1F4L

CRYSTAL STRUCTURE OF THE E.COLI METHIONYL-TRNA SYNTHETASE COMPLEXED WITH METHIONINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

How methionyl-tRNA synthetase creates its amino acid recognition pocket upon L-methionine binding.

Serre, L.Verdon, G.Choinowski, T.Hervouet, N.Risler, J.L.Zelwer, C.

(2001) J Mol Biol 306: 863-876

  • DOI: https://doi.org/10.1006/jmbi.2001.4408
  • Primary Citation of Related Structures:  
    1F4L

  • PubMed Abstract: 

    Amino acid selection by aminoacyl-tRNA synthetases requires efficient mechanisms to avoid incorrect charging of the cognate tRNAs. A proofreading mechanism prevents Escherichia coli methionyl-tRNA synthetase (EcMet-RS) from activating in vivo L-homocysteine, a natural competitor of L-methionine recognised by the enzyme. The crystal structure of the complex between EcMet-RS and L-methionine solved at 1.8 A resolution exhibits some conspicuous differences with the recently published free enzyme structure. Thus, the methionine delta-sulphur atom replaces a water molecule H-bonded to Leu13N and Tyr260O(eta) in the free enzyme. Rearrangements of aromatic residues enable the protein to form a hydrophobic pocket around the ligand side-chain. The subsequent formation of an extended water molecule network contributes to relative displacements, up to 3 A, of several domains of the protein. The structure of this complex supports a plausible mechanism for the selection of L-methionine versus L-homocysteine and suggests the possibility of information transfer between the different functional domains of the enzyme.


  • Organizational Affiliation

    Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique, rue Charles Sadron, Orléans Cedex 2, 45071, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
METHIONYL-TRNA SYNTHETASE551Escherichia coliMutation(s): 0 
Gene Names: SYNTHETIC GENE
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.4α = 90
b = 45.16β = 107.91
c = 86.31γ = 90
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-03-21
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-08-24
    Changes: Structure summary
  • Version 1.4: 2017-10-04
    Changes: Refinement description
  • Version 1.5: 2024-03-13
    Changes: Data collection, Database references, Derived calculations