5vec - Revision history

OCA at 13:47, 4 October 2023

OCA — Wed, 04 Oct 2023 13:47:07 GMT

←Older revision		Revision as of 13:47, 4 October 2023
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	<StructureSection load='5vec' size='340' side='right'caption='[[5vec]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='5vec' size='340' side='right'caption='[[5vec]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vec]] is a 2 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=5VEC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VEC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vec]] is a 2 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=5VEC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VEC FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.2000163Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Related_structure~~\|~~Related:]]</b></td><td class="sblockDat">[[5epc\|5epc~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~PGM1 ([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=5vec FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vec OCA], [https://pdbe.org/5vec PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vec RCSB], [https://www.ebi.ac.uk/pdbsum/5vec PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vec 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/Phosphoglucomutase Phosphoglucomutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.2.2 5.4.2.2]~~ </~~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=5vec FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vec OCA], [~~http~~://pdbe.org/5vec PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5vec RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5vec PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5vec ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/PGM1_HUMAN PGM1_HUMAN]] PGM-CDG;Glycogen storage disease due to phosphoglucomutase deficiency. The disease is caused by mutations affecting the gene represented in this entry.	+	[https://www.uniprot.org/uniprot/PGM1_HUMAN PGM1_HUMAN] PGM-CDG;Glycogen storage disease due to phosphoglucomutase deficiency. The disease is caused by mutations affecting the gene represented in this entry.
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PGM1_HUMAN PGM1_HUMAN]] This enzyme participates in both the breakdown and synthesis of glucose.	+	[https://www.uniprot.org/uniprot/PGM1_HUMAN PGM1_HUMAN] This enzyme participates in both the breakdown and synthesis of glucose.
	<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: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Phosphoglucomutase]]~~	+	[[Category: Beamer LJ]]
-	[[Category: Beamer~~, L J~~]]	+	[[Category: Stiers KM]]
-	[[Category: Stiers~~, K M]]~~	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Pgm1]]~~	+
-	~~[[Category: Phosphoglucomutase-1]]~~	+
-	~~[[Category: Phosphoryl transfer~~]]	+

OCA at 08:03, 27 November 2019

OCA — Wed, 27 Nov 2019 08:03:52 GMT

←Older revision		Revision as of 08:03, 27 November 2019
Line 1:		Line 1:

	==Crystal Structure of the R515L missense variant of human PGM1==		==Crystal Structure of the R515L missense variant of human PGM1==
-	<StructureSection load='5vec' size='340' side='right' caption='[[5vec]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='5vec' size='340' side='right'caption='[[5vec]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5vec]] is a 2 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=5VEC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VEC FirstGlance]. <br>		<table><tr><td colspan='2'>[[5vec]] is a 2 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=5VEC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VEC FirstGlance]. <br>
Line 28:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Phosphoglucomutase]]		[[Category: Phosphoglucomutase]]
	[[Category: Beamer, L J]]		[[Category: Beamer, L J]]

OCA at 10:21, 5 September 2018

OCA — Wed, 05 Sep 2018 10:21:27 GMT

←Older revision		Revision as of 10:21, 5 September 2018
Line 3:		Line 3:
	<StructureSection load='5vec' size='340' side='right' caption='[[5vec]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='5vec' size='340' side='right' caption='[[5vec]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vec]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VEC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VEC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vec]] is a 2 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=5VEC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VEC FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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">[[5epc\|5epc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5epc\|5epc]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PGM1 ([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/Phosphoglucomutase Phosphoglucomutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.2.2 5.4.2.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoglucomutase Phosphoglucomutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.2.2 5.4.2.2] </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=5vec FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vec OCA], [http://pdbe.org/5vec PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vec RCSB], [http://www.ebi.ac.uk/pdbsum/5vec PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vec 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=5vec FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vec OCA], [http://pdbe.org/5vec PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vec RCSB], [http://www.ebi.ac.uk/pdbsum/5vec PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vec ProSAT]</span></td></tr>
Line 13:		Line 14:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/PGM1_HUMAN PGM1_HUMAN]] This enzyme participates in both the breakdown and synthesis of glucose.		[[http://www.uniprot.org/uniprot/PGM1_HUMAN PGM1_HUMAN]] This enzyme participates in both the breakdown and synthesis of glucose.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Human phosphoglucomutase 1 (PGM1) plays a central role in cellular glucose homeostasis, catalyzing the conversion of glucose 1-phosphate and glucose 6-phosphate. Recently, missense variants of this enzyme were identified as causing an inborn error of metabolism, PGM1 deficiency, with features of a glycogen storage disease and a congenital disorder of glycosylation. Previous studies of selected PGM1 variants have revealed various mechanisms for enzyme dysfunction, including regions of structural disorder and side-chain rearrangements within the active site. Here, we examine variants within a substrate-binding loop in domain 4 (D4) of PGM1 that cause extreme impairment of activity. Biochemical, structural, and computational studies demonstrate multiple detrimental impacts resulting from these variants, including loss of conserved ligand-binding interactions and reduced mobility of the D4 loop, due to perturbation of its conformational ensemble. These potentially synergistic effects make this conserved ligand-binding loop a hotspot for disease-related variants in PGM1 and related enzymes.
		+
		+	A Hotspot for Disease-Associated Variants of Human PGM1 Is Associated with Impaired Ligand Binding and Loop Dynamics.,Stiers KM, Beamer LJ Structure. 2018 Aug 7. pii: S0969-2126(18)30251-X. doi:, 10.1016/j.str.2018.07.005. PMID:30122451<ref>PMID:30122451</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5vec" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Phosphoglucomutase]]		[[Category: Phosphoglucomutase]]
	[[Category: Beamer, L J]]		[[Category: Beamer, L J]]

OCA at 05:26, 27 June 2018

OCA — Wed, 27 Jun 2018 05:26:12 GMT

←Older revision		Revision as of 05:26, 27 June 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5vec is ~~ON HOLD until Paper Publication~~	+	==Crystal Structure of the R515L missense variant of human PGM1==
-		+	<StructureSection load='5vec' size='340' side='right' caption='[[5vec]], [[Resolution\|resolution]] 2.20Å' scene=''>
-	~~Authors~~: ~~Stiers~~, K.M., ~~Beamer~~, L.J.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5vec]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VEC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VEC FirstGlance]. <br>
-	~~Description~~: ~~Crystal Structure of~~ the ~~R515L missense variant~~ of ~~human PGM1~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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">[[5epc\|5epc]]</td></tr>
-	[[Category: Beamer, L.J]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoglucomutase Phosphoglucomutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.2.2 5.4.2.2] </span></td></tr>
-	[[Category: Stiers, K.M]]	+	<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=5vec FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vec OCA], [http://pdbe.org/5vec PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vec RCSB], [http://www.ebi.ac.uk/pdbsum/5vec PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vec ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/PGM1_HUMAN PGM1_HUMAN]] PGM-CDG;Glycogen storage disease due to phosphoglucomutase deficiency. The disease is caused by mutations affecting the gene represented in this entry.
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PGM1_HUMAN PGM1_HUMAN]] This enzyme participates in both the breakdown and synthesis of glucose.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Phosphoglucomutase]]
		+	[[Category: Beamer, L J]]
		+	[[Category: Stiers, K M]]
		+	[[Category: Isomerase]]
		+	[[Category: Pgm1]]
		+	[[Category: Phosphoglucomutase-1]]
		+	[[Category: Phosphoryl transfer]]

OCA at 14:00, 27 September 2017

OCA — Wed, 27 Sep 2017 14:00:42 GMT

←Older revision		Revision as of 14:00, 27 September 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5vec is ON HOLD	+	The entry 5vec is ON HOLD until Paper Publication

	Authors: Stiers, K.M., Beamer, L.J.		Authors: Stiers, K.M., Beamer, L.J.

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

OCA — Wed, 12 Apr 2017 09:58:10 GMT

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

←Older revision

Revision as of 09:58, 12 April 2017

OCA: New page: '''Unreleased structure''' The entry 5vec is ON HOLD Authors: Stiers, K.M., Beamer, L.J. Description: Crystal Structure of the R515L missense variant of human PGM1 [[Category: Unreleas...

OCA — Wed, 12 Apr 2017 09:58:09 GMT

New page: '''Unreleased structure''' The entry 5vec is ON HOLD Authors: Stiers, K.M., Beamer, L.J. Description: Crystal Structure of the R515L missense variant of human PGM1 [[Category: Unreleas...

New page

'''Unreleased structure'''

The entry 5vec is ON HOLD

Authors: Stiers, K.M., Beamer, L.J.

Description: Crystal Structure of the R515L missense variant of human PGM1
[[Category: Unreleased Structures]]
[[Category: Beamer, L.J]]
[[Category: Stiers, K.M]]