Methionyl-trna synthetase from escherichia coli complexed with methioninyl adenylate

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Use of analogues of methionine and methionyl adenylate to sample conformational changes during catalysis in Escherichia coli methionyl-tRNA synthetase.

Crepin, T.Schmitt, E.Mechulam, Y.Sampson, P.B.Vaughan, M.D.Honek, J.F.Blanquet, S.

(2003) J Mol Biol 332: 59-72

  • DOI: https://doi.org/10.1016/s0022-2836(03)00917-3
  • Primary Citation of Related Structures:  
    1P7P, 1PFU, 1PFV, 1PFW, 1PFY, 1PG0, 1PG2

  • PubMed Abstract: 

    Binding of methionine to methionyl-tRNA synthetase (MetRS) is known to promote conformational changes within the active site. However, the contribution of these rearrangements to enzyme catalysis is not fully understood. In this study, several methionine and methionyl adenylate analogues were diffused into crystals of the monomeric form of Escherichia coli methionyl-tRNA synthetase. The structures of the corresponding complexes were solved at resolutions below 1.9A and compared to those of the enzyme free or complexed with methionine. Residues Y15 and W253 play key roles in the strength of the binding of the amino acid and of its analogues. Indeed, full motions of these residues are required to recover the maximum in free energy of binding. Residue Y15 also controls the size of the hydrophobic pocket where the amino acid side-chain interacts. H301 appears to participate to the specific recognition of the sulphur atom of methionine. Complexes with methionyl adenylate analogues illustrate the shielding by MetRS of the region joining the methionine and adenosine moieties. Finally, the structure of MetRS complexed to a methionine analogue mimicking the tetrahedral carbon of the transition state in the aminoacylation reaction was solved. On the basis of this model, we propose that, in response to the binding of the 3'-end of tRNA, Y15 moves again in order to deshield the anhydride bond in the natural adenylate.

  • Organizational Affiliation

    Laboratoire de Biochimie, Unité Mixte de Recherche no 7654, CNRS-Ecole Polytechnique, F-91128 Palaiseau cedex, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methionyl-tRNA synthetase551Escherichia coliMutation(s): 0 
Gene Names: metG
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
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MOD

Download Ideal Coordinates CCD File 
C15 H27 N6 O7 P S
Binding Affinity Annotations 
IDSourceBinding Affinity
MOD Binding MOAD:  1PG0 Kd: 1000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.041α = 90
b = 45.574β = 108.37
c = 87.28γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CCP4data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-02-17
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description