1GAX

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 793-803


  • PubMed Abstract: 
  • Valyl-tRNA synthetase (ValRS) strictly discriminates the cognate L-valine from the larger L-isoleucine and the isosteric L-threonine by the tRNA-dependent "double sieve" mechanism. In this study, we determined the 2.9 A crystal structure of a complex ...

    Valyl-tRNA synthetase (ValRS) strictly discriminates the cognate L-valine from the larger L-isoleucine and the isosteric L-threonine by the tRNA-dependent "double sieve" mechanism. In this study, we determined the 2.9 A crystal structure of a complex of Thermus thermophilus ValRS, tRNA(Val), and an analog of the Val-adenylate intermediate. The analog is bound in a pocket, where Pro(41) allows accommodation of the Val and Thr moieties but precludes the Ile moiety (the first sieve), on the aminoacylation domain. The editing domain, which hydrolyzes incorrectly synthesized Thr-tRNA(Val), is bound to the 3' adenosine of tRNA(Val). A contiguous pocket was found to accommodate the Thr moiety, but not the Val moiety (the second sieve). Furthermore, another Thr binding pocket for Thr-adenylate hydrolysis was suggested on the editing domain.


    Organizational Affiliation

    Department of Biophysics and Biochemistry Graduate School of Science The University of Tokyo 7-3-1 Hongo Bunkyo-ku, 113-0033, Tokyo, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
VALYL-TRNA SYNTHETASE
A, B
862Thermus thermophilusGene Names: valS
EC: 6.1.1.9
Find proteins for P96142 (Thermus thermophilus)
Go to UniProtKB:  P96142
Entity ID: 1
MoleculeChainsLengthOrganism
TRNA(VAL)C,D75N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VAA
Query on VAA

Download SDF File 
Download CCD File 
A, B
N-[VALINYL]-N'-[ADENOSYL]-DIAMINOSUFONE
C15 H24 N8 O6 S
ILBDFTSSTCBHRF-CYUGOOACSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.245 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 411.810α = 90.00
b = 411.810β = 90.00
c = 81.970γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
MLPHAREphasing
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-12-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance