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 1.4 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: 10.1006/jmbi.2001.4408

  • 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-homoc ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
METHIONYL-TRNA SYNTHETASE
A
551Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: metG
EC: 6.1.1.10
Find proteins for P00959 (Escherichia coli (strain K12))
Go to UniProtKB:  P00959
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MET
Query on MET

Download SDF File 
Download CCD File 
A
METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
 Ligand Interaction
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 = 78.400α = 90.00
b = 45.160β = 107.91
c = 86.310γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-03-21
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-08-24
    Type: Structure summary
  • Version 1.4: 2017-10-04
    Type: Refinement description