5ws8 - Revision history

OCA at 16:52, 8 November 2023

OCA — Wed, 08 Nov 2023 16:52:28 GMT

←Older revision		Revision as of 16:52, 8 November 2023
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	==Pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate==		==Pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate==
-	<StructureSection load='5ws8' size='340' side='right' caption='[[5ws8]], [[Resolution\|resolution]] 2.62Å' scene=''>	+	<StructureSection load='5ws8' size='340' side='right'caption='[[5ws8]], [[Resolution\|resolution]] 2.62Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ws8]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Myctu Myctu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WS8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5WS8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ws8]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WS8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WS8 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OXL:OXALATE+ION'>OXL</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]] 2.62Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wrp\|5wrp]]~~, [[~~5ws9~~\|~~5ws9]], [[5wsa\|5wsa]], [[5wsb\|5wsb]], [[5wsc\|5wsc~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OXL:OXALATE+ION'>OXL</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>pyk, pykA, Rv1617, MTCY01B2.09 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~83332 MYCTU])</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=5ws8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ws8 OCA], [https://pdbe.org/5ws8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ws8 RCSB], [https://www.ebi.ac.uk/pdbsum/5ws8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ws8 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/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=5ws8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ws8 OCA], [~~http~~://pdbe.org/5ws8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ws8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ws8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ws8 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/KPYK_MYCTU KPYK_MYCTU]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5ws8" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ws8" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Pyruvate kinase 3D structures\|Pyruvate kinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Myctu~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Pyruvate kinase~~]]	+	[[Category: Mycobacterium tuberculosis H37Rv]]
-	[[Category: Cai, Q]]	+	[[Category: Cai Q]]
-	[[Category: Dedon~~, P C~~]]	+	[[Category: Dedon PC]]
-	[[Category: ~~Lescar, J~~]]	+	[[Category: El Sahili A]]
-	[[Category: ~~Sahili, A El~~]]	+	[[Category: Lescar J]]
-	[[Category: Zhong, W]]	+	[[Category: Zhong W]]
-	~~[[Category: Allostery]]~~	+
-	~~[[Category: Glycolysis]]~~	+
-	~~[[Category: Phospho transferase]]~~	+
-	~~[[Category: Synergism]]~~	+
-	~~[[Category: Tetramer]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 08:41, 10 January 2018

OCA — Wed, 10 Jan 2018 08:41:25 GMT

←Older revision		Revision as of 08:41, 10 January 2018
Line 3:		Line 3:
	<StructureSection load='5ws8' size='340' side='right' caption='[[5ws8]], [[Resolution\|resolution]] 2.62Å' scene=''>		<StructureSection load='5ws8' size='340' side='right' caption='[[5ws8]], [[Resolution\|resolution]] 2.62Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ws8]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WS8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WS8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ws8]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Myctu Myctu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WS8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WS8 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OXL:OXALATE+ION'>OXL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OXL:OXALATE+ION'>OXL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wrp\|5wrp]], [[5ws9\|5ws9]], [[5wsa\|5wsa]], [[5wsb\|5wsb]], [[5wsc\|5wsc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wrp\|5wrp]], [[5ws9\|5ws9]], [[5wsa\|5wsa]], [[5wsb\|5wsb]], [[5wsc\|5wsc]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pyk, pykA, Rv1617, MTCY01B2.09 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])</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=5ws8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ws8 OCA], [http://pdbe.org/5ws8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ws8 RCSB], [http://www.ebi.ac.uk/pdbsum/5ws8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ws8 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=5ws8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ws8 OCA], [http://pdbe.org/5ws8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ws8 RCSB], [http://www.ebi.ac.uk/pdbsum/5ws8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ws8 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Pyruvate kinase (PYK) is an essential glycolytic enzyme that controls glycolytic flux and is critical for ATP production in all organisms, with tight regulation by multiple metabolites. Yet the allosteric mechanisms governing PYK activity in bacterial pathogens are poorly understood. Here we report biochemical, structural and metabolomic evidence that Mycobacterium tuberculosis (Mtb) PYK uses AMP and glucose-6-phosphate (G6P) as synergistic allosteric activators that function as a molecular "OR logic gate" to tightly regulate energy and glucose metabolism. G6P was found to bind to a previously unknown site adjacent to the canonical site for AMP. Kinetic data and structural network analysis further show that AMP and G6P work synergistically as allosteric activators. Importantly, metabolome profiling in the Mtb surrogate, Mycobacterium bovis BCG, reveals significant changes in AMP and G6P levels during nutrient deprivation, which provides insights into how a PYK OR gate would function during the stress of Mtb infection.
		+
		+	Allosteric pyruvate kinase-based "logic gate" synergistically senses energy and sugar levels in Mycobacterium tuberculosis.,Zhong W, Cui L, Goh BC, Cai Q, Ho P, Chionh YH, Yuan M, Sahili AE, Fothergill-Gilmore LA, Walkinshaw MD, Lescar J, Dedon PC Nat Commun. 2017 Dec 7;8(1):1986. doi: 10.1038/s41467-017-02086-y. PMID:29215013<ref>PMID:29215013</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ws8" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Myctu]]
	[[Category: Pyruvate kinase]]		[[Category: Pyruvate kinase]]
	[[Category: Cai, Q]]		[[Category: Cai, Q]]

