OCA at 08:20, 16 August 2023

2023-08-16T08:20:37Z

←Older revision		Revision as of 08:20, 16 August 2023
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-	'''Unreleased structure'''

-	~~The entry~~ 8brv is ~~ON HOLD until Paper~~ Publication	+	==Escherichia coli methionyl-tRNA synthetase mutant L13M,I297C complexed with beta3-methionine.==
		+	<StructureSection load='8brv' size='340' side='right'caption='[[8brv]], [[Resolution\|resolution]] 1.53Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8brv]] 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=8BRV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8BRV FirstGlance]. <br>
		+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.53Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B3M:(3R)-3-AMINO-5-(METHYLSULFANYL)PENTANOIC+ACID'>B3M</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</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=8brv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8brv OCA], [https://pdbe.org/8brv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8brv RCSB], [https://www.ebi.ac.uk/pdbsum/8brv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8brv ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/SYM_ECOLI SYM_ECOLI] Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation.[HAMAP-Rule:MF_00098]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Amino acids (AAs) with a noncanonical backbone would be a valuable tool for protein engineering, enabling new structural motifs and building blocks. To incorporate them into an expanded genetic code, the first, key step is to obtain an appropriate aminoacyl-tRNA synthetase (aaRS). Currently, directed evolution is not available to optimize AAs with noncanonical backbones, since an appropriate selective pressure has not been discovered. Computational protein design (CPD) is an alternative. We used a new CPD method to redesign MetRS and increase its activity towards beta-Met, which has an extra backbone methylene. The new method considered a few active site positions for design and used a Monte Carlo exploration of the corresponding sequence space. During the exploration, a bias energy was adaptively learned, such that the free energy landscape of the apo enzyme was flattened. Enzyme variants could then be sampled, in the presence of the ligand and the bias energy, according to their beta-Met binding affinities. 18 predicted variants were chosen for experimental testing; 10 exhibited detectable activity for beta-Met adenylation. Top predicted hits were characterized experimentally in detail. Dissociation constants, catalytic rates, and Michaelis constants for both alpha-Met and beta-Met were measured. The best mutant retained a preference for alpha-Met over beta-Met; however, the preference was reduced, compared to the wildtype, by a factor of 29. For this mutant, high resolution crystal structures were obtained in complex with both alpha-Met and beta-Met, indicating that the predicted, active conformation of beta-Met in the active site was retained. This article is protected by copyright. All rights reserved.

-	~~Authors~~:	+	Redesigning methionyl-tRNA synthetase for beta-methionine activity with adaptive landscape flattening and experiments.,Opuu V, Nigro G, Lazennec-Schurdevin C, Mechulam Y, Schmitt E, Simonson T Protein Sci. 2023 Jul 30:e4738. doi: 10.1002/pro.4738. PMID:37518893<ref>PMID:37518893</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 8brv" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Escherichia coli]]
		+	[[Category: Large Structures]]
		+	[[Category: Lazennec-Schurdevin C]]
		+	[[Category: Mechulam Y]]
		+	[[Category: Nigro G]]
		+	[[Category: Opuu V]]
		+	[[Category: Schmitt E]]
		+	[[Category: Simonson T]]

OCA at 05:13, 7 December 2022

2022-12-07T05:13:03Z

←Older revision		Revision as of 05:13, 7 December 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8brv is ON HOLD	+	The entry 8brv is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "8brv" [edit=sysop:move=sysop]

2022-11-30T08:29:16Z

Protected "8brv" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:29, 30 November 2022

OCA: New page: '''Unreleased structure''' The entry 8brv is ON HOLD Authors: Description: Category: Unreleased Structures

2022-11-30T08:29:15Z

New page: '''Unreleased structure''' The entry 8brv is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 8brv is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

8brv - Revision history

OCA at 08:20, 16 August 2023

OCA at 05:13, 7 December 2022

OCA: Protected "8brv" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 8brv is ON HOLD Authors: Description: Category: Unreleased Structures