Tyrosyl-tRNA synthetase from Thermus thermophilus complexed with tyrosinol

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 

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This is version 1.4 of the entry. See complete history


Class I Tyrosyl-tRNA Synthetase Has a Class II Mode or tRNA Recognition

Yaremchuk, A.Kriklivyi, I.Tukalo, M.Cusack, S.

(2002) EMBO J 21: 3829

  • DOI: https://doi.org/10.1093/emboj/cdf373
  • Primary Citation of Related Structures:  
    1H3E, 1H3F

  • PubMed Abstract: 

    Bacterial tyrosyl-tRNA synthetases (TyrRS) possess a flexibly linked C-terminal domain of approximately 80 residues, which has hitherto been disordered in crystal structures of the enzyme. We have determined the structure of Thermus thermophilus TyrRS at 2.0 A resolution in a crystal form in which the C-terminal domain is ordered, and confirm that the fold is similar to part of the C-terminal domain of ribosomal protein S4. We have also determined the structure at 2.9 A resolution of the complex of T.thermophilus TyrRS with cognate tRNA(tyr)(G Psi A). In this structure, the C-terminal domain binds between the characteristic long variable arm of the tRNA and the anti-codon stem, thus recognizing the unique shape of the tRNA. The anticodon bases have a novel conformation with A-36 stacked on G-34, and both G-34 and Psi-35 are base-specifically recognized. The tRNA binds across the two subunits of the dimeric enzyme and, remarkably, the mode of recognition of the class I TyrRS for its cognate tRNA resembles that of a class II synthetase in being from the major groove side of the acceptor stem.

  • Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble Outstation, c/o ILL, 156X, F-38042 Grenoble cedex 9, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
432Thermus thermophilus HB27Mutation(s): 0 
Find proteins for P83453 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore P83453 
Go to UniProtKB:  P83453
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP83453
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.794α = 90
b = 111.05β = 90
c = 141.226γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-09-12
    Type: Initial release
  • Version 1.1: 2011-06-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-10-17
    Changes: Data collection, Structure summary
  • Version 1.4: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary