Preliminary Structure of Thermus thermophilus Ligand-Free Valyl-tRNA Synthetase

Experimental Data Snapshot

  • Resolution: 4.00 Å
  • R-Value Free: 0.383 
  • R-Value Work: 0.316 
  • R-Value Observed: 0.320 

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Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase

Fukai, S.Nureki, O.Sekine, S.Shimada, A.Vassylyev, D.G.Yokoyama, S.

(2003) RNA 9: 100-111

  • DOI: https://doi.org/10.1261/rna.2760703
  • Primary Citation of Related Structures:  
    1IVS, 1IYW

  • PubMed Abstract: 

    The molecular interactions between valyl-tRNA synthetase (ValRS) and tRNA(Val), with the C34-A35-C36 anticodon, from Thermus thermophilus were studied by crystallographic analysis and structure-based mutagenesis. In the ValRS-bound structure of tRNA(Val), the successive A35-C36 residues (the major identity elements) of tRNA(Val) are base-stacked upon each other, and fit into a pocket on the alpha-helix bundle domain of ValRS. Hydrogen bonds are formed between ValRS and A35-C36 of tRNA(Val) in a base-specific manner. The C-terminal coiled-coil domain of ValRS interacts electrostatically with A20 and hydrophobically with the G19*C56 tertiary base pair. The loss of these interactions by the deletion of the coiled-coil domain of ValRS increased the K(M) value for tRNA(Val) 28-fold and decreased the k(cat) value 19-fold in the aminoacylation. The tRNA(Val) K(M) and k(cat) values were increased 21-fold and decreased 32-fold, respectively, by the disruption of the G18*U55 and G19*C56 tertiary base pairs, which associate the D- and T-loops for the formation of the L-shaped tRNA structure. Therefore, the coiled-coil domain of ValRS is likely to stabilize the L-shaped tRNA structure during the aminoacylation reaction.

  • Organizational Affiliation

    Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Valyl-tRNA Synthetase
A, B
862Thermus thermophilusMutation(s): 0 
Find proteins for P96142 (Thermus thermophilus)
Explore P96142 
Go to UniProtKB:  P96142
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP96142
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 4.00 Å
  • R-Value Free: 0.383 
  • R-Value Work: 0.316 
  • R-Value Observed: 0.320 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 186.562α = 90
b = 207.328β = 90
c = 59.235γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2003-06-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-02-07
    Changes: Experimental preparation
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references