4oqi - Revision history

OCA at 07:39, 25 January 2023

OCA — Wed, 25 Jan 2023 07:39:53 GMT

←Older revision		Revision as of 07:39, 25 January 2023
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	==Crystal structure of stabilized TEM-1 beta-lactamase variant v.13 carrying R164S/G238S mutations==		==Crystal structure of stabilized TEM-1 beta-lactamase variant v.13 carrying R164S/G238S mutations==
-	<StructureSection load='4oqi' size='340' side='right' caption='[[4oqi]], [[Resolution\|resolution]] 1.13Å' scene=''>	+	<StructureSection load='4oqi' size='340' side='right'caption='[[4oqi]], [[Resolution\|resolution]] 1.13Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4oqi]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OQI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4OQI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4oqi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OQI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OQI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ibr\|4ibr]], [[4ibx\|4ibx]], [[4op5\|4op5]], [[4op8\|4op8]], [[4opq\|4opq]], [[4opr\|4opr]], [[4opy\|4opy]], [[4opz\|4opz]], [[4oq0\|4oq0]], [[4oqg\|4oqg]], [[4oqh\|4oqh]]</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=4oqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oqi OCA], [https://pdbe.org/4oqi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4oqi RCSB], [https://www.ebi.ac.uk/pdbsum/4oqi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4oqi ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bla-TEM-94 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=4oqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oqi OCA], [~~http~~://pdbe.org/4oqi PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4oqi RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4oqi PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4oqi ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8KMX3_ECOLX Q8KMX3_ECOLX]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4oqi" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4oqi" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
-	[[Category: Dellus-Gur, E]]	+	[[Category: Large Structures]]
-	[[Category: Elias, M]]	+	[[Category: Dellus-Gur E]]
-	[[Category: Fraser~~, J S~~]]	+	[[Category: Elias M]]
-	[[Category: Tawfik~~, D S]]~~	+	[[Category: Fraser JS]]
-	~~[[Category: Beta-lctamase]]~~	+	[[Category: Tawfik DS]]
-	~~[[Category: Hydrolase-hydrolase inhibitor complex~~]]	+

OCA at 07:53, 17 January 2018

OCA — Wed, 17 Jan 2018 07:53:54 GMT

←Older revision		Revision as of 07:53, 17 January 2018
Line 3:		Line 3:
	<StructureSection load='4oqi' size='340' side='right' caption='[[4oqi]], [[Resolution\|resolution]] 1.13Å' scene=''>		<StructureSection load='4oqi' size='340' side='right' caption='[[4oqi]], [[Resolution\|resolution]] 1.13Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4oqi]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OQI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OQI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4oqi]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OQI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OQI FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ibr\|4ibr]], [[4ibx\|4ibx]], [[4op5\|4op5]], [[4op8\|4op8]], [[4opq\|4opq]], [[4opr\|4opr]], [[4opy\|4opy]], [[4opz\|4opz]], [[4oq0\|4oq0]], [[4oqg\|4oqg]], [[4oqh\|4oqh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ibr\|4ibr]], [[4ibx\|4ibx]], [[4op5\|4op5]], [[4op8\|4op8]], [[4opq\|4opq]], [[4opr\|4opr]], [[4opy\|4opy]], [[4opz\|4opz]], [[4oq0\|4oq0]], [[4oqg\|4oqg]], [[4oqh\|4oqh]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bla-TEM-94 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=4oqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oqi OCA], [http://pdbe.org/4oqi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4oqi RCSB], [http://www.ebi.ac.uk/pdbsum/4oqi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4oqi 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=4oqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oqi OCA], [http://pdbe.org/4oqi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4oqi RCSB], [http://www.ebi.ac.uk/pdbsum/4oqi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4oqi ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Epistasis is a key factor in evolution since it determines which combinations of mutations provide adaptive solutions and which mutational pathways toward these solutions are accessible by natural selection. There is growing evidence for the pervasiveness of sign epistasis--a complete reversion of mutational effects, particularly in protein evolution--yet its molecular basis remains poorly understood. We describe the structural basis of sign epistasis between G238S and R164S, two adaptive mutations in TEM-1 beta-lactamase--an enzyme that endows antibiotics resistance. Separated by 10 A, these mutations initiate two separate trajectories toward increased hydrolysis rates and resistance toward second and third-generation cephalosporins antibiotics. Both mutations allow the enzyme's active site to adopt alternative conformations and accommodate the new antibiotics. By solving the corresponding set of crystal structures, we found that R164S causes local disorder whereas G238S induces discrete conformations. When combined, the mutations in 238 and 164 induce local disorder whereby nonproductive conformations that perturb the enzyme's catalytic preorganization dominate. Specifically, Asn170 that coordinates the deacylating water molecule is misaligned, in both the free form and the inhibitor-bound double mutant. This local disorder is not restored by stabilizing global suppressor mutations and thus leads to an evolutionary cul-de-sac. Conformational dynamism therefore underlines the reshaping potential of protein's structures and functions but also limits protein evolvability because of the fragility of the interactions networks that maintain protein structures.
		+
		+	Negative Epistasis and Evolvability in TEM-1 beta-Lactamase--The Thin Line between an Enzyme's Conformational Freedom and Disorder.,Dellus-Gur E, Elias M, Caselli E, Prati F, Salverda ML, de Visser JA, Fraser JS, Tawfik DS J Mol Biol. 2015 Jul 17;427(14):2396-409. doi: 10.1016/j.jmb.2015.05.011. Epub, 2015 May 22. PMID:26004540<ref>PMID:26004540</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4oqi" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
	[[Category: Dellus-Gur, E]]		[[Category: Dellus-Gur, E]]
	[[Category: Elias, M]]		[[Category: Elias, M]]

OCA at 17:25, 9 March 2017

OCA — Thu, 09 Mar 2017 17:25:04 GMT

←Older revision		Revision as of 17:25, 9 March 2017
Line 1:		Line 1:
		+
	==Crystal structure of stabilized TEM-1 beta-lactamase variant v.13 carrying R164S/G238S mutations==		==Crystal structure of stabilized TEM-1 beta-lactamase variant v.13 carrying R164S/G238S mutations==
	<StructureSection load='4oqi' size='340' side='right' caption='[[4oqi]], [[Resolution\|resolution]] 1.13Å' scene=''>		<StructureSection load='4oqi' size='340' side='right' caption='[[4oqi]], [[Resolution\|resolution]] 1.13Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ibr\|4ibr]], [[4ibx\|4ibx]], [[4op5\|4op5]], [[4op8\|4op8]], [[4opq\|4opq]], [[4opr\|4opr]], [[4opy\|4opy]], [[4opz\|4opz]], [[4oq0\|4oq0]], [[4oqg\|4oqg]], [[4oqh\|4oqh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ibr\|4ibr]], [[4ibx\|4ibx]], [[4op5\|4op5]], [[4op8\|4op8]], [[4opq\|4opq]], [[4opr\|4opr]], [[4opy\|4opy]], [[4opz\|4opz]], [[4oq0\|4oq0]], [[4oqg\|4oqg]], [[4oqh\|4oqh]]</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=4oqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oqi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4oqi RCSB], [http://www.ebi.ac.uk/pdbsum/4oqi 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=4oqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oqi OCA], [http://pdbe.org/4oqi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4oqi RCSB], [http://www.ebi.ac.uk/pdbsum/4oqi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4oqi ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__

OCA at 12:15, 20 May 2015

OCA — Wed, 20 May 2015 12:15:11 GMT

←Older revision		Revision as of 12:15, 20 May 2015
Line 1:		Line 1:
-	~~WITHDRAWN~~: ~~The PDB entry~~ 4OQI ~~was withdrawn~~.	+	==Crystal structure of stabilized TEM-1 beta-lactamase variant v.13 carrying R164S/G238S mutations==
		+	<StructureSection load='4oqi' size='340' side='right' caption='[[4oqi]], [[Resolution\|resolution]] 1.13Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4oqi]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OQI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OQI FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ibr\|4ibr]], [[4ibx\|4ibx]], [[4op5\|4op5]], [[4op8\|4op8]], [[4opq\|4opq]], [[4opr\|4opr]], [[4opy\|4opy]], [[4opz\|4opz]], [[4oq0\|4oq0]], [[4oqg\|4oqg]], [[4oqh\|4oqh]]</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=4oqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oqi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4oqi RCSB], [http://www.ebi.ac.uk/pdbsum/4oqi PDBsum]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Dellus-Gur, E]]
		+	[[Category: Elias, M]]
		+	[[Category: Fraser, J S]]
		+	[[Category: Tawfik, D S]]
		+	[[Category: Beta-lctamase]]
		+	[[Category: Hydrolase-hydrolase inhibitor complex]]

OCA at 11:02, 30 April 2015

OCA — Thu, 30 Apr 2015 11:02:03 GMT

←Older revision		Revision as of 11:02, 30 April 2015
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	WITHDRAWN: The PDB entry 4OQI was withdrawn.
-		+
-	The entry ~~4oqi is ON HOLD until Apr 23 2016~~	+
-		+
-	~~Authors: Dellus-Gur, E., Elias, M., Fraser, J.S., Tawfik, D.S.~~	+
-		+
-	~~Description: Crystal structure of stabilized TEM-1 beta-lactamase variant v.13 carrying R164S/G238S mutations~~	+
-	~~[[Category: Unreleased Structures]]~~	+
-	~~[[Category: Elias, M]]~~	+
-	~~[[Category: Fraser, J.S]]~~	+
-	~~[[Category: Dellus-Gur, E]]~~	+
-	~~[[Category: Tawfik, D~~.~~S]]~~	+

OCA at 07:53, 15 April 2015

OCA — Wed, 15 Apr 2015 07:53:11 GMT

←Older revision		Revision as of 07:53, 15 April 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4oqi is ON HOLD until Apr 11 2016	+	The entry 4oqi is ON HOLD until Apr 23 2016

	Authors: Dellus-Gur, E., Elias, M., Fraser, J.S., Tawfik, D.S.		Authors: Dellus-Gur, E., Elias, M., Fraser, J.S., Tawfik, D.S.

OCA at 11:36, 7 February 2015

OCA — Sat, 07 Feb 2015 11:36:02 GMT

←Older revision		Revision as of 11:36, 7 February 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4oqi is ON HOLD until ~~Paper Publication~~	+	The entry 4oqi is ON HOLD until Apr 11 2016

	Authors: Dellus-Gur, E., Elias, M., Fraser, J.S., Tawfik, D.S.		Authors: Dellus-Gur, E., Elias, M., Fraser, J.S., Tawfik, D.S.

OCA at 14:31, 24 December 2014

OCA — Wed, 24 Dec 2014 14:31:57 GMT

←Older revision		Revision as of 14:31, 24 December 2014
Line 6:		Line 6:

	Description: Crystal structure of stabilized TEM-1 beta-lactamase variant v.13 carrying R164S/G238S mutations		Description: Crystal structure of stabilized TEM-1 beta-lactamase variant v.13 carrying R164S/G238S mutations
		+	[[Category: Unreleased Structures]]
		+	[[Category: Elias, M]]
		+	[[Category: Fraser, J.S]]
		+	[[Category: Dellus-Gur, E]]
		+	[[Category: Tawfik, D.S]]

OCA at 08:26, 2 April 2014

OCA — Wed, 02 Apr 2014 08:26:22 GMT

←Older revision		Revision as of 08:26, 2 April 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4oqi is ON HOLD	+	The entry 4oqi is ON HOLD until Paper Publication

	Authors: Dellus-Gur, E., Elias, M., Fraser, J.S., Tawfik, D.S.		Authors: Dellus-Gur, E., Elias, M., Fraser, J.S., Tawfik, D.S.

	Description: Crystal structure of stabilized TEM-1 beta-lactamase variant v.13 carrying R164S/G238S mutations		Description: Crystal structure of stabilized TEM-1 beta-lactamase variant v.13 carrying R164S/G238S mutations

OCA: Protected "4oqi" [edit=sysop:move=sysop]

OCA — Wed, 19 Feb 2014 16:19:25 GMT

Protected "4oqi" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:19, 19 February 2014