Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Deep Knot Structure for Construction of Active Site and Cofactor Binding Site of tRNA Modification Enzyme

Nureki, O.Watanabe, K.Fukai, S.Ishii, R.Endo, Y.Hori, H.Yokoyama, S.

(2004) Structure 12: 593-602

  • DOI: https://doi.org/10.1016/j.str.2004.03.003
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The tRNA(Gm18) methyltransferase (TrmH) catalyzes the 2'-O methylation of guanosine 18 (Gua18) of tRNA. We solved the crystal structure of Thermus thermophilus TrmH complexed with S-adenosyl-L-methionine at 1.85 A resolution. The catalytic domain contains a deep trefoil knot, which mutational analyses revealed to be crucial for the formation of the catalytic site and the cofactor binding pocket. The tRNA dihydrouridine(D)-arm can be docked onto the dimeric TrmH, so that the tRNA D-stem is clamped by the N- and C-terminal helices from one subunit while the Gua18 is modified by the other subunit. Arg41 from the other subunit enters the catalytic site and forms a hydrogen bond with a bound sulfate ion, an RNA main chain phosphate analog, thus activating its nucleophilic state. Based on Gua18 modeling onto the active site, we propose that once Gua18 binds, the phosphate group activates Arg41, which then deprotonates the 2'-OH group for methylation.

  • Organizational Affiliation

    Department of Biotechnology, Faculty of Engineering, Ehime University, Matsuyama 790-8577, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA (Gm18) methyltransferase194Thermus thermophilusMutation(s): 0 
Find proteins for Q5SM16 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SM16 
Go to UniProtKB:  Q5SM16
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SM16
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.601α = 90
b = 44.023β = 120.78
c = 56.756γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-05-04
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2013-06-26
    Changes: Derived calculations
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references, Derived calculations