Crystal structure of Methanocaldococcus jannaschii Trm5 in complex with adenosine

Experimental Data Snapshot

  • Resolution: 3.05 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.214 

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Differentiating analogous tRNA methyltransferases by fragments of the methyl donor.

Lahoud, G.Goto-Ito, S.Yoshida, K.Ito, T.Yokoyama, S.Hou, Y.M.

(2011) RNA 17: 1236-1246

  • DOI: https://doi.org/10.1261/rna.2706011
  • Primary Citation of Related Structures:  
    3AXZ, 3AY0

  • PubMed Abstract: 

    Bacterial TrmD and eukaryotic-archaeal Trm5 form a pair of analogous tRNA methyltransferase that catalyze methyl transfer from S-adenosyl methionine (AdoMet) to N(1) of G37, using catalytic motifs that share no sequence or structural homology. Here we show that natural and synthetic analogs of AdoMet are unable to distinguish TrmD from Trm5. Instead, fragments of AdoMet, adenosine and methionine, are selectively inhibitory of TrmD rather than Trm5. Detailed structural information of the two enzymes in complex with adenosine reveals how Trm5 escapes targeting by adopting an altered structure, whereas TrmD is trapped by targeting due to its rigid structure that stably accommodates the fragment. Free energy analysis exposes energetic disparities between the two enzymes in how they approach the binding of AdoMet versus fragments and provides insights into the design of inhibitors selective for TrmD.

  • Organizational Affiliation

    Thomas Jefferson University, Department of Biochemistry and Molecular Biology, Philadelphia, Pennsylvania 19107, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein MJ0883
A, B
336Methanocaldococcus jannaschiiMutation(s): 0 
Gene Names: MJ0883Trm5
Find proteins for Q58293 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q58293 
Go to UniProtKB:  Q58293
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ58293
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.05 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.49α = 90
b = 67.127β = 93.75
c = 92.239γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data 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: 2011-08-17
    Type: Initial release
  • Version 1.1: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description