5fqm - Revision history

OCA at 13:19, 26 July 2023

OCA — Wed, 26 Jul 2023 13:19:02 GMT

←Older revision		Revision as of 13:19, 26 July 2023
Line 3:		Line 3:
	<StructureSection load='5fqm' size='340' side='right'caption='[[5fqm]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='5fqm' size='340' side='right'caption='[[5fqm]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fqm]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Synthetic_construct_sequences~~ Synthetic construct ~~sequences~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FQM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5FQM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fqm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FQM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FQM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.5Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5fqm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fqm OCA], [~~http~~://pdbe.org/5fqm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5fqm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5fqm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5fqm ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=5fqm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fqm OCA], [https://pdbe.org/5fqm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fqm RCSB], [https://www.ebi.ac.uk/pdbsum/5fqm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fqm ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 24:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Synthetic construct ~~sequences~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Gavira~~, J A]]~~	+	[[Category: Gavira JA]]
-	~~[[Category: Risso, V A~~]]	+	[[Category: Martinez Rodriguez S]]
-	[[Category: Rodriguez, S ~~Martinez~~]]	+	[[Category: Risso VA]]
-	[[Category: ~~Ruiz, J M.Sanchez~~]]	+	[[Category: Sanchez Ruiz JM]]
-	[[Category: ~~Gnca]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Precambrian]]~~	+
-	~~[[Category: Resurrected beta-lactamase~~]]	+

OCA at 07:32, 6 May 2020

OCA — Wed, 06 May 2020 07:32:27 GMT

←Older revision		Revision as of 07:32, 6 May 2020
Line 1:		Line 1:

	==Last common ancestor of Gram Negative Bacteria (GNCA) Class A beta- lactamase==		==Last common ancestor of Gram Negative Bacteria (GNCA) Class A beta- lactamase==
-	<StructureSection load='5fqm' size='340' side='right' caption='[[5fqm]], [[Resolution\|resolution]] 1.50Å' scene=''>	+	<StructureSection load='5fqm' size='340' side='right'caption='[[5fqm]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fqm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FQM OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5FQM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fqm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FQM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5FQM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=5fqm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fqm OCA], [http://pdbe.org/5fqm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fqm RCSB], [http://www.ebi.ac.uk/pdbsum/5fqm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fqm ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5fqm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fqm OCA], [http://pdbe.org/5fqm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fqm RCSB], [http://www.ebi.ac.uk/pdbsum/5fqm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fqm ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 16:
	</div>		</div>
	<div class="pdbe-citations 5fqm" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5fqm" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Synthetic construct sequences]]		[[Category: Synthetic construct sequences]]
	[[Category: Gavira, J A]]		[[Category: Gavira, J A]]

OCA at 05:53, 16 November 2017

OCA — Thu, 16 Nov 2017 05:53:43 GMT

←Older revision		Revision as of 05:53, 16 November 2017
Line 3:		Line 3:
	<StructureSection load='5fqm' size='340' side='right' caption='[[5fqm]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='5fqm' size='340' side='right' caption='[[5fqm]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fqm]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FQM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FQM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fqm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FQM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FQM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=5fqm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fqm OCA], [http://pdbe.org/5fqm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fqm RCSB], [http://www.ebi.ac.uk/pdbsum/5fqm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fqm 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=5fqm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fqm OCA], [http://pdbe.org/5fqm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fqm RCSB], [http://www.ebi.ac.uk/pdbsum/5fqm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fqm ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Protein engineering studies often suggest the emergence of completely new enzyme functionalities to be highly improbable. However, enzymes likely catalysed many different reactions already in the last universal common ancestor. Mechanisms for the emergence of completely new active sites must therefore either plausibly exist or at least have existed at the primordial protein stage. Here, we use resurrected Precambrian proteins as scaffolds for protein engineering and demonstrate that a new active site can be generated through a single hydrophobic-to-ionizable amino acid replacement that generates a partially buried group with perturbed physico-chemical properties. We provide experimental and computational evidence that conformational flexibility can assist the emergence and subsequent evolution of new active sites by improving substrate and transition-state binding, through the sampling of many potentially productive conformations. Our results suggest a mechanism for the emergence of primordial enzymes and highlight the potential of ancestral reconstruction as a tool for protein engineering.
		+
		+	De novo active sites for resurrected Precambrian enzymes.,Risso VA, Martinez-Rodriguez S, Candel AM, Kruger DM, Pantoja-Uceda D, Ortega-Munoz M, Santoyo-Gonzalez F, Gaucher EA, Kamerlin SCL, Bruix M, Gavira JA, Sanchez-Ruiz JM Nat Commun. 2017 Jul 18;8:16113. doi: 10.1038/ncomms16113. PMID:28719578<ref>PMID:28719578</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5fqm" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Synthetic construct sequences]]
	[[Category: Gavira, J A]]		[[Category: Gavira, J A]]
	[[Category: Risso, V A]]		[[Category: Risso, V A]]

