5fh1 - Revision history

OCA at 06:50, 19 July 2023

OCA — Wed, 19 Jul 2023 06:50:49 GMT

←Older revision		Revision as of 06:50, 19 July 2023
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	<StructureSection load='5fh1' size='340' side='right'caption='[[5fh1]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='5fh1' size='340' side='right'caption='[[5fh1]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fh1]] 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=5FH1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5FH1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fh1]] 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=5FH1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FH1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</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~~></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]] 1.55Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fh0\|5fh0]], [[5fh2\|5fh2]], [[5fh3\|5fh3]], [[5fh4\|5fh4]], [[5fh5\|5fh5]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</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></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=5fh1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fh1 OCA], [https://pdbe.org/5fh1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fh1 RCSB], [https://www.ebi.ac.uk/pdbsum/5fh1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fh1 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=5fh1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fh1 OCA], [~~http~~://pdbe.org/5fh1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5fh1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5fh1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5fh1 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: ~~Holyoak, T~~]]	+	[[Category: Rattus norvegicus]]
-	[[Category: ~~Johnson,~~ T A]]	+	[[Category: Holyoak T]]
-	[[Category: ~~Gluconeogenesis]]~~	+	[[Category: Johnson TA]]
-	~~[[Category: Kinase]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 09:03, 4 December 2019

OCA — Wed, 04 Dec 2019 09:03:43 GMT

←Older revision		Revision as of 09:03, 4 December 2019
Line 1:		Line 1:

	==The structure of rat cytosolic PEPCK variant E89D in complex with GTP==		==The structure of rat cytosolic PEPCK variant E89D in complex with GTP==
-	<StructureSection load='5fh1' size='340' side='right' caption='[[5fh1]], [[Resolution\|resolution]] 1.55Å' scene=''>	+	<StructureSection load='5fh1' size='340' side='right'caption='[[5fh1]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5fh1]] 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=5FH1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FH1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5fh1]] 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=5FH1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FH1 FirstGlance]. <br>
Line 21:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 5fh1" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5fh1" 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 17:16, 15 November 2017

OCA — Wed, 15 Nov 2017 17:16:18 GMT

←Older revision		Revision as of 17:16, 15 November 2017
Line 3:		Line 3:
	<StructureSection load='5fh1' size='340' side='right' caption='[[5fh1]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='5fh1' size='340' side='right' caption='[[5fh1]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fh1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FH1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FH1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fh1]] 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=5FH1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FH1 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</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></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</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></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fh0\|5fh0]], [[5fh2\|5fh2]], [[5fh3\|5fh3]], [[5fh4\|5fh4]], [[5fh5\|5fh5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fh0\|5fh0]], [[5fh2\|5fh2]], [[5fh3\|5fh3]], [[5fh4\|5fh4]], [[5fh5\|5fh5]]</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=5fh1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fh1 OCA], [http://pdbe.org/5fh1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fh1 RCSB], [http://www.ebi.ac.uk/pdbsum/5fh1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fh1 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=5fh1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fh1 OCA], [http://pdbe.org/5fh1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fh1 RCSB], [http://www.ebi.ac.uk/pdbsum/5fh1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fh1 ProSAT]</span></td></tr>
Line 24:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Buffalo rat]]
	[[Category: Holyoak, T]]		[[Category: Holyoak, T]]
	[[Category: Johnson, T A]]		[[Category: Johnson, T A]]

OCA at 16:13, 2 January 2017

OCA — Mon, 02 Jan 2017 16:13:16 GMT

←Older revision		Revision as of 16:13, 2 January 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 5fh1 is ~~ON HOLD until Paper~~ Publication	+	==The structure of rat cytosolic PEPCK variant E89D in complex with GTP==
		+	<StructureSection load='5fh1' size='340' side='right' caption='[[5fh1]], [[Resolution\|resolution]] 1.55Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5fh1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FH1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FH1 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</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></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fh0\|5fh0]], [[5fh2\|5fh2]], [[5fh3\|5fh3]], [[5fh4\|5fh4]], [[5fh5\|5fh5]]</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=5fh1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fh1 OCA], [http://pdbe.org/5fh1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fh1 RCSB], [http://www.ebi.ac.uk/pdbsum/5fh1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fh1 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 ==
		+	Phosphoenolpyruvate carboxykinase (PEPCK) is an essential metabolic enzyme operating in the gluconeogenesis and glyceroneogenesis pathways. Previous work has demonstrated that the enzyme cycles between a catalytically inactive open state and a catalytically active closed state. The transition of the enzyme between these states requires the transition of several active site loops to shift from mobile, disordered structural elements to stable ordered states. The mechanism by which these disorder-order transitions are coupled to the ligation state of the active site however is not fully understood. To further investigate the mechanisms by which the mobility of the active site loops is coupled to enzymatic function and the transitioning of the enzyme between the two conformational states, we have conducted structural and functional studies of point mutants of E89. E89 is a proposed key member of the interaction network of mobile elements as it resides in the R-loop region of the enzyme active site. These new data demonstrate the importance of the R-loop in coordinating interactions between substrates at the OAA/PEP binding site and the mobile R- and Omega-loop domains. In turn, the studies more generally demonstrate the mechanisms by which the intrinsic ligand binding energy can be utilized in catalysis to drive unfavorable conformational changes, changes that are subsequently required for both optimal catalytic activity and fidelity.

-	~~Authors:~~ Johnson, T.A., ~~Holyoak, T~~.	+	Utilization of Substrate Intrinsic Binding Energy for Conformational Change and Catalytic Function in Phosphoenolpyruvate Carboxykinase.,Johnson TA, Mcleod MJ, Holyoak T Biochemistry. 2016 Jan 26;55(3):575-87. doi: 10.1021/acs.biochem.5b01215. Epub, 2016 Jan 13. PMID:26709450<ref>PMID:26709450</ref>

-	~~Description: The structure~~ of ~~rat cytosolic PEPCK variant E89D in complex with GTP~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Johnson, T.A]]~~	+	<div class="pdbe-citations 5fh1" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Holyoak, T]]		[[Category: Holyoak, T]]
		+	[[Category: Johnson, T A]]
		+	[[Category: Gluconeogenesis]]
		+	[[Category: Kinase]]
		+	[[Category: Lyase]]

OCA at 18:14, 13 January 2016

OCA — Wed, 13 Jan 2016 18:14:44 GMT

←Older revision		Revision as of 18:14, 13 January 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5fh1 is ON HOLD	+	The entry 5fh1 is ON HOLD until Paper Publication

	Authors: Johnson, T.A., Holyoak, T.		Authors: Johnson, T.A., Holyoak, T.

OCA: Protected "5fh1" [edit=sysop:move=sysop]

OCA — Wed, 30 Dec 2015 17:56:45 GMT

Protected "5fh1" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:56, 30 December 2015

OCA: New page: '''Unreleased structure''' The entry 5fh1 is ON HOLD Authors: Johnson, T.A., Holyoak, T. Description: The structure of rat cytosolic PEPCK variant E89D in complex with GTP [[Category: ...

OCA — Wed, 30 Dec 2015 17:56:43 GMT

New page: '''Unreleased structure''' The entry 5fh1 is ON HOLD Authors: Johnson, T.A., Holyoak, T. Description: The structure of rat cytosolic PEPCK variant E89D in complex with GTP [[Category: ...

New page

'''Unreleased structure'''

The entry 5fh1 is ON HOLD

Authors: Johnson, T.A., Holyoak, T.

Description: The structure of rat cytosolic PEPCK variant E89D in complex with GTP
[[Category: Unreleased Structures]]
[[Category: Johnson, T.A]]
[[Category: Holyoak, T]]