6eqj - Revision history

OCA at 12:21, 9 May 2024

OCA — Thu, 09 May 2024 12:21:04 GMT

←Older revision		Revision as of 12:21, 9 May 2024
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	==Crystal Structure of Human Glycogenin-1 (GYG1) Tyr195pIPhe mutant, apo form==		==Crystal Structure of Human Glycogenin-1 (GYG1) Tyr195pIPhe mutant, apo form==
-	<StructureSection load='6eqj' size='340' side='right' caption='[[6eqj]], [[Resolution\|resolution]] 2.18Å' scene=''>	+	<StructureSection load='6eqj' size='340' side='right'caption='[[6eqj]], [[Resolution\|resolution]] 2.18Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6eqj]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EQJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6EQJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6eqj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EQJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6EQJ 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>~~</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]] 2.18Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~PHI~~:~~IODO~~-~~PHENYLALANINE~~'>~~PHI~~</scene>~~</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=PHI:IODO-PHENYLALANINE'>PHI</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GYG1~~, ~~GYG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~<~~/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=6eqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6eqj OCA], [https://pdbe.org/6eqj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6eqj RCSB], [https://www.ebi.ac.uk/pdbsum/6eqj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6eqj 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/Glycogenin_glucosyltransferase Glycogenin glucosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.186 2.4.1.186]~~ </~~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=6eqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6eqj OCA], [~~http~~://pdbe.org/6eqj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6eqj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6eqj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6eqj ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/GLYG_HUMAN GLYG_HUMAN]] Glycogen storage disease due to glycogenin deficiency. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry.	+	[https://www.uniprot.org/uniprot/GLYG_HUMAN GLYG_HUMAN] Glycogen storage disease due to glycogenin deficiency. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry.
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/GLYG_HUMAN GLYG_HUMAN]] Self-glucosylates, via an inter-subunit mechanism, to form an oligosaccharide primer that serves as substrate for glycogen synthase.	+	[https://www.uniprot.org/uniprot/GLYG_HUMAN GLYG_HUMAN] Self-glucosylates, via an inter-subunit mechanism, to form an oligosaccharide primer that serves as substrate for glycogen synthase.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 30:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Glycogenin glucosyltransferase~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Human~~]]	+	[[Category: Large Structures]]
-	[[Category: Arrowsmith~~, C H~~]]	+	[[Category: Arrowsmith CH]]
-	[[Category: Bailey~~, H J~~]]	+	[[Category: Bailey HJ]]
-	[[Category: Bezerra~~, G A~~]]	+	[[Category: Bezerra GA]]
-	[[Category: Bilyard~~, M K~~]]	+	[[Category: Bilyard MK]]
-	[[Category: Bountra, C]]	+	[[Category: Bountra C]]
-	[[Category: Davis~~, B G~~]]	+	[[Category: Davis BG]]
-	[[Category: Edwards~~, A M~~]]	+	[[Category: Edwards AM]]
-	[[Category: Kopec, J]]	+	[[Category: Kopec J]]
-	[[Category: Lee, S ~~Seo~~]]	+	[[Category: Seo Lee S]]
-	[[Category: Yue~~, W W]]~~	+	[[Category: Yue WW]]
-	~~[[Category: Glycogenin-1]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 12:46, 7 November 2018

