3moe - Revision history

OCA at 10:25, 21 February 2024

OCA — Wed, 21 Feb 2024 10:25:56 GMT

←Older revision		Revision as of 10:25, 21 February 2024
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	<StructureSection load='3moe' size='340' side='right'caption='[[3moe]], [[Resolution\|resolution]] 1.25Å' scene=''>		<StructureSection load='3moe' size='340' side='right'caption='[[3moe]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3moe]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Buffalo_rat Buffalo rat~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MOE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3MOE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3moe]] 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=3MOE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3MOE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <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]] 1.25Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3moh\|3moh]], [[3mof\|3mof]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <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 ([https://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'>[https://en.wikipedia.org/wiki/Phosphoenolpyruvate_carboxykinase_(GTP) Phosphoenolpyruvate carboxykinase (GTP)], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=3moe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3moe OCA], [https://pdbe.org/3moe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3moe RCSB], [https://www.ebi.ac.uk/pdbsum/3moe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3moe ProSAT]</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=3moe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3moe OCA], [https://pdbe.org/3moe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3moe RCSB], [https://www.ebi.ac.uk/pdbsum/3moe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3moe ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[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.	+	[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.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3moe ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3moe ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Many studies have shown that the dynamic motions of individual protein segments can play an important role in enzyme function. Recent structural studies on the gluconeogenic enzyme PEPCK demonstrate that PEPCK contains a 10-residue Omega-loop domain that acts as an active site lid. Based upon these structural studies we have previously proposed a model for the mechanism of PEPCK catalysis in which the conformation of this mobile lid-domain is energetically coupled to ligand binding resulting in the closed conformation of the lid, necessary for correct substrate positioning, becoming more energetically favorable as ligands associate with the enzyme. Here we test this model by the introduction of a point mutation (A467G) into the center of the Omega-loop lid that is designed to increase the entropic penalty for lid closure. Structural and kinetic characterization of this mutant enzyme demonstrates that the mutation has decreased the favorability of the enzyme adapting the closed lid conformation. As a consequence of this shift in the equilibrium defining the conformation of the active site lid, the enzyme's ability to stabilize the reaction intermediate is reduced resulting in catalytic defect. This stabilization is initially surprising, as the lid domain makes no direct contacts with the enolate intermediate formed during the reaction. Furthermore, during the conversion of OAA to PEP, the destabilization of the lid closed conformation results in the reaction becoming decoupled as the enolate intermediate is protonated rather than phosphorylated resulting in the formation of pyruvate. Taken together, the structural and kinetic characterization of A467G-PEPCK support our model of the role of the active site lid in catalytic function and demonstrate that the shift in the lowest energy conformation between open and closed lid states is a function of the free energy available to the enzyme through ligand binding and the entropic penalty for ordering of the ten-residue Omega-loop lid domain.
-
-	Increasing the conformational entropy of the Omega-loop lid domain in PEPCK impairs catalysis and decreases catalytic fidelity.,Johnson TA, Holyoak T Biochemistry. 2010 May 17. PMID:20476774<ref>PMID:20476774</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3moe" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Phosphoenolpyruvate carboxykinase 3D structures\|Phosphoenolpyruvate carboxykinase 3D structures]]		*[[Phosphoenolpyruvate carboxykinase 3D structures\|Phosphoenolpyruvate carboxykinase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Buffalo rat]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Holyoak, T~~]]	+	[[Category: Rattus norvegicus]]
-	[[Category: ~~Johnson,~~ T A]]	+	[[Category: Holyoak T]]
-	[[Category: ~~Gluconeogenesis]]~~	+	[[Category: Johnson TA]]
-	~~[[Category: Kinase]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 05:42, 6 October 2021

OCA — Wed, 06 Oct 2021 05:42:04 GMT

←Older revision		Revision as of 05:42, 6 October 2021
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	==The structure of rat cytosolic PEPCK mutant A467G in complex with Beta-Sulfopyruvate and GTP==		==The structure of rat cytosolic PEPCK mutant A467G in complex with Beta-Sulfopyruvate and GTP==
-	<StructureSection load='3moe' size='340' side='right' caption='[[3moe]], [[Resolution\|resolution]] 1.25Å' scene=''>	+	<StructureSection load='3moe' size='340' side='right'caption='[[3moe]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3moe]] 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=3MOE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3MOE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3moe]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MOE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3MOE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <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" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <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">[[3moh\|3moh]], [[3mof\|3mof]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3moh\|3moh]], [[3mof\|3mof]]</div></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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pck1 ([https://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'>[https://en.wikipedia.org/wiki/Phosphoenolpyruvate_carboxykinase_(GTP) Phosphoenolpyruvate carboxykinase (GTP)], with EC number [https://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=3moe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3moe OCA], [~~http~~://pdbe.org/3moe PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3moe RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3moe PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3moe ProSAT]</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=3moe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3moe OCA], [https://pdbe.org/3moe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3moe RCSB], [https://www.ebi.ac.uk/pdbsum/3moe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3moe 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.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mo/3moe_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mo/3moe_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
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	</div>		</div>
	<div class="pdbe-citations 3moe" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3moe" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Phosphoenolpyruvate carboxykinase 3D structures\|Phosphoenolpyruvate carboxykinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Buffalo rat]]		[[Category: Buffalo rat]]
		+	[[Category: Large Structures]]
	[[Category: Holyoak, T]]		[[Category: Holyoak, T]]
	[[Category: Johnson, T A]]		[[Category: Johnson, T A]]

OCA at 08:15, 8 November 2017

OCA — Wed, 08 Nov 2017 08:15:43 GMT

←Older revision		Revision as of 08:15, 8 November 2017
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	</div>		</div>
	<div class="pdbe-citations 3moe" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3moe" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Phosphoenolpyruvate carboxykinase\|Phosphoenolpyruvate carboxykinase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 22:47, 4 August 2016

OCA — Thu, 04 Aug 2016 22:47:22 GMT

←Older revision		Revision as of 22:47, 4 August 2016
Line 1:		Line 1:
		+
	==The structure of rat cytosolic PEPCK mutant A467G in complex with Beta-Sulfopyruvate and GTP==		==The structure of rat cytosolic PEPCK mutant A467G in complex with Beta-Sulfopyruvate and GTP==
	<StructureSection load='3moe' size='340' side='right' caption='[[3moe]], [[Resolution\|resolution]] 1.25Å' scene=''>		<StructureSection load='3moe' size='340' side='right' caption='[[3moe]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3moe]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Rattus_norvegicus Rattus norvegicus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MOE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3MOE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3moe]] 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=3MOE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3MOE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <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=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <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">[[3moh\|3moh]], [[3mof\|3mof]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3moh\|3moh]], [[3mof\|3mof]]</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 ~~Rattus norvegicus~~])</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=3moe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3moe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3moe RCSB], [http://www.ebi.ac.uk/pdbsum/3moe PDBsum]</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=3moe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3moe OCA], [http://pdbe.org/3moe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3moe RCSB], [http://www.ebi.ac.uk/pdbsum/3moe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3moe ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3moe ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3moe" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Rattus norvegicus~~]]	+	[[Category: Buffalo rat]]
	[[Category: Holyoak, T]]		[[Category: Holyoak, T]]
	[[Category: Johnson, T A]]		[[Category: Johnson, T A]]

OCA at 13:44, 25 December 2014

OCA — Thu, 25 Dec 2014 13:44:21 GMT

←Older revision		Revision as of 13:44, 25 December 2014
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	<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=3moe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3moe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3moe RCSB], [http://www.ebi.ac.uk/pdbsum/3moe PDBsum]</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=3moe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3moe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3moe RCSB], [http://www.ebi.ac.uk/pdbsum/3moe PDBsum]</span></td></tr>
	</table>		</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.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 15:53, 18 December 2014

OCA — Thu, 18 Dec 2014 15:53:11 GMT

←Older revision		Revision as of 15:53, 18 December 2014
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-	~~{{STRUCTURE_3moe\| PDB=3moe \| SCENE= }}~~	+	==The structure of rat cytosolic PEPCK mutant A467G in complex with Beta-Sulfopyruvate and GTP==
-	===The structure of rat cytosolic PEPCK mutant A467G in complex with Beta-Sulfopyruvate and GTP===	+	<StructureSection load='3moe' size='340' side='right' caption='[[3moe]], [[Resolution\|resolution]] 1.25Å' scene=''>
-	~~{{ABSTRACT_PUBMED_20476774}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3moe]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MOE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3MOE FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <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">[[3moh\|3moh]], [[3mof\|3mof]]</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 Rattus norvegicus])</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=3moe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3moe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3moe RCSB], [http://www.ebi.ac.uk/pdbsum/3moe PDBsum]</span></td></tr>
		+	</table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mo/3moe_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Many studies have shown that the dynamic motions of individual protein segments can play an important role in enzyme function. Recent structural studies on the gluconeogenic enzyme PEPCK demonstrate that PEPCK contains a 10-residue Omega-loop domain that acts as an active site lid. Based upon these structural studies we have previously proposed a model for the mechanism of PEPCK catalysis in which the conformation of this mobile lid-domain is energetically coupled to ligand binding resulting in the closed conformation of the lid, necessary for correct substrate positioning, becoming more energetically favorable as ligands associate with the enzyme. Here we test this model by the introduction of a point mutation (A467G) into the center of the Omega-loop lid that is designed to increase the entropic penalty for lid closure. Structural and kinetic characterization of this mutant enzyme demonstrates that the mutation has decreased the favorability of the enzyme adapting the closed lid conformation. As a consequence of this shift in the equilibrium defining the conformation of the active site lid, the enzyme's ability to stabilize the reaction intermediate is reduced resulting in catalytic defect. This stabilization is initially surprising, as the lid domain makes no direct contacts with the enolate intermediate formed during the reaction. Furthermore, during the conversion of OAA to PEP, the destabilization of the lid closed conformation results in the reaction becoming decoupled as the enolate intermediate is protonated rather than phosphorylated resulting in the formation of pyruvate. Taken together, the structural and kinetic characterization of A467G-PEPCK support our model of the role of the active site lid in catalytic function and demonstrate that the shift in the lowest energy conformation between open and closed lid states is a function of the free energy available to the enzyme through ligand binding and the entropic penalty for ordering of the ten-residue Omega-loop lid domain.