OCA at 00:37, 19 January 2017

OCA — Thu, 19 Jan 2017 00:37:44 GMT

←Older revision		Revision as of 00:37, 19 January 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5fqm is ~~ON HOLD until Paper Publication~~	+	==Last common ancestor of Gram Negative Bacteria (GNCA) Class A beta- lactamase==
-		+	<StructureSection load='5fqm' size='340' side='right' caption='[[5fqm]], [[Resolution\|resolution]] 1.50Å' scene=''>
-	~~Authors~~: ~~Martinez Rodriguez~~, S., ~~Gavira~~, J.A., ~~Risso, V~~.A., ~~Sanchez Ruiz, J~~.M.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5fqm]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FQM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FQM FirstGlance]. <br>
-	~~Description~~: ~~Last common ancestor of Gram Negative Bacteria (GNCA) Class~~ A ~~beta-lactamase~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5fqm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fqm OCA], [http://pdbe.org/5fqm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fqm RCSB], [http://www.ebi.ac.uk/pdbsum/5fqm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fqm ProSAT]</span></td></tr>
-	[[Category: ~~Sanchez Ruiz~~, ~~J.M~~]]	+	</table>
-	[[Category: ~~Gavira~~, J.A]]	+	__TOC__
-	[[Category: ~~Martinez Rodriguez, S~~]]	+	</StructureSection>
-	[[Category: ~~Risso, V.A~~]]	+	[[Category: Gavira, J A]]
		+	[[Category: Risso, V A]]
		+	[[Category: Rodriguez, S Martinez]]
		+	[[Category: Ruiz, J M.Sanchez]]
		+	[[Category: Gnca]]
		+	[[Category: Hydrolase]]
		+	[[Category: Precambrian]]
		+	[[Category: Resurrected beta-lactamase]]

OCA at 18:32, 13 January 2016

OCA — Wed, 13 Jan 2016 18:32:43 GMT

←Older revision		Revision as of 18:32, 13 January 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Martinez Rodriguez, S., Gavira, J.A., Risso, V.A., Sanchez Ruiz, J.M.		Authors: Martinez Rodriguez, S., Gavira, J.A., Risso, V.A., Sanchez Ruiz, J.M.

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

OCA — Wed, 23 Dec 2015 11:48:21 GMT

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

←Older revision

Revision as of 11:48, 23 December 2015

OCA: New page: '''Unreleased structure''' The entry 5fqm is ON HOLD Authors: Martinez Rodriguez, S., Gavira, J.A., Risso, V.A., Sanchez Ruiz, J.M. Description: Last common ancestor of Gram Negative B...

OCA — Wed, 23 Dec 2015 11:48:20 GMT

New page: '''Unreleased structure''' The entry 5fqm is ON HOLD Authors: Martinez Rodriguez, S., Gavira, J.A., Risso, V.A., Sanchez Ruiz, J.M. Description: Last common ancestor of Gram Negative B...

New page

'''Unreleased structure'''

The entry 5fqm is ON HOLD

Authors: Martinez Rodriguez, S., Gavira, J.A., Risso, V.A., Sanchez Ruiz, J.M.

Description: Last common ancestor of Gram Negative Bacteria (GNCA) Class A beta-lactamase
[[Category: Unreleased Structures]]
[[Category: Sanchez Ruiz, J.M]]
[[Category: Gavira, J.A]]
[[Category: Martinez Rodriguez, S]]
[[Category: Risso, V.A]]