OCA — Wed, 07 Nov 2018 12:46:42 GMT

←Older revision		Revision as of 12:46, 7 November 2018
Line 14:		Line 14:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/GLYG_HUMAN GLYG_HUMAN]] Self-glucosylates, via an inter-subunit mechanism, to form an oligosaccharide primer that serves as substrate for glycogen synthase.		[[http://www.uniprot.org/uniprot/GLYG_HUMAN GLYG_HUMAN]] Self-glucosylates, via an inter-subunit mechanism, to form an oligosaccharide primer that serves as substrate for glycogen synthase.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Biosynthesis of glycogen, the essential glucose (and hence energy) storage molecule in humans, animals and fungi(1), is initiated by the glycosyltransferase enzyme, glycogenin (GYG). Deficiencies in glycogen formation cause neurodegenerative and metabolic disease(2-4), and mouse knockout(5) and inherited human mutations(6) of GYG impair glycogen synthesis. GYG acts as a 'seed core' for the formation of the glycogen particle by catalysing its own stepwise autoglucosylation to form a covalently bound gluco-oligosaccharide chain at initiation site Tyr 195. Precise mechanistic studies have so far been prevented by an inability to access homogeneous glycoforms of this protein, which unusually acts as both catalyst and substrate. Here we show that unprecedented direct access to different, homogeneously glucosylated states of GYG can be accomplished through a palladium-mediated enzyme activation 'shunt' process using on-protein C-C bond formation. Careful mimicry of GYG intermediates recapitulates catalytic activity at distinct stages, which in turn allows discovery of triphasic kinetics and substrate plasticity in GYG's use of sugar substrates. This reveals a tolerant but 'proof-read' mechanism that underlies the precision of this metabolic process. The present demonstration of direct, chemically controlled access to intermediate states of active enzymes suggests that such ligation-dependent activation could be a powerful tool in the study of mechanism.
		+
		+	Palladium-mediated enzyme activation suggests multiphase initiation of glycogenesis.,Bilyard MK, Bailey HJ, Raich L, Gafitescu MA, Machida T, Iglesias-Fernandez J, Lee SS, Spicer CD, Rovira C, Yue WW, Davis BG Nature. 2018 Oct 24. pii: 10.1038/s41586-018-0644-7. doi:, 10.1038/s41586-018-0644-7. PMID:30356213<ref>PMID:30356213</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6eqj" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Glycogenin\|Glycogenin]]		*[[Glycogenin\|Glycogenin]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:54, 24 October 2018

OCA — Wed, 24 Oct 2018 06:54:19 GMT

←Older revision		Revision as of 06:54, 24 October 2018
Line 3:		Line 3:
	<StructureSection load='6eqj' size='340' side='right' caption='[[6eqj]], [[Resolution\|resolution]] 2.18Å' scene=''>		<StructureSection load='6eqj' size='340' side='right' caption='[[6eqj]], [[Resolution\|resolution]] 2.18Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6eqj]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EQJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EQJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6eqj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EQJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EQJ 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></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></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PHI:IODO-PHENYLALANINE'>PHI</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PHI:IODO-PHENYLALANINE'>PHI</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GYG1, GYG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycogenin_glucosyltransferase Glycogenin glucosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.186 2.4.1.186] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycogenin_glucosyltransferase Glycogenin glucosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.186 2.4.1.186] </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=6eqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6eqj OCA], [http://pdbe.org/6eqj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6eqj RCSB], [http://www.ebi.ac.uk/pdbsum/6eqj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6eqj 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=6eqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6eqj OCA], [http://pdbe.org/6eqj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6eqj RCSB], [http://www.ebi.ac.uk/pdbsum/6eqj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6eqj ProSAT]</span></td></tr>
Line 13:		Line 14:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/GLYG_HUMAN GLYG_HUMAN]] Self-glucosylates, via an inter-subunit mechanism, to form an oligosaccharide primer that serves as substrate for glycogen synthase.		[[http://www.uniprot.org/uniprot/GLYG_HUMAN GLYG_HUMAN]] Self-glucosylates, via an inter-subunit mechanism, to form an oligosaccharide primer that serves as substrate for glycogen synthase.
		+
		+	==See Also==
		+	*[[Glycogenin\|Glycogenin]]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Glycogenin glucosyltransferase]]		[[Category: Glycogenin glucosyltransferase]]
		+	[[Category: Human]]
	[[Category: Arrowsmith, C H]]		[[Category: Arrowsmith, C H]]
	[[Category: Bailey, H J]]		[[Category: Bailey, H J]]

