Crystal structure of Trm14 from Pyrococcus furiosus in complex with S-adenosylmethionine

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

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Crystal structures of the tRNA:m2G6 methyltransferase Trm14/TrmN from two domains of life.

Fislage, M.Roovers, M.Tuszynska, I.Bujnicki, J.M.Droogmans, L.Versees, W.

(2012) Nucleic Acids Res 40: 5149-5161

  • DOI: https://doi.org/10.1093/nar/gks163
  • Primary Citation of Related Structures:  
    3TLJ, 3TM4, 3TM5, 3TMA

  • PubMed Abstract: 

    Methyltransferases (MTases) form a major class of tRNA-modifying enzymes needed for the proper functioning of tRNA. Recently, RNA MTases from the TrmN/Trm14 family that are present in Archaea, Bacteria and Eukaryota have been shown to specifically modify tRNA(Phe) at guanosine 6 in the tRNA acceptor stem. Here, we report the first X-ray crystal structures of the tRNA m(2)G6 (N(2)-methylguanosine) MTase (TTC)TrmN from Thermus thermophilus and its ortholog (Pf)Trm14 from Pyrococcus furiosus. Structures of (Pf)Trm14 were solved in complex with the methyl donor S-adenosyl-l-methionine (SAM or AdoMet), as well as the reaction product S-adenosyl-homocysteine (SAH or AdoHcy) and the inhibitor sinefungin. (TTC)TrmN and (Pf)Trm14 consist of an N-terminal THUMP domain fused to a catalytic Rossmann-fold MTase (RFM) domain. These results represent the first crystallographic structure analysis of proteins containing both THUMP and RFM domain, and hence provide further insight in the contribution of the THUMP domain in tRNA recognition and catalysis. Electrostatics and conservation calculations suggest a main tRNA binding surface in a groove between the THUMP domain and the MTase domain. This is further supported by a docking model of TrmN in complex with tRNA(Phe) of T. thermophilus and via site-directed mutagenesis.

  • Organizational Affiliation

    VIB Department of Structural Biology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA (guanine N2-)-methyltransferase Trm14
A, B
373Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: PF1002
EC: 2.1.1
Find proteins for Q8U248 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U248 
Go to UniProtKB:  Q8U248
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8U248
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.08α = 90
b = 45.17β = 91.79
c = 121.43γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-14
    Type: Initial release
  • Version 1.1: 2012-05-09
    Changes: Other
  • Version 1.2: 2012-10-03
    Changes: Database references
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description