OCA at 07:36, 15 November 2017

OCA — Wed, 15 Nov 2017 07:36:56 GMT

←Older revision		Revision as of 07:36, 15 November 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ws8 is ~~ON HOLD until Paper Publication~~	+	==Pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate==
-		+	<StructureSection load='5ws8' size='340' side='right' caption='[[5ws8]], [[Resolution\|resolution]] 2.62Å' scene=''>
-	~~Authors~~: ~~Zhong~~, W., ~~Cai~~, Q., ~~El Sahili~~, A., ~~Lescar~~, J., ~~Dedon~~, P.C.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ws8]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WS8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WS8 FirstGlance]. <br>
-	~~Description: Pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OXL:OXALATE+ION'>OXL</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wrp\|5wrp]], [[5ws9\|5ws9]], [[5wsa\|5wsa]], [[5wsb\|5wsb]], [[5wsc\|5wsc]]</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=5ws8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ws8 OCA], [http://pdbe.org/5ws8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ws8 RCSB], [http://www.ebi.ac.uk/pdbsum/5ws8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ws8 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Pyruvate kinase]]
	[[Category: Cai, Q]]		[[Category: Cai, Q]]
-	[[Category: ~~El Sahili~~, A]]	+	[[Category: Dedon, P C]]
	[[Category: Lescar, J]]		[[Category: Lescar, J]]
-	[[Category: ~~Dedon~~, ~~P.C~~]]	+	[[Category: Sahili, A El]]
	[[Category: Zhong, W]]		[[Category: Zhong, W]]
		+	[[Category: Allostery]]
		+	[[Category: Glycolysis]]
		+	[[Category: Phospho transferase]]
		+	[[Category: Synergism]]
		+	[[Category: Tetramer]]
		+	[[Category: Transferase]]

OCA at 20:39, 22 December 2016

OCA — Thu, 22 Dec 2016 20:39:08 GMT

←Older revision		Revision as of 20:39, 22 December 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ws8 is ON HOLD	+	The entry 5ws8 is ON HOLD until Paper Publication

	Authors: Zhong, W., Cai, Q., El Sahili, A., Lescar, J., Dedon, P.C.		Authors: Zhong, W., Cai, Q., El Sahili, A., Lescar, J., Dedon, P.C.

OCA: Protected "5ws8" [edit=sysop:move=sysop]

OCA — Thu, 15 Dec 2016 17:55:03 GMT

Protected "5ws8" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:55, 15 December 2016

OCA: New page: '''Unreleased structure''' The entry 5ws8 is ON HOLD Authors: Zhong, W., Cai, Q., El Sahili, A., Lescar, J., Dedon, P.C. Description: Pyruvate kinase (PYK) from Mycobacterium tuberculo...

OCA — Thu, 15 Dec 2016 17:55:02 GMT

New page: '''Unreleased structure''' The entry 5ws8 is ON HOLD Authors: Zhong, W., Cai, Q., El Sahili, A., Lescar, J., Dedon, P.C. Description: Pyruvate kinase (PYK) from Mycobacterium tuberculo...

New page

'''Unreleased structure'''

The entry 5ws8 is ON HOLD

Authors: Zhong, W., Cai, Q., El Sahili, A., Lescar, J., Dedon, P.C.

Description: Pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate
[[Category: Unreleased Structures]]
[[Category: Cai, Q]]
[[Category: El Sahili, A]]
[[Category: Lescar, J]]
[[Category: Dedon, P.C]]
[[Category: Zhong, W]]