1TKE

Crystal structure of the editing domain of threonyl-tRNA synthetase complexed with serine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Achieving Error-Free Translation; The Mechanism of Proofreading of Threonyl-tRNA Synthetase at Atomic Resolution.

Dock-Bregeon, A.C.Rees, B.Torres-Larios, A.Bey, G.Caillet, J.Moras, D.

(2004) Mol.Cell 16: 375-386

  • DOI: 10.1016/j.molcel.2004.10.002
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The fidelity of aminoacylation of tRNA(Thr) by the threonyl-tRNA synthetase (ThrRS) requires the discrimination of the cognate substrate threonine from the noncognate serine. Misacylation by serine is corrected in a proofreading or editing step. An e ...

    The fidelity of aminoacylation of tRNA(Thr) by the threonyl-tRNA synthetase (ThrRS) requires the discrimination of the cognate substrate threonine from the noncognate serine. Misacylation by serine is corrected in a proofreading or editing step. An editing site has been located 39 A away from the aminoacylation site. We report the crystal structures of this editing domain in its apo form and in complex with the serine product, and with two nonhydrolyzable analogs of potential substrates: the terminal tRNA adenosine charged with serine, and seryl adenylate. The structures show how serine is recognized, and threonine rejected, and provide the structural basis for the editing mechanism, a water-mediated hydrolysis of the mischarged tRNA. When the adenylate analog binds in the editing site, a phosphate oxygen takes the place of one of the catalytic water molecules, thereby blocking the reaction. This rules out a correction mechanism that would occur before the binding of the amino acid on the tRNA.


    Organizational Affiliation

    IGBMC (CNRS/INSERM/Université Louis Pasteur), Laboratoire de Biologie et Génomique Structurales, 1, rue Laurent Fries, BP 10142, 67400 Illkirch, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Threonyl-tRNA synthetase
A
224Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: thrS
EC: 6.1.1.3
Find proteins for P0A8M3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A8M3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SER
Query on SER

Download SDF File 
Download CCD File 
A
SERINE
C3 H7 N O3
MTCFGRXMJLQNBG-REOHCLBHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 43.697α = 90.00
b = 44.913β = 90.00
c = 116.607γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
HKL-2000data reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-30
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance