6FDF

Crystal structure of S. pombe Dnmt2 methyltransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.697 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

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: 10.1038/s41598-018-27118-5

  • PubMed Abstract: 
  • Dnmt2 methylates cytosine at position 38 of tRNA <sup>Asp </sup> in a variety of eukaryotic organisms. A correlation between the presence of the hypermodified nucleoside queuosine (Q) at position 34 of tRNA <sup>Asp </sup> and the Dnmt2 dependent C38 ...

    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. rficner@uni-goettingen.de.,Bioanalytical Mass Spectrometry Research Group, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany.,Institut für Pharmazeutische Chemie der Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany.,Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, 37077, Göttingen, Germany.,Bioanalytics, Department of Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Straße 40, 37075, Göttingen, Germany.,Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstrasse 2, 37077, Göttingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
tRNA (cytosine(38)-C(5))-methyltransferase
A, B, C, D
334Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: pmt1
EC: 2.1.1.204
Find proteins for P40999 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  P40999
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
SAH
Query on SAH

Download SDF File 
Download CCD File 
A, B, C, D
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.697 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.174 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 153.817α = 90.00
b = 114.781β = 131.05
c = 113.759γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySPP1784

Revision History 

  • Version 1.0: 2018-06-20
    Type: Initial release