crystal structure of apo M. jannashii tyrosyl-tRNA synthetase

Experimental Data Snapshot

  • Resolution: 2.65 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

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Crystal structures of apo wild-type M. jannaschii tyrosyl-tRNA synthetase (TyrRS) and an engineered TyrRS specific for O-methyl-L-tyrosine.

Zhang, Y.Wang, L.Schultz, P.G.Wilson, I.A.

(2005) Protein Sci 14: 1340-1349

  • DOI: https://doi.org/10.1110/ps.041239305
  • Primary Citation of Related Structures:  
    1U7D, 1U7X

  • PubMed Abstract: 

    The Methanococcus jannaschii tRNA(Tyr)/TyrRS pair has been engineered to incorporate unnatural amino acids into proteins in E. coli. To reveal the structural basis for the altered specificity of mutant TyrRS for O-methyl-L-tyrosine (OMeTyr), the crystal structures for the apo wild-type and mutant M. jannaschii TyrRS were determined at 2.66 and 3.0 A, respectively, for comparison with the published structure of TyrRS complexed with tRNA(Tyr) and substrate tyrosine. A large conformational change was found for the anticodon recognition loop 257-263 of wild-type TyrRS upon tRNA binding in order to facilitate recognition of G34 of the anticodon loop through pi-stacking and hydrogen bonding interactions. Loop 133-143, which is close to the tRNA acceptor stem-binding site, also appears to be stabilized by interaction with the tRNA(Tyr). Binding of the substrate tyrosine results in subtle and cooperative movements of the side chains within the tyrosine-binding pocket. In the OMeTyr-specific mutant synthetase structure, the signature motif KMSKS loop and acceptor stem-binding loop 133-143 were surprisingly ordered in the absence of bound ATP and tRNA. The active-site mutations result in altered hydrogen bonding and steric interactions which favor binding of OMeTyr over L-tyrosine. The structure of the mutant and wild-type TyrRS now provide a basis for generating new active-site libraries to evolve synthetases specific for other unnatural amino acids.

  • Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, 10550 Torrey Pines Road, La Jolla, CA 92037, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosyl-tRNA synthetase
A, B
306Methanocaldococcus jannaschiiMutation(s): 0 
Gene Names: tyrS
Find proteins for Q57834 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q57834 
Go to UniProtKB:  Q57834
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ57834
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.65 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.119α = 90
b = 185.292β = 90
c = 95.482γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-05-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Refinement description