Crystal structure of E.coli TrmJ

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

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This is version 1.2 of the entry. See complete history


Characterization of Two Homologous 2'-O-Methyltransferases Showing Different Specificities for Their tRNA Substrates.

Somme, J.Van Laer, B.Roovers, M.Steyaert, J.Versees, W.Droogmans, L.

(2014) RNA 20: 1257

  • DOI: https://doi.org/10.1261/rna.044503.114
  • Primary Citation of Related Structures:  
    4CND, 4CNE, 4CNF, 4CNG

  • PubMed Abstract: 

    The 2'-O-methylation of the nucleoside at position 32 of tRNA is found in organisms belonging to the three domains of life. Unrelated enzymes catalyzing this modification in Bacteria (TrmJ) and Eukarya (Trm7) have already been identified, but until now, no information is available for the archaeal enzyme. In this work we have identified the methyltransferase of the archaeon Sulfolobus acidocaldarius responsible for the 2'-O-methylation at position 32. This enzyme is a homolog of the bacterial TrmJ. Remarkably, both enzymes have different specificities for the nature of the nucleoside at position 32. While the four canonical nucleosides are substrates of the Escherichia coli enzyme, the archaeal TrmJ can only methylate the ribose of a cytidine. Moreover, the two enzymes recognize their tRNA substrates in a different way. We have solved the crystal structure of the catalytic domain of both enzymes to gain better understanding of these differences at a molecular level.

  • Organizational Affiliation

    Laboratoire de Microbiologie, Université libre de Bruxelles (ULB), 6041 Gosselies, Belgium.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
267Escherichia coli K-12Mutation(s): 1 
Find proteins for P0AE01 (Escherichia coli (strain K12))
Explore P0AE01 
Go to UniProtKB:  P0AE01
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AE01
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PEG

Download Ideal Coordinates CCD File 
C4 H10 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.4α = 90
b = 73.03β = 105.13
c = 53.33γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-02
    Type: Initial release
  • Version 1.1: 2014-07-30
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description