>XDX</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]] 2.8Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jsx\|5jsx]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene>, <scene name='pdbligand=XDX:(2R)-2-(ALPHA-D-GLUCOPYRANOSYLOXY)-3-(PHOSPHONOOXY)PROPANOIC+ACID'>XDX</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gpgS, Rv1208 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])</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=5jt0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jt0 OCA], [https://pdbe.org/5jt0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jt0 RCSB], [https://www.ebi.ac.uk/pdbsum/5jt0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jt0 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/Glucosyl-3-phosphoglycerate_synthase Glucosyl-3-phosphoglycerate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.266 2.4.1.266] </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=5jt0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jt0 OCA], [~~http~~://pdbe.org/5jt0 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jt0 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jt0 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jt0 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/GPGS_MYCTU GPGS_MYCTU]] Involved in the biosynthesis of methylglucose lipopolysaccharides (MGLPs). Catalyzes the condensation of NDP-glucose and 3-phospho-glycerate (3-PGA) to yield glucosyl-3-phosphoglycerate (GPG).<ref>PMID:22637481</ref>	+	[https://www.uniprot.org/uniprot/GPGS_MYCTU GPGS_MYCTU] Involved in the biosynthesis of methylglucose lipopolysaccharides (MGLPs). Catalyzes the condensation of NDP-glucose and 3-phospho-glycerate (3-PGA) to yield glucosyl-3-phosphoglycerate (GPG).<ref>PMID:22637481</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: ~~Glucosyl-3-phosphoglycerate synthase~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Myctu~~]]	+	[[Category: Mycobacterium tuberculosis H37Rv]]
-	[[Category: Albesa-Jove, D]]	+	[[Category: Albesa-Jove D]]
-	[[Category: Arrasate, P]]	+	[[Category: Arrasate P]]
-	[[Category: Carreras-Gonzalez, A]]	+	[[Category: Carreras-Gonzalez A]]
-	[[Category: Comino, N]]	+	[[Category: Comino N]]
-	[[Category: Guerin~~, M E~~]]	+	[[Category: Guerin ME]]
-	[[Category: Rodrigo-Unzueta, A]]	+	[[Category: Rodrigo-Unzueta A]]
-	[[Category: Sancho-Vaello, E]]	+	[[Category: Sancho-Vaello E]]
-	[[Category: Urresti, S]]	+	[[Category: Urresti S]]
-	~~[[Category: Transferase~~]]	+

OCA at 06:57, 5 December 2018

OCA — Wed, 05 Dec 2018 06:57:09 GMT

←Older revision		Revision as of 06:57, 5 December 2018
Line 3:		Line 3:
	<StructureSection load='5jt0' size='340' side='right' caption='[[5jt0]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='5jt0' size='340' side='right' caption='[[5jt0]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jt0]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JT0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JT0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jt0]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Myctu Myctu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JT0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JT0 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene>, <scene name='pdbligand=XDX:(2R)-2-(ALPHA-D-GLUCOPYRANOSYLOXY)-3-(PHOSPHONOOXY)PROPANOIC+ACID'>XDX</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene>, <scene name='pdbligand=XDX:(2R)-2-(ALPHA-D-GLUCOPYRANOSYLOXY)-3-(PHOSPHONOOXY)PROPANOIC+ACID'>XDX</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jsx\|5jsx]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jsx\|5jsx]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gpgS, Rv1208 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucosyl-3-phosphoglycerate_synthase Glucosyl-3-phosphoglycerate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.266 2.4.1.266] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucosyl-3-phosphoglycerate_synthase Glucosyl-3-phosphoglycerate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.266 2.4.1.266] </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=5jt0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jt0 OCA], [http://pdbe.org/5jt0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jt0 RCSB], [http://www.ebi.ac.uk/pdbsum/5jt0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jt0 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=5jt0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jt0 OCA], [http://pdbe.org/5jt0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jt0 RCSB], [http://www.ebi.ac.uk/pdbsum/5jt0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jt0 ProSAT]</span></td></tr>
Line 11:		Line 12:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/GPGS_MYCTU GPGS_MYCTU]] Involved in the biosynthesis of methylglucose lipopolysaccharides (MGLPs). Catalyzes the condensation of NDP-glucose and 3-phospho-glycerate (3-PGA) to yield glucosyl-3-phosphoglycerate (GPG).<ref>PMID:22637481</ref>		[[http://www.uniprot.org/uniprot/GPGS_MYCTU GPGS_MYCTU]] Involved in the biosynthesis of methylglucose lipopolysaccharides (MGLPs). Catalyzes the condensation of NDP-glucose and 3-phospho-glycerate (3-PGA) to yield glucosyl-3-phosphoglycerate (GPG).<ref>PMID:22637481</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Glycosyltransferases (GTs) play a central role in nature. They catalyze the transfer of a sugar moiety to a broad range of acceptor substrates. GTs are highly selective enzymes, allowing the recognition of subtle structural differences in the sequences and stereochemistry of their sugar and acceptor substrates. We report here a series of structural snapshots of the reaction center of the retaining glucosyl-3-phosphoglycerate synthase (GpgS). During this sequence of events, we visualize how the enzyme guides the substrates into the reaction center where the glycosyl transfer reaction takes place, and unveil the mechanism of product release, involving multiple conformational changes not only in the substrates/products but also in the enzyme. The structural data are further complemented by metadynamics free-energy calculations, revealing how the equilibrium of loop conformations is modulated along these itineraries. The information reported here represent an important contribution for the understanding of GT enzymes at the molecular level.
		+
		+	Structural Snapshots and Loop Dynamics along the Catalytic Cycle of Glycosyltransferase GpgS.,Albesa-Jove D, Romero-Garcia J, Sancho-Vaello E, Contreras FX, Rodrigo-Unzueta A, Comino N, Carreras-Gonzalez A, Arrasate P, Urresti S, Biarnes X, Planas A, Guerin ME Structure. 2017 Jul 5;25(7):1034-1044.e3. doi: 10.1016/j.str.2017.05.009. Epub, 2017 Jun 15. PMID:28625787<ref>PMID:28625787</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5jt0" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 16:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Glucosyl-3-phosphoglycerate synthase]]		[[Category: Glucosyl-3-phosphoglycerate synthase]]
		+	[[Category: Myctu]]
	[[Category: Albesa-Jove, D]]		[[Category: Albesa-Jove, D]]
	[[Category: Arrasate, P]]		[[Category: Arrasate, P]]

OCA at 13:43, 24 May 2017

OCA — Wed, 24 May 2017 13:43:46 GMT

←Older revision		Revision as of 13:43, 24 May 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5jt0 is ~~ON HOLD~~ ~~until Paper Publication~~	+	==Crystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis in complex with Mn2+, uridine-diphosphate (UDP) and glucosyl-3-phosphoglycerate (GPG) - GpgSGPGUDP*Mn2+==
-		+	<StructureSection load='5jt0' size='340' side='right' caption='[[5jt0]], [[Resolution\|resolution]] 2.80Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5jt0]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JT0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JT0 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene>, <scene name='pdbligand=XDX:(2R)-2-(ALPHA-D-GLUCOPYRANOSYLOXY)-3-(PHOSPHONOOXY)PROPANOIC+ACID'>XDX</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jsx\|5jsx]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucosyl-3-phosphoglycerate_synthase Glucosyl-3-phosphoglycerate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.266 2.4.1.266] </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=5jt0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jt0 OCA], [http://pdbe.org/5jt0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jt0 RCSB], [http://www.ebi.ac.uk/pdbsum/5jt0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jt0 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GPGS_MYCTU GPGS_MYCTU]] Involved in the biosynthesis of methylglucose lipopolysaccharides (MGLPs). Catalyzes the condensation of NDP-glucose and 3-phospho-glycerate (3-PGA) to yield glucosyl-3-phosphoglycerate (GPG).<ref>PMID:22637481</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Glucosyl-3-phosphoglycerate synthase]]
		+	[[Category: Albesa-Jove, D]]
		+	[[Category: Arrasate, P]]
		+	[[Category: Carreras-Gonzalez, A]]
		+	[[Category: Comino, N]]
		+	[[Category: Guerin, M E]]
		+	[[Category: Rodrigo-Unzueta, A]]
		+	[[Category: Sancho-Vaello, E]]
		+	[[Category: Urresti, S]]
		+	[[Category: Transferase]]

OCA: Protected "5jt0" [edit=sysop:move=sysop]

OCA — Wed, 01 Jun 2016 13:47:42 GMT

Protected "5jt0" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:47, 1 June 2016

OCA: New page: '''Unreleased structure''' The entry 5jt0 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 01 Jun 2016 13:47:40 GMT

New page: '''Unreleased structure''' The entry 5jt0 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5jt0 is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]