OCA at 06:26, 20 December 2017

OCA — Wed, 20 Dec 2017 06:26:46 GMT

←Older revision		Revision as of 06:26, 20 December 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6eqj ~~is ON HOLD~~	+	==Crystal Structure of Human Glycogenin-1 (GYG1) Tyr195pIPhe mutant, apo form==
-		+	<StructureSection load='6eqj' size='340' side='right' caption='[[6eqj]], [[Resolution\|resolution]] 2.18Å' scene=''>
-	~~Authors~~: ~~Bailey, H~~.J.~~, Kopec, J~~.~~, Bilyard, M~~.K.~~, Bezerra, G~~.A., ~~Seo Lee, S~~., ~~Arrowsmith, C~~.H., ~~Edwards, A~~.M., ~~Bountra~~, C., ~~Davis, B~~.G., ~~Yue, W~~.W.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6eqj]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EQJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EQJ FirstGlance]. <br>
-	~~Description~~: ~~Crystal Structure of Human Glycogenin~~-~~1 (GYG1) Tyr195pIPhe mutant~~, ~~apo~~ form	+	</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></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PHI:IODO-PHENYLALANINE'>PHI</scene></td></tr>
-	[[Category: ~~Seo Lee~~, S]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycogenin_glucosyltransferase Glycogenin glucosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.186 2.4.1.186] </span></td></tr>
-	[[Category: Bailey, H.J]]	+	<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=6eqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6eqj OCA], [http://pdbe.org/6eqj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6eqj RCSB], [http://www.ebi.ac.uk/pdbsum/6eqj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6eqj ProSAT]</span></td></tr>
-	[[Category: ~~Arrowsmith~~, C.H]]	+	</table>
-	[[Category: ~~Bezerra~~, G.A]]	+	== Disease ==
-	[[Category: ~~Yue~~, ~~W.W~~]]	+	[[http://www.uniprot.org/uniprot/GLYG_HUMAN GLYG_HUMAN]] Glycogen storage disease due to glycogenin deficiency. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry.
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GLYG_HUMAN GLYG_HUMAN]] Self-glucosylates, via an inter-subunit mechanism, to form an oligosaccharide primer that serves as substrate for glycogen synthase.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Glycogenin glucosyltransferase]]
		+	[[Category: Arrowsmith, C H]]
		+	[[Category: Bailey, H J]]
		+	[[Category: Bezerra, G A]]
		+	[[Category: Bilyard, M K]]
		+	[[Category: Bountra, C]]
		+	[[Category: Davis, B G]]
		+	[[Category: Edwards, A M]]
	[[Category: Kopec, J]]		[[Category: Kopec, J]]
-	[[Category: ~~Davis~~, ~~B.G~~]]	+	[[Category: Lee, S Seo]]
-	[[Category: ~~Edwards~~, ~~A.M~~]]	+	[[Category: Yue, W W]]
-	[[Category: ~~Bilyard, M.K~~]]	+	[[Category: Glycogenin-1]]
-	[[Category: ~~Bountra, C~~]]	+	[[Category: Hydrolase]]

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

OCA — Wed, 25 Oct 2017 05:56:29 GMT

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

←Older revision

Revision as of 05:56, 25 October 2017

OCA: New page: '''Unreleased structure''' The entry 6eqj is ON HOLD Authors: Bailey, H.J., Kopec, J., Bilyard, M.K., Bezerra, G.A., Seo Lee, S., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Davis, B....

OCA — Wed, 25 Oct 2017 05:56:27 GMT

New page: '''Unreleased structure''' The entry 6eqj is ON HOLD Authors: Bailey, H.J., Kopec, J., Bilyard, M.K., Bezerra, G.A., Seo Lee, S., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Davis, B....

New page

'''Unreleased structure'''

The entry 6eqj is ON HOLD

Authors: Bailey, H.J., Kopec, J., Bilyard, M.K., Bezerra, G.A., Seo Lee, S., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Davis, B.G., Yue, W.W.

Description: Crystal Structure of Human Glycogenin-1 (GYG1) Tyr195pIPhe mutant, apo form
[[Category: Unreleased Structures]]
[[Category: Seo Lee, S]]
[[Category: Bailey, H.J]]
[[Category: Arrowsmith, C.H]]
[[Category: Bezerra, G.A]]
[[Category: Yue, W.W]]
[[Category: Kopec, J]]
[[Category: Davis, B.G]]
[[Category: Edwards, A.M]]
[[Category: Bilyard, M.K]]
[[Category: Bountra, C]]