6bm9 - Revision history

OCA at 14:45, 4 October 2023

OCA — Wed, 04 Oct 2023 14:45:35 GMT

←Older revision		Revision as of 14:45, 4 October 2023
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	<StructureSection load='6bm9' size='340' side='right'caption='[[6bm9]], [[Resolution\|resolution]] 2.19Å' scene=''>		<StructureSection load='6bm9' size='340' side='right'caption='[[6bm9]], [[Resolution\|resolution]] 2.19Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6bm9]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BM9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6BM9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6bm9]] is a 4 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=6BM9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BM9 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=ZN:ZINC+ION'>ZN</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]] 2.19Å</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=6bm9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bm9 OCA], [~~http~~://pdbe.org/6bm9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6bm9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6bm9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6bm9 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=ZN:ZINC+ION'>ZN</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=6bm9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bm9 OCA], [https://pdbe.org/6bm9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6bm9 RCSB], [https://www.ebi.ac.uk/pdbsum/6bm9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6bm9 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q5U7L7_ECOLX Q5U7L7_ECOLX]
	<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: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Carr~~, P D~~]]	+	[[Category: Carr PD]]
-	[[Category: Hong, N S]]	+	[[Category: Hong N-S]]
-	[[Category: Jackson~~, C J]]~~	+	[[Category: Jackson CJ]]
-	~~[[Category: Directed evolution]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Mbl super family]]~~	+
-	~~[[Category: Ndm-1]]~~	+
-	~~[[Category: Phosphatase~~]]	+

OCA at 08:35, 8 January 2020

OCA — Wed, 08 Jan 2020 08:35:57 GMT

←Older revision		Revision as of 08:35, 8 January 2020
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	==Directed evolutionary changes in MBL super family - VIM-2 Round 10==		==Directed evolutionary changes in MBL super family - VIM-2 Round 10==
-	<StructureSection load='6bm9' size='340' side='right' caption='[[6bm9]], [[Resolution\|resolution]] 2.19Å' scene=''>	+	<StructureSection load='6bm9' size='340' side='right'caption='[[6bm9]], [[Resolution\|resolution]] 2.19Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6bm9]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BM9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BM9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6bm9]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BM9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BM9 FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 6bm9" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6bm9" 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: Carr, P D]]		[[Category: Carr, P D]]
	[[Category: Hong, N S]]		[[Category: Hong, N S]]

OCA at 07:52, 21 February 2019

OCA — Thu, 21 Feb 2019 07:52:50 GMT

←Older revision		Revision as of 07:52, 21 February 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6bm9 is ~~ON HOLD until Paper~~ Publication	+	==Directed evolutionary changes in MBL super family - VIM-2 Round 10==
		+	<StructureSection load='6bm9' size='340' side='right' caption='[[6bm9]], [[Resolution\|resolution]] 2.19Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6bm9]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BM9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BM9 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=ZN:ZINC+ION'>ZN</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=6bm9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bm9 OCA], [http://pdbe.org/6bm9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bm9 RCSB], [http://www.ebi.ac.uk/pdbsum/6bm9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bm9 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Genetic variation among orthologous proteins can cause cryptic phenotypic properties that only manifest in changing environments. Such variation may impact the evolvability of proteins, but the underlying molecular basis remains unclear. Here, we performed comparative directed evolution of four orthologous metallo-beta-lactamases toward a new function and found that different starting genotypes evolved to distinct evolutionary outcomes. Despite a low initial fitness, one ortholog reached a significantly higher fitness plateau than its counterparts, via increasing catalytic activity. By contrast, the ortholog with the highest initial activity evolved to a less-optimal and phenotypically distinct outcome through changes in expression, oligomerization and activity. We show how cryptic molecular properties and conformational variation of active site residues in the initial genotypes cause epistasis, that could lead to distinct evolutionary outcomes. Our work highlights the importance of understanding the molecular details that connect genetic variation to protein function to improve the prediction of protein evolution.

-	~~Authors: Hong~~, N~~.-S.~~, ~~Jackson~~, ~~C.J.~~, Carr, P.D.	+	Cryptic genetic variation shapes the adaptive evolutionary potential of enzymes.,Baier F, Hong N, Yang G, Pabis A, Miton CM, Barrozo A, Carr PD, Kamerlin SC, Jackson CJ, Tokuriki N Elife. 2019 Feb 5;8. pii: 40789. doi: 10.7554/eLife.40789. PMID:30719972<ref>PMID:30719972</ref>

-	~~Description: Directed evolutionary changes in MBL super family~~ -~~VIM~~-~~2 Round 10~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Hong, N.-S]]	+	<div class="pdbe-citations 6bm9" style="background-color:#fffaf0;"></div>
-	[[Category: Jackson, C.J]]	+	== References ==
-	[[Category: ~~Carr, P.D~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Carr, P D]]
		+	[[Category: Hong, N S]]
		+	[[Category: Jackson, C J]]
		+	[[Category: Directed evolution]]
		+	[[Category: Hydrolase]]
		+	[[Category: Mbl super family]]
		+	[[Category: Ndm-1]]
		+	[[Category: Phosphatase]]

OCA at 03:58, 30 May 2018

OCA — Wed, 30 May 2018 03:58:04 GMT

←Older revision		Revision as of 03:58, 30 May 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6bm9 is ON HOLD	+	The entry 6bm9 is ON HOLD until Paper Publication

	Authors: Hong, N.-S., Jackson, C.J., Carr, P.D.		Authors: Hong, N.-S., Jackson, C.J., Carr, P.D.

OCA: Protected "6bm9" [edit=sysop:move=sysop]

OCA — Wed, 22 Nov 2017 06:35:59 GMT

Protected "6bm9" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:35, 22 November 2017

OCA: New page: '''Unreleased structure''' The entry 6bm9 is ON HOLD Authors: Hong, N.-S., Jackson, C.J., Carr, P.D. Description: Directed evolutionary changes in MBL super family -VIM-2 Round 10 [[Ca...

OCA — Wed, 22 Nov 2017 06:35:58 GMT

New page: '''Unreleased structure''' The entry 6bm9 is ON HOLD Authors: Hong, N.-S., Jackson, C.J., Carr, P.D. Description: Directed evolutionary changes in MBL super family -VIM-2 Round 10 [[Ca...

New page

'''Unreleased structure'''

The entry 6bm9 is ON HOLD

Authors: Hong, N.-S., Jackson, C.J., Carr, P.D.

Description: Directed evolutionary changes in MBL super family -VIM-2 Round 10
[[Category: Unreleased Structures]]
[[Category: Hong, N.-S]]
[[Category: Jackson, C.J]]
[[Category: Carr, P.D]]