1IYW

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4 Å
  • R-Value Free: 0.383 
  • R-Value Work: 0.316 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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

  • Primary Citation of Related Structures:  

  • 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( ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Valyl-tRNA Synthetase
A, B
862Thermus thermophilusMutation(s): 0 
Gene Names: valS
EC: 6.1.1.9
Find proteins for P96142 (Thermus thermophilus)
Go to UniProtKB:  P96142
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4 Å
  • R-Value Free: 0.383 
  • R-Value Work: 0.316 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 186.562α = 90.00
b = 207.328β = 90.00
c = 59.235γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-02-07
    Type: Experimental preparation