6asn - Revision history

OCA at 14:18, 13 March 2024

OCA — Wed, 13 Mar 2024 14:18:18 GMT

←Older revision		Revision as of 14:18, 13 March 2024
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	<StructureSection load='6asn' size='340' side='right'caption='[[6asn]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='6asn' size='340' side='right'caption='[[6asn]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6asn]] 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=6ASN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6ASN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6asn]] 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=6ASN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ASN FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=03S:METHANESULFONIC+ACID'>03S</scene~~>, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.549Å</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=03S:METHANESULFONIC+ACID'>03S</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6asn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6asn OCA], [https://pdbe.org/6asn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6asn RCSB], [https://www.ebi.ac.uk/pdbsum/6asn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6asn 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=6asn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6asn OCA], [~~http~~://pdbe.org/6asn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6asn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6asn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6asn ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/PCKA_ECOLI PCKA_ECOLI]
-	Protein engineering to alter recognition underlying ligand binding and activity has enormous potential. Here, ligand binding for Escherichia coli phosphoenolpyruvate carboxykinase (PEPCK), which converts oxaloacetate into CO2 and phosphoenolpyruvate as the first committed step in gluconeogenesis, was engineered to accommodate alternative ligands as an exemplary system with structural information. From our identification of bicarbonate binding in the PEPCK active site at the supposed CO2 binding site, we probed binding of nonnative ligands with three oxygen atoms arranged to resemble the bicarbonate geometry. Crystal structures of PEPCK and point mutants with bound nonnative ligands thiosulfate and methanesulfonate along with strained ATP and reoriented oxaloacetate intermediates and unexpected bicarbonate were determined and analyzed. The mutations successfully altered the bound ligand position and orientation and its specificity: mutated PEPCKs bound either thiosulfate or methanesulfonate but never both. Computational calculations predicted a methanesulfonate binding mutant and revealed that release of the active site ordered solvent exerts a strong influence on ligand binding. Besides nonnative ligand binding, one mutant altered the Mn(2+) coordination sphere: instead of the canonical octahedral ligand arrangement, the mutant in question had an only five-coordinate arrangement. From this work, critical features of ligand binding, position, and metal ion cofactor geometry required for all downstream events can be engineered with small numbers of mutations to provide insights into fundamental underpinnings of protein-ligand recognition. Through structural and computational knowledge, the combination of designed and random mutations aids in the robust design of predetermined changes to ligand binding and activity to engineer protein function.	+
-		+
-	Structural Control of Nonnative Ligand Binding in Engineered Mutants of Phosphoenolpyruvate Carboxykinase.,Tang HYH, Shin DS, Hura GL, Yang Y, Hu X, Lightstone FC, McGee MD, Padgett HS, Yannone SM, Tainer JA Biochemistry. 2018 Dec 4;57(48):6688-6700. doi: 10.1021/~~acs.biochem.8b00963. Epub, 2018 Nov 15. PMID:30376300<ref>PMID:30376300<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6asn" 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: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Shin~~, D S~~]]	+	[[Category: Shin DS]]
-	[[Category: Tainer~~, J A~~]]	+	[[Category: Tainer JA]]
-	[[Category: Tang~~, H Y.H]]~~	+	[[Category: Tang HYH]]
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Nonnative ligand~~]]	+

OCA at 09:47, 4 December 2019

OCA — Wed, 04 Dec 2019 09:47:15 GMT

←Older revision		Revision as of 09:47, 4 December 2019
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 6asn" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6asn" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Phosphoenolpyruvate carboxykinase 3D structures\|Phosphoenolpyruvate carboxykinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:05, 1 May 2019

OCA — Wed, 01 May 2019 09:05:05 GMT

←Older revision		Revision as of 09:05, 1 May 2019
Line 1:		Line 1:

	==E. coli phosphoenolpyruvate carboxykinase K212I F216V mutant bound to methanesulfonate==		==E. coli phosphoenolpyruvate carboxykinase K212I F216V mutant bound to methanesulfonate==
-	<StructureSection load='6asn' size='340' side='right' caption='[[6asn]], [[Resolution\|resolution]] 1.55Å' scene=''>	+	<StructureSection load='6asn' size='340' side='right'caption='[[6asn]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6asn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ASN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ASN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6asn]] 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=6ASN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ASN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=03S:METHANESULFONIC+ACID'>03S</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=03S:METHANESULFONIC+ACID'>03S</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6asn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6asn OCA], [http://pdbe.org/6asn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6asn RCSB], [http://www.ebi.ac.uk/pdbsum/6asn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6asn 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=6asn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6asn OCA], [http://pdbe.org/6asn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6asn RCSB], [http://www.ebi.ac.uk/pdbsum/6asn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6asn ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Protein engineering to alter recognition underlying ligand binding and activity has enormous potential. Here, ligand binding for Escherichia coli phosphoenolpyruvate carboxykinase (PEPCK), which converts oxaloacetate into CO2 and phosphoenolpyruvate as the first committed step in gluconeogenesis, was engineered to accommodate alternative ligands as an exemplary system with structural information. From our identification of bicarbonate binding in the PEPCK active site at the supposed CO2 binding site, we probed binding of nonnative ligands with three oxygen atoms arranged to resemble the bicarbonate geometry. Crystal structures of PEPCK and point mutants with bound nonnative ligands thiosulfate and methanesulfonate along with strained ATP and reoriented oxaloacetate intermediates and unexpected bicarbonate were determined and analyzed. The mutations successfully altered the bound ligand position and orientation and its specificity: mutated PEPCKs bound either thiosulfate or methanesulfonate but never both. Computational calculations predicted a methanesulfonate binding mutant and revealed that release of the active site ordered solvent exerts a strong influence on ligand binding. Besides nonnative ligand binding, one mutant altered the Mn(2+) coordination sphere: instead of the canonical octahedral ligand arrangement, the mutant in question had an only five-coordinate arrangement. From this work, critical features of ligand binding, position, and metal ion cofactor geometry required for all downstream events can be engineered with small numbers of mutations to provide insights into fundamental underpinnings of protein-ligand recognition. Through structural and computational knowledge, the combination of designed and random mutations aids in the robust design of predetermined changes to ligand binding and activity to engineer protein function.
		+
		+	Structural Control of Nonnative Ligand Binding in Engineered Mutants of Phosphoenolpyruvate Carboxykinase.,Tang HYH, Shin DS, Hura GL, Yang Y, Hu X, Lightstone FC, McGee MD, Padgett HS, Yannone SM, Tainer JA Biochemistry. 2018 Dec 4;57(48):6688-6700. doi: 10.1021/acs.biochem.8b00963. Epub, 2018 Nov 15. PMID:30376300<ref>PMID:30376300</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6asn" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: Shin, D S]]		[[Category: Shin, D S]]
	[[Category: Tainer, J A]]		[[Category: Tainer, J A]]

OCA at 07:25, 29 August 2018

OCA — Wed, 29 Aug 2018 07:25:11 GMT

←Older revision		Revision as of 07:25, 29 August 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6asn is ~~ON HOLD until Paper Publication~~	+	==E. coli phosphoenolpyruvate carboxykinase K212I F216V mutant bound to methanesulfonate==
-		+	<StructureSection load='6asn' size='340' side='right' caption='[[6asn]], [[Resolution\|resolution]] 1.55Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6asn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ASN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ASN FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=03S:METHANESULFONIC+ACID'>03S</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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>
		+	<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=6asn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6asn OCA], [http://pdbe.org/6asn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6asn RCSB], [http://www.ebi.ac.uk/pdbsum/6asn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6asn ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Shin, D S]]
		+	[[Category: Tainer, J A]]
		+	[[Category: Tang, H Y.H]]
		+	[[Category: Lyase]]
		+	[[Category: Nonnative ligand]]

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

OCA — Wed, 27 Sep 2017 16:44:55 GMT

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

←Older revision

Revision as of 16:44, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 6asn is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Sep 2017 16:44:54 GMT

New page: '''Unreleased structure''' The entry 6asn is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6asn is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]