Crystal Structure of dual specific Trm10 construct from Thermococcus kodakaraensis.

Experimental Data Snapshot

  • Resolution: 1.79 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Structural and biochemical analysis of the dual-specificity Trm10 enzyme fromThermococcus kodakaraensisprompts reconsideration of its catalytic mechanism.

Singh, R.K.Feller, A.Roovers, M.Van Elder, D.Wauters, L.Droogmans, L.Versees, W.

(2018) RNA 24: 1080-1092

  • DOI: https://doi.org/10.1261/rna.064345.117
  • Primary Citation of Related Structures:  
    6EMS, 6EMT, 6EMU, 6EMV

  • PubMed Abstract: 

    tRNA molecules get heavily modified post-transcriptionally. The N-1 methylation of purines at position 9 of eukaryal and archaeal tRNA is catalyzed by the SPOUT methyltranferase Trm10. Remarkably, while certain Trm10 orthologs are specific for either guanosine or adenosine, others show a dual specificity. Structural and functional studies have been performed on guanosine- and adenosine-specific enzymes. Here we report the structure and biochemical analysis of the dual-specificity enzyme from Thermococcus kodakaraensis ( Tk Trm10). We report the first crystal structure of a construct of this enzyme, consisting of the N-terminal domain and the catalytic SPOUT domain. Moreover, crystal structures of the SPOUT domain, either in the apo form or bound to S -adenosyl-l-methionine or S -adenosyl-l-homocysteine reveal the conformational plasticity of two active site loops upon substrate binding. Kinetic analysis shows that Tk Trm10 has a high affinity for its tRNA substrates, while the enzyme on its own has a very low methyltransferase activity. Mutation of either of two active site aspartate residues (Asp206 and Asp245) to Asn or Ala results in only modest effects on the N-1 methylation reaction, with a small shift toward a preference for m 1 G formation over m 1 A formation. Only a double D206A/D245A mutation severely impairs activity. These results are in line with the recent finding that the single active-site aspartate was dispensable for activity in the guanosine-specific Trm10 from yeast, and suggest that also dual-specificity Trm10 orthologs use a noncanonical tRNA methyltransferase mechanism without residues acting as general base catalysts.

  • Organizational Affiliation

    Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA (guanine(9)-/adenine(9)-N1)-methyltransferase197Thermococcus kodakarensisMutation(s): 1 
Gene Names: TK0422
EC: (PDB Primary Data), (PDB Primary Data)
Find proteins for Q5JD38 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JD38 
Go to UniProtKB:  Q5JD38
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5JD38
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on TRS

Download Ideal Coordinates CCD File 
C4 H12 N O3
Query on GOL

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A]
C3 H8 O3
Query on ACT

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
C2 H3 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.79 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.262α = 90
b = 62.262β = 90
c = 203.51γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Fonds voor Wetenschappelijk Onderzoek (FWO)Belgium--

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-13
    Type: Initial release
  • Version 1.1: 2018-07-25
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description