Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 25.47 kDa 
• Atom Count: 2109 
• Modelled Residue Count: 224 
• Deposited Residue Count: 224 
• Unique protein chains: 1

1TJE

Crystal structure of the editing domain of threonyl-tRNA synthetase

• PDB DOI: 10.2210/pdb1TJE/pdb

• Classification: LIGASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2004-06-04 Released: 2004-11-30 
• Deposition Author(s): Dock-Bregeon, A.C., Rees, B., Torres-Larios, A., Bey, G., Caillet, J., Moras, D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.224 
• R-Value Work: 0.202 
• R-Value Observed: 0.203 

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

• PubMed: 15525511 
• DOI: 10.1016/j.molcel.2004.10.002
• Primary Citation of Related Structures:  
  1TJE, 1TKE, 1TKG, 1TKY


• 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 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Threonyl-tRNA synthetase	A	224	Escherichia coli	Mutation(s): 0  Gene Names: thrS, b1719, C2116, SF1512, S1630 EC: 6.1.1.3
UniProt
Find proteins for P0A8M3 (Escherichia coli (strain K12)) Explore P0A8M3  Go to UniProtKB:  P0A8M3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.224 
• R-Value Work: 0.202 
• R-Value Observed: 0.203 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.566	α = 90
b = 45.243	β = 90
c = 116.602	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-06-04 
• Released Date: 2004-11-30 
Deposition Author(s): Dock-Bregeon, A.C., Rees, B., Torres-Larios, A., Bey, G., Caillet, J., Moras, D.

Revision History  

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