Crystal Structure of A. aeolicus TrmH/SpoU tRNA modifying enzyme

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.237 

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This is version 1.3 of the entry. See complete history


Structure of a class II TrmH tRNA-modifying enzyme from Aquifex aeolicus.

Pleshe, E.Truesdell, J.Batey, R.T.

(2005) Acta Crystallogr Sect F Struct Biol Cryst Commun 61: 722-728

  • DOI: https://doi.org/10.1107/S1744309105022980
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Biological RNAs contain a variety of post-transcriptional modifications that facilitate their efficient function in the cellular environment. One of the two most common forms of modification is methylation of the 2'-hydroxyl group of the ribose sugar, which is performed by a number of S-adenosylmethionine (SAM) dependent methyltransferases. In bacteria, many of these modifications in tRNA and rRNA are carried out by the alpha/beta-knot superfamily of enzymes, whose SAM-binding pocket is created by a characteristic deep trefoil knot. TrmH, an enzyme found throughout all three kingdoms of life, modifies the universally conserved guanosine 18 position of tRNA. The crystal structure of TrmH from the thermophilic bacterium Aquifex aeolicus has been determined at 1.85 A resolution using data collected from a synchrotron-radiation source. The protein reveals a fold typical of members of the SpoU clan of proteins, a subfamily of the alpha/beta-knot superfamily, with alpha-helical extensions at the N- and C-termini that are likely to be involved in tRNA binding.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Colorado, Campus Box 215, Boulder, CO 80309-0215, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA (Guanosine-2'-O-)-methyltransferase211Aquifex aeolicusMutation(s): 0 
Gene Names: trmHspoU
Find proteins for O67577 (Aquifex aeolicus (strain VF5))
Explore O67577 
Go to UniProtKB:  O67577
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO67577
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.85 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.237 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.658α = 90
b = 66.658β = 90
c = 194.884γ = 120
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: 2005-08-09
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description