Crystal structure of S. pombe Dnmt2 methyltransferase

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 

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Structural insights into the stimulation of S. pombe Dnmt2 catalytic efficiency by the tRNA nucleoside queuosine.

Johannsson, S.Neumann, P.Wulf, A.Welp, L.M.Gerber, H.D.Krull, M.Diederichsen, U.Urlaub, H.Ficner, R.

(2018) Sci Rep 8: 8880-8880

  • DOI: https://doi.org/10.1038/s41598-018-27118-5
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Dnmt2 methylates cytosine at position 38 of tRNA Asp in a variety of eukaryotic organisms. A correlation between the presence of the hypermodified nucleoside queuosine (Q) at position 34 of tRNA Asp and the Dnmt2 dependent C38 methylation was recently found in vivo for S. pombe and D. discoideum. We demonstrate a direct effect of the Q-modification on the methyltransferase catalytic efficiency in vitro, as V max /K 0.5 of purified S. pombe Dnmt2 shows an increase for in vitro transcribed tRNA Asp containing Q34 to 6.27 ∗ 10 -3  s -1  µM -1 compared to 1.51 ∗ 10 -3  s -1  µM -1 for the unmodified substrate. Q34tRNA Asp exhibits an only slightly increased affinity for Dnmt2 in comparison to unmodified G34tRNA. In order to get insight into the structural basis for the Q-dependency, the crystal structure of S. pombe Dnmt2 was determined at 1.7 Å resolution. It closely resembles the known structures of human and E. histolytica Dnmt2, and contains the entire active site loop. The interaction with tRNA was analyzed by means of mass-spectrometry using UV cross-linked Dnmt2-tRNA complex. These cross-link data and computational docking of Dnmt2 and tRNA Asp reveal Q34 positioned adjacent to the S-adenosylmethionine occupying the active site, suggesting that the observed increase of Dnmt2 catalytic efficiency by queuine originates from optimal positioning of the substrate molecules and residues relevant for methyl transfer.

  • Organizational Affiliation

    Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, 37077, Göttingen, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA (cytosine(38)-C(5))-methyltransferase
A, B, C, D
334Schizosaccharomyces pombeMutation(s): 0 
Gene Names: pmt1SPBC19C2.02
Find proteins for P40999 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore P40999 
Go to UniProtKB:  P40999
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40999
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SAH

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
N [auth C],
Q [auth D]
C14 H20 N6 O5 S
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
K [auth B]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
K [auth B],
L [auth B],
M [auth B],
O [auth C],
P [auth C],
R [auth D],
S [auth D]
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.817α = 90
b = 114.781β = 131.05
c = 113.759γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research FoundationGermanySPP1784

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Data collection, Database references