Crystal structure of the non-discriminating and archaeal-type aspartyl-tRNA synthetase from Thermus thermophilus

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 

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Non-discriminating and discriminating aspartyl-tRNA synthetases differ in the anticodon-binding domain

Charron, C.Roy, H.Blaise, M.Giege, R.Kern, D.

(2003) EMBO J 22: 1632-1643

  • DOI: https://doi.org/10.1093/emboj/cdg148
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    In most organisms, tRNA aminoacylation is ensured by 20 aminoacyl-tRNA synthetases (aaRSs). In eubacteria, however, synthetases can be duplicated as in Thermus thermophilus, which contains two distinct AspRSs. While AspRS-1 is specific, AspRS-2 is non-discriminating and aspartylates tRNA(Asp) and tRNA(Asn). The structure at 2.3 A resolution of AspRS-2, the first of a non-discriminating synthetase, was solved. It differs from that of AspRS-1 but has resemblance to that of discriminating and archaeal AspRS from Pyrococcus kodakaraensis. The protein presents non-conventional features in its OB-fold anticodon-binding domain, namely the absence of a helix inserted between two beta-strands of this fold and a peculiar L1 loop differing from the large loops known to interact with tRNA(Asp) identity determinant C36 in conventional AspRSs. In AspRS-2, this loop is small and structurally homologous to that in AsnRSs, including conservation of a proline. In discriminating Pyrococcus AspRS, the L1 loop, although small, lacks this proline and is not superimposable with that of AspRS-2 or AsnRS. Its particular status is demonstrated by a loop-exchange experiment that renders the Pyrococcus AspRS non-discriminating.

  • Organizational Affiliation

    Département Mécanismes et Macromolécules de la Synthèse Protéique et Cristallogenèse, UPR 9002, 15 rue René Descartes, 67084 Strasbourg cedex, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
aspartyl-tRNA synthetase 2
A, B
422Thermus thermophilusMutation(s): 0 
Find proteins for Q5SIC2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SIC2 
Go to UniProtKB:  Q5SIC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SIC2
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.361α = 90
b = 122.554β = 90
c = 167.137γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-04-08
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references