1FYF

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Transfer RNA-mediated editing in threonyl-tRNA synthetase. The class II solution to the double discrimination problem.

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

(2000) Cell 103: 877-884


  • PubMed Abstract: 
  • Threonyl-tRNA synthetase, a class II synthetase, uses a unique zinc ion to discriminate against the isosteric valine at the activation step. The crystal structure of the enzyme with an analog of seryl adenylate shows that the noncognate serine cannot ...

    Threonyl-tRNA synthetase, a class II synthetase, uses a unique zinc ion to discriminate against the isosteric valine at the activation step. The crystal structure of the enzyme with an analog of seryl adenylate shows that the noncognate serine cannot be fully discriminated at that step. We show that hydrolysis of the incorrectly formed ser-tRNA(Thr) is performed at a specific site in the N-terminal domain of the enzyme. The present study suggests that both classes of synthetases use effectively the ability of the CCA end of tRNA to switch between a hairpin and a helical conformation for aminoacylation and editing. As a consequence, the editing mechanism of both classes of synthetases can be described as mirror images, as already seen for tRNA binding and amino acid activation.


    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
    • 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


    Organizational Affiliation

    UPR 9004 Biologie Structurale IGBMC, CNRS/INSERM/ULP BP163 67404 Cedex, 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
SSA
Query on SSA

Download SDF File 
Download CCD File 
A, B
5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE
C13 H19 N7 O8 S
HQXFJGONGJPTLZ-YTMOPEAISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 86.950α = 90.00
b = 109.520β = 90.00
c = 115.370γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-12-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance