6com - Revision history

OCA at 15:08, 4 October 2023

2023-10-04T15:08:37Z

← Older revision		Revision as of 15:08, 4 October 2023
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	<StructureSection load='6com' size='340' side='right'caption='[[6com]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='6com' size='340' side='right'caption='[[6com]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6com]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6COM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6COM FirstGlance]. <br>		<table><tr><td colspan='2'>[[6com]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6COM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6COM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</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]] 2.3Å</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pckA, pck, b3403, JW3366 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene></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_(ATP) Phosphoenolpyruvate carboxykinase (ATP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.49 4.1.1.49] </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=6com FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6com OCA], [https://pdbe.org/6com PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6com RCSB], [https://www.ebi.ac.uk/pdbsum/6com PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6com 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=6com FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6com OCA], [~~http~~://pdbe.org/6com PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6com RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6com PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6com ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/PCKA_ECOLI PCKA_ECOLI]
	<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: ~~Ecoli~~]]		[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Cotelesage~~, J H~~]]		[[Category: Cotelesage JH]]
	[[Category: Goldie, H]]		[[Category: Goldie H]]
	[[Category: Novakovski, B]]		[[Category: Novakovski B]]
	[[Category: Sanders, D]]		[[Category: Sanders D]]
	[[Category: Sokaribo~~, A S]]~~		[[Category: Sokaribo AS]]
	~~[[Category: Enzyme]]~~
	~~[[Category: Lyase]]~~
	~~[[Category: Pepcarboxykinase~~]]

OCA at 16:30, 22 January 2020

2020-01-22T16:30:48Z

← Older revision		Revision as of 16:30, 22 January 2020
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	==~~Mutagenic studies~~ of E.coli ~~PCK with~~ Asp269Asn ~~mutation was purified crystallized and the structure was solved to 2.3A~~==		==2.3A crystal structure of E. coli phosphoenolpyruvate carboxykinase mutant Asp269Asn==
	<StructureSection load='6com' size='340' side='right' caption='[[6com]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='6com' size='340' side='right'caption='[[6com]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6com]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6COM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6COM FirstGlance]. <br>		<table><tr><td colspan='2'>[[6com]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6COM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6COM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene></td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pckA, pck, b3403, JW3366 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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_(ATP) Phosphoenolpyruvate carboxykinase (ATP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.49 4.1.1.49] </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_(ATP) Phosphoenolpyruvate carboxykinase (ATP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.49 4.1.1.49] </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=6com FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6com OCA], [http://pdbe.org/6com PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6com RCSB], [http://www.ebi.ac.uk/pdbsum/6com PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6com 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=6com FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6com OCA], [http://pdbe.org/6com PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6com RCSB], [http://www.ebi.ac.uk/pdbsum/6com PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6com ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			BACKGROUND: Phosphoenolpyruvate carboxykinase (PEPCK) is a metabolic enzyme in the gluconeogenesis pathway, where it catalyzes the reversible conversion of oxaloacetate (OAA) to phosphoenolpyruvate (PEP) and CO2. The substrates for Escherichia coli PEPCK are OAA and MgATP, with Mn(2+) acting as a cofactor. Analysis of PEPCK structures have revealed amino acid residues involved in substrate/cofactor coordination during catalysis. METHODS: Key residues involved in coordinating the different substrates and cofactor bound to E. coli PEPCK were mutated. Purified mutant enzymes were used for kinetic assays. The structure of some mutant enzymes were determined using X-ray crystallography. RESULTS: Mutation of residues D269 and H232, which comprise part of the coordination sphere of Mn(2+), reduced kcat by 14-fold, and significantly increased the Km values for Mn(2+) and OAA. Mutation of K254 a key residue in the P-loop motif that interacts with MgATP, significantly elevated the Km value for MgATP and reduced kcat. R65 and R333 are key residues that interacts with OAA. The R65Q and R333Q mutations significantly increased the Km value for OAA and reduced kcat respectively. CONCLUSIONS: Our results show that mutation of residues involved in coordinating OAA, MgATP and Mn(2+) significantly reduce PEPCK activity. K254 plays an important role in phosphoryl transfer, while R333 is involved in both OAA decarboxylation and phosphoryl transfer by E. coli PEPCK. GENERAL SIGNIFICANCE: In higher organisms including humans, PEPCK helps to regulate blood glucose levels, hence PEPCK is a potential drug target for patients with non-insulin dependent diabetes mellitus.

			Kinetic and structural analysis of Escherichia coli phosphoenolpyruvate carboxykinase mutants.,Sokaribo A, Novakovski BAA, Cotelesage J, White AP, Sanders D, Goldie H Biochim Biophys Acta Gen Subj. 2020 Jan 3;1864(4):129517. doi:, 10.1016/j.bbagen.2020.129517. PMID:31911238<ref>PMID:31911238</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 6com" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Phosphoenolpyruvate carboxykinase 3D structures\|Phosphoenolpyruvate carboxykinase 3D structures]]
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Ecoli]]
			[[Category: Large Structures]]
	[[Category: Cotelesage, J H]]		[[Category: Cotelesage, J H]]
	[[Category: Goldie, H]]		[[Category: Goldie, H]]

OCA at 06:00, 4 April 2018

2018-04-04T06:00:33Z

← Older revision		Revision as of 06:00, 4 April 2018
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry 6com is ON HOLD~~		==Mutagenic studies of E.coli PCK with Asp269Asn mutation was purified crystallized and the structure was solved to 2.3A==
			<StructureSection load='6com' size='340' side='right' caption='[[6com]], [[Resolution\|resolution]] 2.30Å' scene=''>
	~~Authors: Sokaribo, A.S., Cotelesage, J.H., Novakovski, B., Goldie, H., Sanders, D.~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[6com]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6COM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6COM FirstGlance]. <br>
	~~Description:~~ Mutagenic studies of E.coli PCK with Asp269Asn mutation was purified crystallized and the structure was solved to 2.3A		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene></td></tr>
	[[~~Category~~: ~~Unreleased Structures~~]]		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoenolpyruvate_carboxykinase_(ATP) Phosphoenolpyruvate carboxykinase (ATP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.49 4.1.1.49] </span></td></tr>
	[[~~Category~~: ~~Sokaribo~~, A.S]]		<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=6com FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6com OCA], [http://pdbe.org/6com PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6com RCSB], [http://www.ebi.ac.uk/pdbsum/6com PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6com ProSAT]</span></td></tr>
	[[Category: ~~Sanders~~, D]]		</table>
			__TOC__
			</StructureSection>
			[[Category: Cotelesage, J H]]
	[[Category: Goldie, H]]		[[Category: Goldie, H]]
	[[Category: Novakovski, B]]		[[Category: Novakovski, B]]
	[[Category: ~~Cotelesage~~, ~~J.H~~]]		[[Category: Sanders, D]]
			[[Category: Sokaribo, A S]]
			[[Category: Enzyme]]
			[[Category: Lyase]]
			[[Category: Pepcarboxykinase]]

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

2018-03-21T06:10:48Z

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

← Older revision	Revision as of 06:10, 21 March 2018
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6com is ON HOLD Authors: Sokaribo, A.S., Cotelesage, J.H., Novakovski, B., Goldie, H., Sanders, D. Description: Mutagenic studies of E.coli PCK wit...

2018-03-21T06:10:46Z

New page: '''Unreleased structure''' The entry 6com is ON HOLD Authors: Sokaribo, A.S., Cotelesage, J.H., Novakovski, B., Goldie, H., Sanders, D. Description: Mutagenic studies of E.coli PCK wit...

New page

'''Unreleased structure'''

The entry 6com is ON HOLD

Authors: Sokaribo, A.S., Cotelesage, J.H., Novakovski, B., Goldie, H., Sanders, D.

Description: Mutagenic studies of E.coli PCK with Asp269Asn mutation was purified crystallized and the structure was solved to 2.3A
[[Category: Unreleased Structures]]
[[Category: Sokaribo, A.S]]
[[Category: Sanders, D]]
[[Category: Goldie, H]]
[[Category: Novakovski, B]]
[[Category: Cotelesage, J.H]]