5o7d - Revision history

OCA at 19:10, 29 November 2023

2023-11-29T19:10:27Z

← Older revision		Revision as of 19:10, 29 November 2023
Line 1:		Line 1:

	==The X-ray structure of human R38M phosphoglycerate kinase 1 mutant==		==The X-ray structure of human R38M phosphoglycerate kinase 1 mutant==
	<StructureSection load='5o7d' size='340' side='right' caption='[[5o7d]], [[Resolution\|resolution]] 1.84Å' scene=''>		<StructureSection load='5o7d' size='340' side='right'caption='[[5o7d]], [[Resolution\|resolution]] 1.84Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5o7d]] 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=5O7D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5O7D FirstGlance]. <br>		<table><tr><td colspan='2'>[[5o7d]] 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=5O7D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5O7D FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</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]] 1.84Å</td></tr>
	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">PGK1, PGKA, MIG10, OK/SW-cl~~.~~110 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5~~&~~id=9606 HUMAN])~~</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>
	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[http://en.wikipedia.org/wiki/Phosphoglycerate_kinase Phosphoglycerate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.2.3 2.7.2.3]~~ </~~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=5o7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o7d OCA], [https://pdbe.org/5o7d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5o7d RCSB], [https://www.ebi.ac.uk/pdbsum/5o7d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5o7d 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=5o7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o7d OCA], [~~http~~://pdbe.org/5o7d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5o7d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5o7d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5o7d ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
	[~~[http~~://www.uniprot.org/uniprot/PGK1_HUMAN PGK1_HUMAN]] Defects in PGK1 are the cause of phosphoglycerate kinase 1 deficiency (PGK1D) [MIM:[~~http~~://omim.org/entry/300653 300653]]. It is a condition with a highly variable clinical phenotype that includes hemolytic anemia, rhabdomyolysis, myopathy and neurologic involvement. Patients can express one or more of these manifestations.<ref>PMID:8673469</ref> <ref>PMID:8043870</ref> <ref>PMID:8615693</ref> <ref>PMID:9744480</ref> <ref>PMID:2001457</ref> <ref>PMID:1586722</ref> <ref>PMID:1547346</ref> <ref>PMID:6941312</ref> <ref>PMID:6933565</ref>		[https://www.uniprot.org/uniprot/PGK1_HUMAN PGK1_HUMAN] Defects in PGK1 are the cause of phosphoglycerate kinase 1 deficiency (PGK1D) [MIM:[https://omim.org/entry/300653 300653]. It is a condition with a highly variable clinical phenotype that includes hemolytic anemia, rhabdomyolysis, myopathy and neurologic involvement. Patients can express one or more of these manifestations.<ref>PMID:8673469</ref> <ref>PMID:8043870</ref> <ref>PMID:8615693</ref> <ref>PMID:9744480</ref> <ref>PMID:2001457</ref> <ref>PMID:1586722</ref> <ref>PMID:1547346</ref> <ref>PMID:6941312</ref> <ref>PMID:6933565</ref>
	== Function ==		== Function ==
	[~~[http~~://www.uniprot.org/uniprot/PGK1_HUMAN PGK1_HUMAN]] In addition to its role as a glycolytic enzyme, it seems that PGK-1 acts as a polymerase alpha cofactor protein (primer recognition protein).		[https://www.uniprot.org/uniprot/PGK1_HUMAN PGK1_HUMAN] In addition to its role as a glycolytic enzyme, it seems that PGK-1 acts as a polymerase alpha cofactor protein (primer recognition protein).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 23:

	==See Also==		==See Also==
	*[[Phosphoglycerate ~~Kinase~~\|Phosphoglycerate ~~Kinase~~]]		*[[Phosphoglycerate kinase 3D structures\|Phosphoglycerate kinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Human~~]]		[[Category: Homo sapiens]]
	[[Category: ~~Phosphoglycerate kinase~~]]		[[Category: Large Structures]]
	[[Category: Cipollone, A]]		[[Category: Cipollone A]]
	[[Category: Fiorillo, A]]		[[Category: Fiorillo A]]
	[[Category: Ilari, A]]		[[Category: Ilari A]]
	[[Category: Petrosino, M]]		[[Category: Petrosino M]]
	~~[[Category: Transferase~~]]

OCA at 07:04, 12 December 2018

2018-12-12T07:04:35Z

← Older revision		Revision as of 07:04, 12 December 2018
Line 3:		Line 3:
	<StructureSection load='5o7d' size='340' side='right' caption='[[5o7d]], [[Resolution\|resolution]] 1.84Å' scene=''>		<StructureSection load='5o7d' size='340' side='right' caption='[[5o7d]], [[Resolution\|resolution]] 1.84Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5o7d]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O7D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O7D FirstGlance]. <br>		<table><tr><td colspan='2'>[[5o7d]] 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=5O7D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O7D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PGK1, PGKA, MIG10, OK/SW-cl.110 ([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/Phosphoglycerate_kinase Phosphoglycerate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.2.3 2.7.2.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoglycerate_kinase Phosphoglycerate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.2.3 2.7.2.3] </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=5o7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o7d OCA], [http://pdbe.org/5o7d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o7d RCSB], [http://www.ebi.ac.uk/pdbsum/5o7d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o7d 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=5o7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o7d OCA], [http://pdbe.org/5o7d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o7d RCSB], [http://www.ebi.ac.uk/pdbsum/5o7d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o7d ProSAT]</span></td></tr>
Line 12:		Line 13:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/PGK1_HUMAN PGK1_HUMAN]] In addition to its role as a glycolytic enzyme, it seems that PGK-1 acts as a polymerase alpha cofactor protein (primer recognition protein).		[[http://www.uniprot.org/uniprot/PGK1_HUMAN PGK1_HUMAN]] In addition to its role as a glycolytic enzyme, it seems that PGK-1 acts as a polymerase alpha cofactor protein (primer recognition protein).
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Cancer cells are able to survive in difficult conditions, reprogramming their metabolism according to their requirements. Under hypoxic conditions they shift from oxidative phosphorylation to aerobic glycolysis, a behavior known as Warburg effect. In the last years, glycolytic enzymes have been identified as potential targets for alternative anticancer therapies. Recently, phosphoglycerate kinase 1 (PGK1), an ubiquitous enzyme expressed in all somatic cells that catalyzes the seventh step of glycolysis which consists of the reversible phosphotransfer reaction from 1,3-bisphosphoglycerate to ADP, has been discovered to be overexpressed in many cancer types. Moreover, several somatic variants of PGK1 have been identified in tumors. In this study we analyzed the effect of the single nucleotide variants found in cancer tissues on the PGK1 structure and function. Our results clearly show that the variants display a decreased catalytic efficiency and/or thermodynamic stability and an altered local tertiary structure, as shown by the solved X-ray structures. The changes in the catalytic properties and in the stability of the PGK1 variants, mainly due to the local changes evidenced by the X-ray structures, suggest also changes in the functional role of PGK to support the biosynthetic need of the growing and proliferating tumour cells.

			The phosphoglycerate kinase 1 variants found in carcinoma cells display different catalytic activity and conformational stability compared to the native enzyme.,Fiorillo A, Petrosino M, Ilari A, Pasquo A, Cipollone A, Maggi M, Chiaraluce R, Consalvi V PLoS One. 2018 Jul 11;13(7):e0199191. doi: 10.1371/journal.pone.0199191., eCollection 2018. PMID:29995887<ref>PMID:29995887</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 5o7d" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Phosphoglycerate Kinase\|Phosphoglycerate Kinase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Human]]
	[[Category: Phosphoglycerate kinase]]		[[Category: Phosphoglycerate kinase]]
	[[Category: Cipollone, A]]		[[Category: Cipollone, A]]

OCA at 05:37, 20 June 2018

2018-06-20T05:37:51Z

← Older revision		Revision as of 05:37, 20 June 2018
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	The ~~entry~~ 5o7d is ~~ON HOLD~~		==The X-ray structure of human R38M phosphoglycerate kinase 1 mutant==
			<StructureSection load='5o7d' size='340' side='right' caption='[[5o7d]], [[Resolution\|resolution]] 1.84Å' scene=''>
	~~Authors~~: ~~Ilari~~, A., ~~Fiorillo~~, A., ~~Cipollone~~, A., ~~Petrosino, M~~.		== Structural highlights ==
			<table><tr><td colspan='2'>[[5o7d]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O7D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O7D FirstGlance]. <br>
	~~Description~~: ~~The X-ray structure~~ of ~~human R38M~~ phosphoglycerate kinase 1 ~~mutant~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>
	[[Category: ~~Unreleased Structures~~]]		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoglycerate_kinase Phosphoglycerate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.2.3 2.7.2.3] </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=5o7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o7d OCA], [http://pdbe.org/5o7d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o7d RCSB], [http://www.ebi.ac.uk/pdbsum/5o7d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o7d ProSAT]</span></td></tr>
			</table>
			== Disease ==
			[[http://www.uniprot.org/uniprot/PGK1_HUMAN PGK1_HUMAN]] Defects in PGK1 are the cause of phosphoglycerate kinase 1 deficiency (PGK1D) [MIM:[http://omim.org/entry/300653 300653]]. It is a condition with a highly variable clinical phenotype that includes hemolytic anemia, rhabdomyolysis, myopathy and neurologic involvement. Patients can express one or more of these manifestations.<ref>PMID:8673469</ref> <ref>PMID:8043870</ref> <ref>PMID:8615693</ref> <ref>PMID:9744480</ref> <ref>PMID:2001457</ref> <ref>PMID:1586722</ref> <ref>PMID:1547346</ref> <ref>PMID:6941312</ref> <ref>PMID:6933565</ref>
			== Function ==
			[[http://www.uniprot.org/uniprot/PGK1_HUMAN PGK1_HUMAN]] In addition to its role as a glycolytic enzyme, it seems that PGK-1 acts as a polymerase alpha cofactor protein (primer recognition protein).
			== References ==
			<references/>
			__TOC__
			</StructureSection>
			[[Category: Phosphoglycerate kinase]]
	[[Category: Cipollone, A]]		[[Category: Cipollone, A]]
	[[Category: Fiorillo, A]]		[[Category: Fiorillo, A]]
			[[Category: Ilari, A]]
	[[Category: Petrosino, M]]		[[Category: Petrosino, M]]
	[[Category: ~~Ilari, A~~]]		[[Category: Transferase]]

OCA: Protected "5o7d" [edit=sysop:move=sysop]

2017-09-27T12:06:43Z

Protected "5o7d" [edit=sysop:move=sysop]

← Older revision	Revision as of 12:06, 27 September 2017
(No difference)

OCA: New page: '''Unreleased structure''' The entry 5o7d is ON HOLD Authors: Ilari, A., Fiorillo, A., Cipollone, A., Petrosino, M. Description: The X-ray structure of human R38M phosphoglycerate kina...

2017-09-27T12:06:42Z

New page: '''Unreleased structure''' The entry 5o7d is ON HOLD Authors: Ilari, A., Fiorillo, A., Cipollone, A., Petrosino, M. Description: The X-ray structure of human R38M phosphoglycerate kina...

New page

'''Unreleased structure'''

The entry 5o7d is ON HOLD

Authors: Ilari, A., Fiorillo, A., Cipollone, A., Petrosino, M.

Description: The X-ray structure of human R38M phosphoglycerate kinase 1 mutant
[[Category: Unreleased Structures]]
[[Category: Cipollone, A]]
[[Category: Fiorillo, A]]
[[Category: Petrosino, M]]
[[Category: Ilari, A]]