1Y2Q

Crystal structure of the editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A D-amino acid editing module coupled to the translational apparatus in archaea

Dwivedi, S.Kruparani, S.P.Sankaranarayanan, R.

(2005) Nat.Struct.Mol.Biol. 12: 556-557

  • DOI: 10.1038/nsmb943
  • Also Cited By: 2HKZ, 2HL0, 2HL1, 2HL2

  • PubMed Abstract: 
  • We report the crystal structure of an archaea-specific editing domain of threonyl-tRNA synthetase that reveals a marked structural similarity to D-amino acid deacylases found in eubacteria and eukaryotes. The domain can bind D-amino acids despite a l ...

    We report the crystal structure of an archaea-specific editing domain of threonyl-tRNA synthetase that reveals a marked structural similarity to D-amino acid deacylases found in eubacteria and eukaryotes. The domain can bind D-amino acids despite a low sequence identity to other D-amino acid deacylases. These results together indicate the presence of these deacylases in all three kingdoms of life. This underlines an important role they may have played in enforcing homochirality during translation.


    Related Citations: 
    • Cloning, expression, purification, crystallization and preliminary X-ray crystallographic investigations of a unique editing domain from archaebacteria
      Dwivedi, S.,Kruparani, S.P.,Sankaranarayanan, R.
      (2004) Acta Crystallogr.,Sect.D 60: 1662


    Organizational Affiliation

    Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Threonyl-tRNA synthetase
A
143Pyrococcus abyssi (strain GE5 / Orsay)Gene Names: thrS
EC: 6.1.1.3
Find proteins for Q9UZ14 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9UZ14
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.205 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 61.752α = 90.00
b = 61.752β = 90.00
c = 64.894γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-06-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance