8BRW

Escherichia coli methionyl-tRNA synthetase mutant L13C,I297C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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.

(2023) Protein Sci 32: e4738-e4738

  • DOI: https://doi.org/10.1002/pro.4738
  • Primary Citation of Related Structures:  
    8BRU, 8BRV, 8BRW, 8BRX

  • PubMed Abstract: 

    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. 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 β-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 β-Met binding affinities. Eighteen predicted variants were chosen for experimental testing; 10 exhibited detectable activity for β-Met adenylation. Top predicted hits were characterized experimentally in detail. Dissociation constants, catalytic rates, and Michaelis constants for both α-Met and β-Met were measured. The best mutant retained a preference for α-Met over β-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 α-Met and β-Met, indicating that the predicted, active conformation of β-Met in the active site was retained.


  • Organizational Affiliation

    Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methionine--tRNA ligase568Escherichia coliMutation(s): 2 
Gene Names: metGb2114JW2101
EC: 6.1.1.10
UniProt
Find proteins for P00959 (Escherichia coli (strain K12))
Explore P00959 
Go to UniProtKB:  P00959
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00959
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.81α = 90
b = 45.58β = 107.44
c = 86.47γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Centre National de la Recherche Scientifique (CNRS)FranceUMR7654
Other governmentUMR7654

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-16
    Type: Initial release
  • Version 1.1: 2023-09-06
    Changes: Database references