1IVS

CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.248 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.-I.Shimada, A.Vassylyev, D.G.Yokoyama, S.

(2003) RNA 9: 100-111

  • DOI: 10.1261/rna.2760703
  • Structures With Same Primary Citation

  • 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.


    Related Citations: 
    • STRUCTURAL BASIS FOR DOUBLE-SIEVE DISCRIMINATION OF L-VALINE FROM L-ISOLEUCINE AND L-THREONINE BY THE COMPLEX OF TRNA(VAL) AND VALYL-TRNA SYNTHETASE
      Fukai, S., Nureki, O., Sekine, S., Shimada, A., Tao, J., Vassylyev, D.G., Yokoyama, S.
      (2000) Cell 103: 793

    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: 2
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
Protein Feature View
  • Reference Sequence

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
tRNA (Val)C, D75N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VAA
Query on VAA

Download CCD File 
A, B
N-[VALINYL]-N'-[ADENOSYL]-DIAMINOSUFONE
C15 H24 N8 O6 S
ILBDFTSSTCBHRF-CYUGOOACSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.248 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 411.81α = 90
b = 411.81β = 90
c = 81.97γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-02-11
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance