1EVK

CRYSTAL STRUCTURE OF A TRUNCATED FORM OF THREONYL-TRNA SYNTHETASE WITH THE LIGAND THREONINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Zinc ion mediated amino acid discrimination by threonyl-tRNA synthetase.

Sankaranarayanan, R.Dock-Bregeon, A.C.Rees, B.Bovee, M.Caillet, J.Romby, P.Francklyn, C.S.Moras, D.

(2000) Nat.Struct.Mol.Biol. 7: 461-465

  • DOI: 10.1038/75856
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Accurate translation of the genetic code depends on the ability of aminoacyl-tRNA synthetases to distinguish between similar amino acids. In order to investigate the basis of amino acid recognition and to understand the role played by the zinc ion pr ...

    Accurate translation of the genetic code depends on the ability of aminoacyl-tRNA synthetases to distinguish between similar amino acids. In order to investigate the basis of amino acid recognition and to understand the role played by the zinc ion present in the active site of threonyl-tRNA synthetase, we have determined the crystal structures of complexes of an active truncated form of the enzyme with a threonyl adenylate analog or threonine. The zinc ion is directly involved in threonine recognition, forming a pentacoordinate intermediate with both the amino group and the side chain hydroxyl. Amino acid activation experiments reveal that the enzyme shows no activation of isosteric valine, and activates serine at a rate 1,000-fold less than that of cognate threonine. This study demonstrates that the zinc ion is neither strictly catalytic nor structural and suggests how the zinc ion ensures that only amino acids that possess a hydroxyl group attached to the beta-position are activated.


    Related Citations: 
    • The Structure of Threonyl-tRNA Synthetase-tRNA(Thr) Complex Enlightens its Repressor Activity and Reveals an Essential Zinc Ion in the Active Site
      Sankaranarayanan, R.,Dock-Bregeon, A.C.,Romby, P.,Caillet, J.,Springer, M.,Rees, B.,Ehresmann, C.,Ehresmann, B.,Moras, D.
      (1999) Cell 97: 371


    Organizational Affiliation

    UPR 9004 Biologie Structurale, IGBMC, CNRS/INSERM/ULP, Illkirch, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THREONYL-TRNA SYNTHETASE
A, B
401Escherichia 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
B
THREONINE
C4 H9 N O3
AYFVYJQAPQTCCC-GBXIJSLDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 107.050α = 90.00
b = 117.340β = 90.00
c = 87.080γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-07-19
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance