5x0i - Revision history

OCA at 10:07, 15 November 2023

OCA — Wed, 15 Nov 2023 10:07:25 GMT

←Older revision		Revision as of 10:07, 15 November 2023
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	<StructureSection load='5x0i' size='340' side='right'caption='[[5x0i]], [[Resolution\|resolution]] 2.64Å' scene=''>		<StructureSection load='5x0i' size='340' side='right'caption='[[5x0i]], [[Resolution\|resolution]] 2.64Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x0i]] is a 4 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=5X0I OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5X0I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x0i]] is a 4 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=5X0I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X0I FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FBP:BETA-FRUCTOSE-1,6-DIPHOSPHATE'>FBP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene>, <scene name='pdbligand=SER:SERINE'>SER</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]] 2.64Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PKM, OIP3, PK2, PK3, PKM2 ([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=FBP:BETA-FRUCTOSE-1,6-DIPHOSPHATE'>FBP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene>, <scene name='pdbligand=SER:SERINE'>SER</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyruvate_kinase Pyruvate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.40 2.7.1.40] </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=5x0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x0i OCA], [https://pdbe.org/5x0i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x0i RCSB], [https://www.ebi.ac.uk/pdbsum/5x0i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x0i 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=5x0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x0i OCA], [~~http~~://pdbe.org/5x0i PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5x0i RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5x0i PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5x0i ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/KPYM_HUMAN KPYM_HUMAN]] Glycolytic enzyme that catalyzes the transfer of a phosphoryl group from phosphoenolpyruvate (PEP) to ADP, generating ATP. Stimulates POU5F1-mediated transcriptional activation. Plays a general role in caspase independent cell death of tumor cells. The ratio betwween the highly active tetrameric form and nearly inactive dimeric form determines whether glucose carbons are channeled to biosynthetic processes or used for glycolytic ATP production. The transition between the 2 forms contributes to the control of glycolysis and is important for tumor cell proliferation and survival.<ref>PMID:17308100</ref> <ref>PMID:18191611</ref> <ref>PMID:21620138</ref>	+	[https://www.uniprot.org/uniprot/KPYM_HUMAN KPYM_HUMAN] Glycolytic enzyme that catalyzes the transfer of a phosphoryl group from phosphoenolpyruvate (PEP) to ADP, generating ATP. Stimulates POU5F1-mediated transcriptional activation. Plays a general role in caspase independent cell death of tumor cells. The ratio betwween the highly active tetrameric form and nearly inactive dimeric form determines whether glucose carbons are channeled to biosynthetic processes or used for glycolytic ATP production. The transition between the 2 forms contributes to the control of glycolysis and is important for tumor cell proliferation and survival.<ref>PMID:17308100</ref> <ref>PMID:18191611</ref> <ref>PMID:21620138</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
-	*[[Pyruvate ~~Kinase~~\|Pyruvate ~~Kinase~~]]	+	*[[Pyruvate kinase 3D structures\|Pyruvate kinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Pyruvate kinase]]~~	+	[[Category: Chen TJ]]
-	[[Category: Chen~~, T J~~]]	+	[[Category: Wang WC]]
-	[[Category: Wang~~, W C]]~~	+
-	~~[[Category: Glycolysis]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 17:03, 20 November 2019

OCA — Wed, 20 Nov 2019 17:03:17 GMT

←Older revision		Revision as of 17:03, 20 November 2019
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/KPYM_HUMAN KPYM_HUMAN]] Glycolytic enzyme that catalyzes the transfer of a phosphoryl group from phosphoenolpyruvate (PEP) to ADP, generating ATP. Stimulates POU5F1-mediated transcriptional activation. Plays a general role in caspase independent cell death of tumor cells. The ratio betwween the highly active tetrameric form and nearly inactive dimeric form determines whether glucose carbons are channeled to biosynthetic processes or used for glycolytic ATP production. The transition between the 2 forms contributes to the control of glycolysis and is important for tumor cell proliferation and survival.<ref>PMID:17308100</ref> <ref>PMID:18191611</ref> <ref>PMID:21620138</ref>		[[http://www.uniprot.org/uniprot/KPYM_HUMAN KPYM_HUMAN]] Glycolytic enzyme that catalyzes the transfer of a phosphoryl group from phosphoenolpyruvate (PEP) to ADP, generating ATP. Stimulates POU5F1-mediated transcriptional activation. Plays a general role in caspase independent cell death of tumor cells. The ratio betwween the highly active tetrameric form and nearly inactive dimeric form determines whether glucose carbons are channeled to biosynthetic processes or used for glycolytic ATP production. The transition between the 2 forms contributes to the control of glycolysis and is important for tumor cell proliferation and survival.<ref>PMID:17308100</ref> <ref>PMID:18191611</ref> <ref>PMID:21620138</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	PKM2 is a key metabolic enzyme central to glucose metabolism and energy expenditure. Multiple stimuli regulate PKM2's activity through allosteric modulation and post-translational modifications. Furthermore, PKM2 can partner with KDM8, an oncogenic demethylase and enter the nucleus to serve as a HIF1alpha co-activator. Yet, the mechanistic basis of the exon-10 region in allosteric regulation and nuclear translocation remains unclear. Here, we determined the crystal structures and kinetic coupling constants of exon-10 tumor-related mutants (H391Y and R399E), showing altered structural plasticity and reduced allostery. Immunoprecipitation analysis revealed increased interaction with KDM8 for H391Y, R399E, and G415R. We also found a higher degree of HIF1alpha-mediated transactivation activity, particularly in the presence of KDM8. Furthermore, overexpression of PKM2 mutants significantly elevated cell growth and migration. Together, PKM2 exon-10 mutations lead to structure-allostery alterations and increased nuclear functions mediated by KDM8 in breast cancer cells. Targeting the PKM2-KDM8 complex may provide a potential therapeutic intervention.
		+
		+	Mutations in the PKM2 exon-10 region are associated with reduced allostery and increased nuclear translocation.,Chen TJ, Wang HJ, Liu JS, Cheng HH, Hsu SC, Wu MC, Lu CH, Wu YF, Wu JW, Liu YY, Kung HJ, Wang WC Commun Biol. 2019 Mar 15;2:105. doi: 10.1038/s42003-019-0343-4. eCollection 2019. PMID:30911680<ref>PMID:30911680</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5x0i" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 08:04, 3 April 2019

OCA — Wed, 03 Apr 2019 08:04:11 GMT

←Older revision		Revision as of 08:04, 3 April 2019
Line 1:		Line 1:

	==Crystal structure of PKM2 R399E mutant complexed with FBP and serine==		==Crystal structure of PKM2 R399E mutant complexed with FBP and serine==
-	<StructureSection load='5x0i' size='340' side='right' caption='[[5x0i]], [[Resolution\|resolution]] 2.64Å' scene=''>	+	<StructureSection load='5x0i' size='340' side='right'caption='[[5x0i]], [[Resolution\|resolution]] 2.64Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x0i]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X0I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X0I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x0i]] is a 4 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=5X0I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X0I FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FBP:BETA-FRUCTOSE-1,6-DIPHOSPHATE'>FBP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene>, <scene name='pdbligand=SER:SERINE'>SER</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FBP:BETA-FRUCTOSE-1,6-DIPHOSPHATE'>FBP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene>, <scene name='pdbligand=SER:SERINE'>SER</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PKM, OIP3, PK2, PK3, PKM2 ([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/Pyruvate_kinase Pyruvate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.40 2.7.1.40] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyruvate_kinase Pyruvate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.40 2.7.1.40] </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=5x0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x0i OCA], [http://pdbe.org/5x0i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x0i RCSB], [http://www.ebi.ac.uk/pdbsum/5x0i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x0i 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=5x0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x0i OCA], [http://pdbe.org/5x0i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x0i RCSB], [http://www.ebi.ac.uk/pdbsum/5x0i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x0i ProSAT]</span></td></tr>
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/KPYM_HUMAN KPYM_HUMAN]] Glycolytic enzyme that catalyzes the transfer of a phosphoryl group from phosphoenolpyruvate (PEP) to ADP, generating ATP. Stimulates POU5F1-mediated transcriptional activation. Plays a general role in caspase independent cell death of tumor cells. The ratio betwween the highly active tetrameric form and nearly inactive dimeric form determines whether glucose carbons are channeled to biosynthetic processes or used for glycolytic ATP production. The transition between the 2 forms contributes to the control of glycolysis and is important for tumor cell proliferation and survival.<ref>PMID:17308100</ref> <ref>PMID:18191611</ref> <ref>PMID:21620138</ref>		[[http://www.uniprot.org/uniprot/KPYM_HUMAN KPYM_HUMAN]] Glycolytic enzyme that catalyzes the transfer of a phosphoryl group from phosphoenolpyruvate (PEP) to ADP, generating ATP. Stimulates POU5F1-mediated transcriptional activation. Plays a general role in caspase independent cell death of tumor cells. The ratio betwween the highly active tetrameric form and nearly inactive dimeric form determines whether glucose carbons are channeled to biosynthetic processes or used for glycolytic ATP production. The transition between the 2 forms contributes to the control of glycolysis and is important for tumor cell proliferation and survival.<ref>PMID:17308100</ref> <ref>PMID:18191611</ref> <ref>PMID:21620138</ref>
		+
		+	==See Also==
		+	*[[Pyruvate Kinase\|Pyruvate Kinase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Pyruvate kinase]]		[[Category: Pyruvate kinase]]
	[[Category: Chen, T J]]		[[Category: Chen, T J]]

OCA at 05:53, 31 January 2018

OCA — Wed, 31 Jan 2018 05:53:20 GMT

←Older revision		Revision as of 05:53, 31 January 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5x0i is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of PKM2 R399E mutant complexed with FBP and serine==
-		+	<StructureSection load='5x0i' size='340' side='right' caption='[[5x0i]], [[Resolution\|resolution]] 2.64Å' scene=''>
-	~~Authors~~: ~~Wang~~, W.C., ~~Chen~~, T.J.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5x0i]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X0I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X0I FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure~~ of ~~PKM2 R399E mutant complexed with FBP~~ and ~~serine~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FBP:BETA-FRUCTOSE-1,6-DIPHOSPHATE'>FBP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene>, <scene name='pdbligand=SER:SERINE'>SER</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/Pyruvate_kinase Pyruvate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.40 2.7.1.40] </span></td></tr>
-	[[Category: Chen, T.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=5x0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x0i OCA], [http://pdbe.org/5x0i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x0i RCSB], [http://www.ebi.ac.uk/pdbsum/5x0i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x0i ProSAT]</span></td></tr>
-	[[Category: Wang, W.C]]	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/KPYM_HUMAN KPYM_HUMAN]] Glycolytic enzyme that catalyzes the transfer of a phosphoryl group from phosphoenolpyruvate (PEP) to ADP, generating ATP. Stimulates POU5F1-mediated transcriptional activation. Plays a general role in caspase independent cell death of tumor cells. The ratio betwween the highly active tetrameric form and nearly inactive dimeric form determines whether glucose carbons are channeled to biosynthetic processes or used for glycolytic ATP production. The transition between the 2 forms contributes to the control of glycolysis and is important for tumor cell proliferation and survival.<ref>PMID:17308100</ref> <ref>PMID:18191611</ref> <ref>PMID:21620138</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Pyruvate kinase]]
		+	[[Category: Chen, T J]]
		+	[[Category: Wang, W C]]
		+	[[Category: Glycolysis]]
		+	[[Category: Transferase]]

OCA at 17:08, 1 February 2017

OCA — Wed, 01 Feb 2017 17:08:33 GMT

←Older revision		Revision as of 17:08, 1 February 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5x0i is ON HOLD	+	The entry 5x0i is ON HOLD until Paper Publication

	Authors: Wang, W.C., Chen, T.J.		Authors: Wang, W.C., Chen, T.J.

OCA: Protected "5x0i" [edit=sysop:move=sysop]

OCA — Wed, 25 Jan 2017 22:40:34 GMT

Protected "5x0i" [edit=sysop:move=sysop]

←Older revision

Revision as of 22:40, 25 January 2017

OCA: New page: '''Unreleased structure''' The entry 5x0i is ON HOLD Authors: Wang, W.C., Chen, T.J. Description: Crystal structure of PKM2 R399E mutant complexed with FBP and serine [[Category: Unrel...

OCA — Wed, 25 Jan 2017 22:40:32 GMT

New page: '''Unreleased structure''' The entry 5x0i is ON HOLD Authors: Wang, W.C., Chen, T.J. Description: Crystal structure of PKM2 R399E mutant complexed with FBP and serine [[Category: Unrel...

New page

'''Unreleased structure'''

The entry 5x0i is ON HOLD

Authors: Wang, W.C., Chen, T.J.

Description: Crystal structure of PKM2 R399E mutant complexed with FBP and serine
[[Category: Unreleased Structures]]
[[Category: Chen, T.J]]
[[Category: Wang, W.C]]