6ito - Revision history

OCA at 09:52, 22 November 2023

OCA — Wed, 22 Nov 2023 09:52:52 GMT

←Older revision		Revision as of 09:52, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='6ito' size='340' side='right'caption='[[6ito]], [[Resolution\|resolution]] 2.55Å' scene=''>		<StructureSection load='6ito' size='340' side='right'caption='[[6ito]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ito]] 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=6ITO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6ITO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ito]] 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=6ITO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ITO FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene~~>, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OXL:OXALATE+ION'>OXL</scene>, <scene name='pdbligand=R5P:RIBOSE-5-PHOSPHATE'>R5P</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]] 2.55Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5wsc\|5wsc]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OXL:OXALATE+ION'>OXL</scene>, <scene name='pdbligand=R5P:RIBOSE-5-PHOSPHATE'>R5P</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=6ito FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ito OCA], [https://pdbe.org/6ito PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ito RCSB], [https://www.ebi.ac.uk/pdbsum/6ito PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ito 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=6ito FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ito OCA], [~~http~~://pdbe.org/6ito PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ito RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ito PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ito 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 6ito" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6ito" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Pyruvate kinase 3D structures\|Pyruvate kinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 24:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Myctu~~]]	+	[[Category: Mycobacterium tuberculosis H37Rv]]
-	[[Category: ~~Pyruvate kinase~~]]	+	[[Category: Cai Q]]
-	[[Category: ~~Cai, Q~~]]	+	[[Category: Dedon PC]]
-	[[Category: ~~Dedon, P C~~]]	+	[[Category: El Sahili A]]
-	[[Category: Lescar, J]]	+	[[Category: Lescar J]]
-	[[Category: Mu, Y]]	+	[[Category: Mu Y]]
-	~~[[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 06:34, 21 August 2019

OCA — Wed, 21 Aug 2019 06:34:20 GMT

←Older revision		Revision as of 06:34, 21 August 2019
Line 3:		Line 3:
	<StructureSection load='6ito' size='340' side='right'caption='[[6ito]], [[Resolution\|resolution]] 2.55Å' scene=''>		<StructureSection load='6ito' size='340' side='right'caption='[[6ito]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ito]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ITO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ITO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ito]] 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=6ITO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ITO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OXL:OXALATE+ION'>OXL</scene>, <scene name='pdbligand=R5P:RIBOSE-5-PHOSPHATE'>R5P</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OXL:OXALATE+ION'>OXL</scene>, <scene name='pdbligand=R5P:RIBOSE-5-PHOSPHATE'>R5P</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wsc\|5wsc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[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=6ito FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ito OCA], [http://pdbe.org/6ito PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ito RCSB], [http://www.ebi.ac.uk/pdbsum/6ito PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ito 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=6ito FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ito OCA], [http://pdbe.org/6ito PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ito RCSB], [http://www.ebi.ac.uk/pdbsum/6ito PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ito ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In response to the stress of infection, Mycobacterium tuberculosis (Mtb) reprograms its metabolism to accommodate nutrient and energetic demands in a changing environment. Pyruvate kinase (PYK) is an essential glycolytic enzyme in the phosphoenolpyruvate-pyruvate-oxaloacetate node that is a central switch point for carbon flux distribution. Here we show that the competitive binding of pentose monophosphate inhibitors or the activator glucose 6-phosphate (G6P) to MtbPYK tightly regulates the metabolic flux. Intriguingly, pentose monophosphates were found to share the same binding site with G6P. The determination of a crystal structure of MtbPYK with bound ribose 5-phosphate (R5P), combined with biochemical analyses and molecular dynamic simulations, revealed that the allosteric inhibitor pentose monophosphate increases PYK structural dynamics, weakens the structural network communication, and impairs substrate binding. G6P, on the other hand, primes and activates the tetramer by decreasing protein flexibility and strengthening allosteric coupling. Therefore, we propose that MtbPYK uses these differences in conformational dynamics to up- and down-regulate enzymic activity. Importantly, metabolome profiling in mycobacteria reveals a significant increase in the levels of pentose monophosphate during hypoxia, which provides insights into how PYK uses dynamics of the tetramer as a competitive allosteric mechanism to retard glycolysis and facilitate metabolic reprogramming toward the pentose-phosphate pathway for achieving redox balance and an anticipatory metabolic response in Mtb.
		+
		+	Pyruvate Kinase Regulates the Pentose-Phosphate Pathway in Response to Hypoxia in Mycobacterium tuberculosis.,Zhong W, Guo J, Cui L, Chionh YH, Li K, El Sahili A, Cai Q, Yuan M, Michels PAM, Fothergill-Gilmore LA, Walkinshaw MD, Mu Y, Lescar J, Dedon PC J Mol Biol. 2019 Aug 2. pii: S0022-2836(19)30484-X. doi:, 10.1016/j.jmb.2019.07.033. PMID:31381898<ref>PMID:31381898</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6ito" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Myctu]]
	[[Category: Pyruvate kinase]]		[[Category: Pyruvate kinase]]
	[[Category: Cai, Q]]		[[Category: Cai, Q]]

OCA at 16:32, 14 August 2019

OCA — Wed, 14 Aug 2019 16:32:01 GMT

←Older revision		Revision as of 16:32, 14 August 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6ito is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate, AMP and inhibitor Ribose 5-Phosphate==
-		+	<StructureSection load='6ito' size='340' side='right'caption='[[6ito]], [[Resolution\|resolution]] 2.55Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6ito]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ITO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ITO FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OXL:OXALATE+ION'>OXL</scene>, <scene name='pdbligand=R5P:RIBOSE-5-PHOSPHATE'>R5P</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[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=6ito FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ito OCA], [http://pdbe.org/6ito PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ito RCSB], [http://www.ebi.ac.uk/pdbsum/6ito PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ito ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Pyruvate kinase]]
		+	[[Category: Cai, Q]]
		+	[[Category: Dedon, P C]]
		+	[[Category: Lescar, J]]
		+	[[Category: Mu, Y]]
		+	[[Category: Sahili, A El]]
		+	[[Category: Zhong, W]]
		+	[[Category: Allostery]]
		+	[[Category: Glycolysis]]
		+	[[Category: Phospho transferase]]
		+	[[Category: Synergism]]
		+	[[Category: Tetramer]]
		+	[[Category: Transferase]]

OCA at 09:55, 13 March 2019

OCA — Wed, 13 Mar 2019 09:55:13 GMT

←Older revision		Revision as of 09:55, 13 March 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6ito is ON HOLD	+	The entry 6ito is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6ito" [edit=sysop:move=sysop]

OCA — Wed, 05 Dec 2018 05:09:45 GMT

Protected "6ito" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:09, 5 December 2018

OCA: New page: '''Unreleased structure''' The entry 6ito is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 05 Dec 2018 05:09:44 GMT

New page: '''Unreleased structure''' The entry 6ito is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6ito is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]