Structure of a mutant methionyl-tRNA synthetase with modified specificity complexed with methionine

Experimental Data Snapshot

  • Resolution: 1.40 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.168 

Starting Model: experimental
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Switching from an induced-fit to a lock-and-key mechanism in an aminoacyl-tRNA synthetase with modified specificity.

Schmitt, E.Tanrikulu, I.C.Yoo, T.H.Panvert, M.Tirrell, D.A.Mechulam, Y.

(2009) J Mol Biol 394: 843-851

  • DOI: https://doi.org/10.1016/j.jmb.2009.10.016
  • Primary Citation of Related Structures:  
    3H97, 3H99, 3H9B, 3H9C

  • PubMed Abstract: 

    Methionyl-tRNA synthetase (MetRS) specifically binds its methionine substrate in an induced-fit mechanism, with methionine binding causing large rearrangements. Mutated MetRS able to efficiently aminoacylate the methionine (Met) analog azidonorleucine (Anl) have been identified by saturation mutagenesis combined with in vivo screening procedures. Here, the crystal structure of such a mutated MetRS was determined in the apo form as well as complexed with Met or Anl (1.4 to 1.7 A resolution) to reveal the structural basis for the altered specificity. The mutations result in both the loss of important contacts with Met and the creation of new contacts with Anl, thereby explaining the specificity shift. Surprisingly, the conformation induced by Met binding in wild-type MetRS already occurs in the apo form of the mutant enzyme. Therefore, the mutations cause the enzyme to switch from an induced-fit mechanism to a lock-and-key one, thereby enhancing its catalytic efficiency.

  • Organizational Affiliation

    Ecole Polytechnique, Laboratoire de Biochimie, F-91128 Palaiseau Cedex, France; CNRS, UMR7654, Laboratoire de Biochimie, Ecole Polytechnique, F-91128 Palaiseau Cedex, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methionyl-tRNA synthetase560Escherichia coli K-12Mutation(s): 3 
Gene Names: b2114JW2101metG
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
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.40 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.172α = 90
b = 45.293β = 107.25
c = 85.967γ = 90
Software Package:
Software NamePurpose
XSCALEdata processing
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2021-10-13
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-09-06
    Changes: Data collection, Refinement description