1EVL

CRYSTAL STRUCTURE OF A TRUNCATED FORM OF THREONYL-TRNA SYNTHETASE WITH A THREONYL ADENYLATE ANALOG

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.215 

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, C, D
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, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
TSB
Query on TSB
Download SDF File 
Download CCD File 
A, B, C, D
5'-O-(N-(L-THREONYL)-SULFAMOYL)ADENOSINE
C14 H21 N7 O8 S
UPVAPSGKXAAHBG-CKTDUXNWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.215 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 86.700α = 90.00
b = 111.100β = 93.50
c = 135.200γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

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