1ILE | pdb_00001ile

ISOLEUCYL-TRNA SYNTHETASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.298 (Depositor) 
  • R-Value Work: 
    0.222 (Depositor) 
  • R-Value Observed: 
    0.222 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1ILE

This is version 1.3 of the entry. See complete history

Literature

Enzyme structure with two catalytic sites for double-sieve selection of substrate.

Nureki, O.Vassylyev, D.G.Tateno, M.Shimada, A.Nakama, T.Fukai, S.Konno, M.Hendrickson, T.L.Schimmel, P.Yokoyama, S.

(1998) Science 280: 578-582

  • DOI: https://doi.org/10.1126/science.280.5363.578
  • Primary Citation Related Structures: 
    1ILE

  • PubMed Abstract: 

    High-fidelity transfers of genetic information in the central dogma can be achieved by a reaction called editing. The crystal structure of an enzyme with editing activity in translation is presented here at 2.5 angstroms resolution. The enzyme, isoleucyl-transfer RNA synthetase, activates not only the cognate substrate L-isoleucine but also the minimally distinct L-valine in the first, aminoacylation step. Then, in a second, "editing" step, the synthetase itself rapidly hydrolyzes only the valylated products. For this two-step substrate selection, a "double-sieve" mechanism has already been proposed. The present crystal structures of the synthetase in complexes with L-isoleucine and L-valine demonstrate that the first sieve is on the aminoacylation domain containing the Rossmann fold, whereas the second, editing sieve exists on a globular beta-barrel domain that protrudes from the aminoacylation domain.


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

Macromolecule Content 

  • Total Structure Weight: 94.81 kDa 
  • Atom Count: 7,022 
  • Modeled Residue Count: 821 
  • Deposited Residue Count: 821 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ISOLEUCYL-TRNA SYNTHETASE821Thermus thermophilus HB8Mutation(s): 0 
EC: 6.1.1.5
UniProt
Find proteins for P56690 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P56690 
Go to UniProtKB:  P56690
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56690
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.298 (Depositor) 
  • R-Value Work:  0.222 (Depositor) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.1α = 90
b = 94.8β = 126.3
c = 126.5γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 1999-04-13
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary