5tr2 - Revision history

OCA at 13:08, 4 October 2023

OCA — Wed, 04 Oct 2023 13:08:50 GMT

←Older revision		Revision as of 13:08, 4 October 2023
Line 3:		Line 3:
	<StructureSection load='5tr2' size='340' side='right'caption='[[5tr2]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='5tr2' size='340' side='right'caption='[[5tr2]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5tr2]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TR2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5TR2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5tr2]] 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=5TR2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TR2 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>~~, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.5Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~SEP~~:~~PHOSPHOSERINE~~'>~~SEP~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</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]]~~, ~~[[5f9c\|5f9c]], [[5hsh\|5hsh]], [[5jn5\|5jn5]]~~<~~/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=5tr2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tr2 OCA], [https://pdbe.org/5tr2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5tr2 RCSB], [https://www.ebi.ac.uk/pdbsum/5tr2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5tr2 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~~://proteopedia.org/fgij/fg.htm?mol=5tr2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tr2 OCA], [~~http~~://pdbe.org/5tr2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5tr2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5tr2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5tr2 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 ==
Line 27:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[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: Enzyme]]~~	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Phosphohexomutase~~]]	+

OCA at 12:17, 23 September 2020

OCA — Wed, 23 Sep 2020 12:17:33 GMT

←Older revision		Revision as of 12:17, 23 September 2020
Line 1:		Line 1:

	==Crystal structure of the D263G missense variant of human PGM1==		==Crystal structure of the D263G missense variant of human PGM1==
-	<StructureSection load='5tr2' size='340' side='right' caption='[[5tr2]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='5tr2' size='340' side='right'caption='[[5tr2]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5tr2]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TR2 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5TR2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5tr2]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TR2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5TR2 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5epc\|5epc]], [[5f9c\|5f9c]], [[5hsh\|5hsh]], [[5jn5\|5jn5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5epc\|5epc]], [[5f9c\|5f9c]], [[5hsh\|5hsh]], [[5jn5\|5jn5]]</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=5tr2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tr2 OCA], [http://pdbe.org/5tr2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tr2 RCSB], [http://www.ebi.ac.uk/pdbsum/5tr2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tr2 ProSAT]</span></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=5tr2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tr2 OCA], [http://pdbe.org/5tr2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tr2 RCSB], [http://www.ebi.ac.uk/pdbsum/5tr2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tr2 ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 27:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Phosphoglucomutase]]		[[Category: Phosphoglucomutase]]
	[[Category: Beamer, L J]]		[[Category: Beamer, L J]]

OCA at 07:41, 9 March 2017

OCA — Thu, 09 Mar 2017 07:41:08 GMT

←Older revision		Revision as of 07:41, 9 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5tr2 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of the D263G missense variant of human PGM1==
		+	<StructureSection load='5tr2' size='340' side='right' caption='[[5tr2]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5tr2]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TR2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TR2 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5epc\|5epc]], [[5f9c\|5f9c]], [[5hsh\|5hsh]], [[5jn5\|5jn5]]</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=5tr2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tr2 OCA], [http://pdbe.org/5tr2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tr2 RCSB], [http://www.ebi.ac.uk/pdbsum/5tr2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tr2 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.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The enzyme phosphoglucomutase 1 (PGM1) plays a central role in glucose homeostasis. Clinical studies have identified mutations in human PGM1 as the cause of PGM1 deficiency, an inherited metabolic disease. One residue, Asp263, has two known variants associated with disease: D263G and D263Y. Biochemical studies have shown that these mutants are soluble and well folded, but have significant catalytic impairment. To better understand this catalytic defect, we determined crystal structures of these two missense variants, both of which reveal a similar and indirect structural change due to the loss of a conserved salt bridge between Asp263 and Arg293. The arginine reorients into the active site, making interactions with residues responsible for substrate binding. Biochemical studies also show that the catalytic phosphoserine of the missense variants is more stable to hydrolysis relative to wild-type enzyme. The structural perturbation resulting from mutation of this single amino acid reveals the molecular mechanism underlying PGM1 deficiency in these missense variants. DATABASE: Structural data are available in the PDB under the accession numbers 5JN5 and 5TR2.

-	~~Authors: Beamer, L.J~~., Stiers, K.M.	+	Asp263 missense variants perturb the active site of human phosphoglucomutase 1.,Stiers KM, Graham AC, Kain BN, Beamer LJ FEBS J. 2017 Jan 24. doi: 10.1111/febs.14025. PMID:28117557<ref>PMID:28117557</ref>

-	~~Description: Crystal structure~~ of the ~~D263G missense variant~~ of ~~human PGM1~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Beamer, L.J]]	+	<div class="pdbe-citations 5tr2" style="background-color:#fffaf0;"></div>
-	[[Category: Stiers, K.M]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Phosphoglucomutase]]
		+	[[Category: Beamer, L J]]
		+	[[Category: Stiers, K M]]
		+	[[Category: Enzyme]]
		+	[[Category: Isomerase]]
		+	[[Category: Phosphohexomutase]]

OCA at 20:01, 22 December 2016

OCA — Thu, 22 Dec 2016 20:01:27 GMT

←Older revision		Revision as of 20:01, 22 December 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5tr2 is ON HOLD	+	The entry 5tr2 is ON HOLD until Paper Publication

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

OCA: Protected "5tr2" [edit=sysop:move=sysop]

OCA — Wed, 02 Nov 2016 17:04:07 GMT

Protected "5tr2" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:04, 2 November 2016

OCA: New page: '''Unreleased structure''' The entry 5tr2 is ON HOLD Authors: Beamer, L.J., Stiers, K.M. Description: Crystal structure of the D263G missense variant of human PGM1 [[Category: Unreleas...

OCA — Wed, 02 Nov 2016 17:04:06 GMT

New page: '''Unreleased structure''' The entry 5tr2 is ON HOLD Authors: Beamer, L.J., Stiers, K.M. Description: Crystal structure of the D263G missense variant of human PGM1 [[Category: Unreleas...

New page

'''Unreleased structure'''

The entry 5tr2 is ON HOLD

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

Description: Crystal structure of the D263G missense variant of human PGM1
[[Category: Unreleased Structures]]
[[Category: Beamer, L.J]]
[[Category: Stiers, K.M]]