-	~~==Function==~~	+	Increasing the conformational entropy of the Omega-loop lid domain in PEPCK impairs catalysis and decreases catalytic fidelity.,Johnson TA, Holyoak T Biochemistry. 2010 May 17. PMID:20476774<ref>PMID:20476774</ref>
-	~~[[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~~.	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3moe]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Rattus_norvegicus Rattus norvegicus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3MOE OCA].~~	+	</div>

	==See Also==		==See Also==
	*[[Phosphoenolpyruvate carboxykinase\|Phosphoenolpyruvate carboxykinase]]		*[[Phosphoenolpyruvate carboxykinase\|Phosphoenolpyruvate carboxykinase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:020476774</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
-	[[Category: Holyoak, T.]]	+	[[Category: Holyoak, T]]
-	[[Category: Johnson, T A.]]	+	[[Category: Johnson, T A]]
	[[Category: Gluconeogenesis]]		[[Category: Gluconeogenesis]]
	[[Category: Kinase]]		[[Category: Kinase]]
	[[Category: Lyase]]		[[Category: Lyase]]

OCA at 20:52, 17 April 2013

OCA — Wed, 17 Apr 2013 20:52:54 GMT

←Older revision		Revision as of 20:52, 17 April 2013
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-	[[Image:3moe.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3moe", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
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	{{STRUCTURE_3moe\| PDB=3moe \| SCENE= }}		{{STRUCTURE_3moe\| PDB=3moe \| SCENE= }}
-
	===The structure of rat cytosolic PEPCK mutant A467G in complex with Beta-Sulfopyruvate and GTP===		===The structure of rat cytosolic PEPCK mutant A467G in complex with Beta-Sulfopyruvate and GTP===
		+	{{ABSTRACT_PUBMED_20476774}}

-		+	==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.
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_20476774}}, adds the Publication Abstract to the page~~	+
-	~~(as it appears on PubMed at~~ http://www.~~pubmed~~.~~gov~~), ~~where 20476774 is~~ the ~~PubMed ID number~~.	+
-	~~-->~~	+
-	~~{{ABSTRACT_PUBMED_20476774}}~~	+

	==About this Structure==		==About this Structure==
	[[3moe]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MOE OCA].		[[3moe]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MOE OCA].
		+
		+	==See Also==
		+	*[[Phosphoenolpyruvate carboxykinase\|Phosphoenolpyruvate carboxykinase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20476774~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020476774</ref><references group="xtra"/><references/>
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
	[[Category: Holyoak, T.]]		[[Category: Holyoak, T.]]
	[[Category: Johnson, T A.]]		[[Category: Johnson, T A.]]
		+	[[Category: Gluconeogenesis]]
		+	[[Category: Kinase]]
		+	[[Category: Lyase]]

OCA: Protected "3moe" [edit=sysop:move=sysop]

OCA — Wed, 12 Jan 2011 05:25:31 GMT

Protected "3moe" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:25, 12 January 2011

OCA at 05:25, 12 January 2011

OCA — Wed, 12 Jan 2011 05:25:29 GMT

←Older revision		Revision as of 05:25, 12 January 2011
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-	{{Seed}}
	[[Image:3moe.png\|left\|200px]]		[[Image:3moe.png\|left\|200px]]

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	==About this Structure==		==About this Structure==
-	~~3MOE~~ is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MOE OCA].	+	[[3moe]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MOE OCA].

	==Reference==		==Reference==
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	[[Category: Holyoak, T.]]		[[Category: Holyoak, T.]]
	[[Category: Johnson, T A.]]		[[Category: Johnson, T A.]]
-	[[Category: Gluconeogenesis]]
-	[[Category: Kinase]]
-	[[Category: Lyase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jun 10 10:49:23 2010''

OCA at 06:44, 10 June 2010

OCA — Thu, 10 Jun 2010 06:44:37 GMT

←Older revision		Revision as of 06:44, 10 June 2010
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	{{Seed}}		{{Seed}}
-	[[Image:3moe.~~jpg~~\|left\|200px]]	+	[[Image:3moe.png\|left\|200px]]

	<!--		<!--
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	[[Category: Lyase]]		[[Category: Lyase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed~~ Jun ~~2 08~~:35:13 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jun 10 10:49:23 2010''