6FDF | pdb_00006fdf

Crystal structure of S. pombe Dnmt2 methyltransferase

PDB DOI: https://doi.org/10.2210/pdb6FDF/pdb

Classification: TRANSFERASE
Organism(s): Schizosaccharomyces pombe
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-12-22 Released: 2018-06-20
Deposition Author(s): Johannsson, S., Neumann, P., Ficner, R.
Funding Organization(s): German Research Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.195 (Depositor), 0.198 (DCC)
R-Value Work:
0.174 (Depositor), 0.177 (DCC)
R-Value Observed:
0.174 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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

PubMed: 29892076 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41598-018-27118-5
Primary Citation Related Structures:
6FDF

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.

Macromolecule Content

Total Structure Weight: 155.75 kDa
Atom Count: 11,492
Modeled Residue Count: 1,269
Deposited Residue Count: 1,336
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (cytosine(38)-C(5))-methyltransferase	A, B, C, D	334	Schizosaccharomyces pombe	Mutation(s): 0 Gene Names: pmt1, SPBC19C2.02 EC: 2.1.1.204
UniProt
Find proteins for P40999 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore P40999 Go to UniProtKB: P40999
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40999
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain N [auth C] SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain N [auth C] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain N [auth C] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B], N [auth C], Q [auth D]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain Q [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain P [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain P [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain O [auth C] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain P [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D]