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 
  • R-Value Observed: 0.216 

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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 Biol 7: 461-465

  • DOI: 10.1038/75856
  • Primary Citation of Related Structures:  
    1EVK, 1EVL

  • 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 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 ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
THREONYL-TRNA SYNTHETASEA, B, C, D401Escherichia coliMutation(s): 0 
EC: 6.1.1.3
UniProt
Find proteins for P0A8M3 (Escherichia coli (strain K12))
Explore P0A8M3 
Go to UniProtKB:  P0A8M3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A8M3
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.7α = 90
b = 111.1β = 93.5
c = 135.2γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

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