5v9f - Revision history

OCA at 13:44, 4 October 2023

OCA — Wed, 04 Oct 2023 13:44:14 GMT

←Older revision		Revision as of 13:44, 4 October 2023
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	<StructureSection load='5v9f' size='340' side='right'caption='[[5v9f]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='5v9f' size='340' side='right'caption='[[5v9f]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5v9f]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Buffalo_rat Buffalo rat~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V9F OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5V9F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5v9f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V9F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5V9F FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SPV:SULFOPYRUVATE'>SPV</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]] 2.05Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5v95\|5v95]]~~, [[~~5v97~~\|~~5v97]], [[5v9h\|5v9h]], [[5v9g\|5v9g~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SPV:SULFOPYRUVATE'>SPV</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~Pck1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=5~~&id=10116 Buffalo rat])</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=5v9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v9f OCA], [https://pdbe.org/5v9f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5v9f RCSB], [https://www.ebi.ac.uk/pdbsum/5v9f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5v9f 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/Phosphoenolpyruvate_carboxykinase_(GTP) Phosphoenolpyruvate carboxykinase (GTP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.32 4.1.1.32] </~~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=5v9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v9f OCA], [~~http~~://pdbe.org/5v9f PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5v9f RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5v9f PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5v9f ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PCKGC_RAT PCKGC_RAT]] Catalyzes the conversion of oxaloacetate (OAA) to phosphoenolpyruvate (PEP), the rate-limiting step in the metabolic pathway that produces glucose from lactate and other precursors derived from the citric acid cycle.	+	[https://www.uniprot.org/uniprot/PCKGC_RAT PCKGC_RAT] Catalyzes the conversion of oxaloacetate (OAA) to phosphoenolpyruvate (PEP), the rate-limiting step in the metabolic pathway that produces glucose from lactate and other precursors derived from the citric acid cycle.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Buffalo rat]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Cui, D S~~]]	+	[[Category: Rattus norvegicus]]
-	[[Category: ~~Holyoak, T~~]]	+	[[Category: Cui DS]]
-	[[Category: ~~Lyase]]~~	+	[[Category: Holyoak T]]
-	~~[[Category: Phosphoenolpyruvate carboxykinase~~]]	+

OCA at 08:25, 8 January 2020

OCA — Wed, 08 Jan 2020 08:25:37 GMT

←Older revision		Revision as of 08:25, 8 January 2020
Line 1:		Line 1:

	==Structure of the H477R variant of rat cytosolic PEPCK in complex with beta sulfopyruvate and GTP.==		==Structure of the H477R variant of rat cytosolic PEPCK in complex with beta sulfopyruvate and GTP.==
-	<StructureSection load='5v9f' size='340' side='right' caption='[[5v9f]], [[Resolution\|resolution]] 2.05Å' scene=''>	+	<StructureSection load='5v9f' size='340' side='right'caption='[[5v9f]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5v9f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V9F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V9F FirstGlance]. <br>		<table><tr><td colspan='2'>[[5v9f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V9F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V9F FirstGlance]. <br>
Line 21:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 5v9f" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5v9f" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Phosphoenolpyruvate carboxykinase 3D structures\|Phosphoenolpyruvate carboxykinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 26:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Buffalo rat]]		[[Category: Buffalo rat]]
		+	[[Category: Large Structures]]
	[[Category: Cui, D S]]		[[Category: Cui, D S]]
	[[Category: Holyoak, T]]		[[Category: Holyoak, T]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Phosphoenolpyruvate carboxykinase]]		[[Category: Phosphoenolpyruvate carboxykinase]]

OCA at 14:40, 6 November 2017

OCA — Mon, 06 Nov 2017 14:40:24 GMT

←Older revision		Revision as of 14:40, 6 November 2017
Line 3:		Line 3:
	<StructureSection load='5v9f' size='340' side='right' caption='[[5v9f]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='5v9f' size='340' side='right' caption='[[5v9f]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5v9f]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V9F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V9F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5v9f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V9F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V9F FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SPV:SULFOPYRUVATE'>SPV</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SPV:SULFOPYRUVATE'>SPV</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5v95\|5v95]], [[5v97\|5v97]], [[5v9h\|5v9h]], [[5v9g\|5v9g]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5v95\|5v95]], [[5v97\|5v97]], [[5v9h\|5v9h]], [[5v9g\|5v9g]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pck1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoenolpyruvate_carboxykinase_(GTP) Phosphoenolpyruvate carboxykinase (GTP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.32 4.1.1.32] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoenolpyruvate_carboxykinase_(GTP) Phosphoenolpyruvate carboxykinase (GTP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.32 4.1.1.32] </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=5v9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v9f OCA], [http://pdbe.org/5v9f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v9f RCSB], [http://www.ebi.ac.uk/pdbsum/5v9f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v9f 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=5v9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v9f OCA], [http://pdbe.org/5v9f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v9f RCSB], [http://www.ebi.ac.uk/pdbsum/5v9f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v9f ProSAT]</span></td></tr>
Line 24:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Buffalo rat]]
	[[Category: Cui, D S]]		[[Category: Cui, D S]]
	[[Category: Holyoak, T]]		[[Category: Holyoak, T]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Phosphoenolpyruvate carboxykinase]]		[[Category: Phosphoenolpyruvate carboxykinase]]

OCA at 11:34, 12 April 2017

OCA — Wed, 12 Apr 2017 11:34:11 GMT

←Older revision		Revision as of 11:34, 12 April 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5v9f is ~~ON HOLD~~	+	==Structure of the H477R variant of rat cytosolic PEPCK in complex with beta sulfopyruvate and GTP.==
		+	<StructureSection load='5v9f' size='340' side='right' caption='[[5v9f]], [[Resolution\|resolution]] 2.05Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5v9f]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V9F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V9F FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SPV:SULFOPYRUVATE'>SPV</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5v95\|5v95]], [[5v97\|5v97]], [[5v9h\|5v9h]], [[5v9g\|5v9g]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoenolpyruvate_carboxykinase_(GTP) Phosphoenolpyruvate carboxykinase (GTP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.32 4.1.1.32] </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=5v9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v9f OCA], [http://pdbe.org/5v9f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v9f RCSB], [http://www.ebi.ac.uk/pdbsum/5v9f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v9f ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PCKGC_RAT PCKGC_RAT]] Catalyzes the conversion of oxaloacetate (OAA) to phosphoenolpyruvate (PEP), the rate-limiting step in the metabolic pathway that produces glucose from lactate and other precursors derived from the citric acid cycle.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Mobile Omega-loops play essential roles in the function of many enzymes. Here we investigated the importance of a residue lying outside of the mobile Omega-loop element in the catalytic function of an H477R variant of cytosolic phosphoenolpyruvate carboxykinase using crystallographic, kinetic, and computational analysis. The crystallographic data suggest that the efficient transition of the Omega-loop to the closed conformation requires stabilization of the N-terminus of the loop through contacts between R461 and E588. In contrast, the C-terminal end of the Omega-loop undergoes changing interactions with the enzyme body through contacts between H477 at the C-terminus of the loop and E591 located on the enzyme body. Potential of mean force calculations demonstrated that altering the anchoring of the C-terminus of the Omega-loop via the H477R substitution results in the destabilization of the closed state of the Omega-loop by 3.4 kcal mol-1. The kinetic parameters for the enzyme were altered in an asymmetric fashion with the predominant effect being observed in the direction of oxaloacetate synthesis. This is exemplified by a reduction in kcat for the H477R mutant by an order of magnitude in the direction of OAA synthesis, while in the direction of PEP synthesis, it decreased by a factor of only 2. The data are consistent with a mechanism for loop conformational exchange between open and closed states in which a balance between fixed anchoring of the N-terminus of the Omega-loop and a flexible, unattached C-terminus drives the transition between a disordered (open) state and an ordered (closed) state.

-	~~Authors: Holyoak, T~~., Cui, D.S.	+	Asymmetric Anchoring Is Required for Efficient Omega-Loop Opening and Closing in Cytosolic Phosphoenolpyruvate Carboxykinase.,Cui DS, Broom A, Mcleod MJ, Meiering EM, Holyoak T Biochemistry. 2017 Apr 4. doi: 10.1021/acs.biochem.7b00178. PMID:28345895<ref>PMID:28345895</ref>

-	~~Description: Structure~~ of the ~~H477R variant~~ of ~~rat cytosolic PEPCK in complex with beta sulfopyruvate and GTP~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5v9f" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Cui, D S]]
	[[Category: Holyoak, T]]		[[Category: Holyoak, T]]
-	[[Category: ~~Cui, D.S~~]]	+	[[Category: Lyase]]
		+	[[Category: Phosphoenolpyruvate carboxykinase]]

OCA: Protected "5v9f" [edit=sysop:move=sysop]

OCA — Wed, 05 Apr 2017 11:49:40 GMT

Protected "5v9f" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:49, 5 April 2017

OCA: New page: '''Unreleased structure''' The entry 5v9f is ON HOLD Authors: Holyoak, T., Cui, D.S. Description: Structure of the H477R variant of rat cytosolic PEPCK in complex with beta sulfopyruva...

OCA — Wed, 05 Apr 2017 11:49:39 GMT

New page: '''Unreleased structure''' The entry 5v9f is ON HOLD Authors: Holyoak, T., Cui, D.S. Description: Structure of the H477R variant of rat cytosolic PEPCK in complex with beta sulfopyruva...

New page

'''Unreleased structure'''

The entry 5v9f is ON HOLD

Authors: Holyoak, T., Cui, D.S.

Description: Structure of the H477R variant of rat cytosolic PEPCK in complex with beta sulfopyruvate and GTP.
[[Category: Unreleased Structures]]
[[Category: Holyoak, T]]
[[Category: Cui, D.S]]