4ONQ image
Deposition Date 2014-01-28
Release Date 2014-06-04
Last Version Date 2023-09-20
Entry Detail
PDB ID:
4ONQ
Title:
Crystal structure of ntDRM E283S/R309S/F310S/Y590S/D591S mutant
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.50 Å
R-Value Free:
0.23
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 65
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:DNA methyltransferase
Gene (Uniprot):NtDRM1
Mutations:E283S/R309S/F310S/Y590S/D591S
Chain IDs:A, B
Chain Length:357
Number of Molecules:2
Biological Source:Nicotiana tabacum
Ligand Molecules
Primary Citation
Molecular Mechanism of Action of Plant DRM De Novo DNA Methyltransferases.
Cell(Cambridge,Mass.) 157 1050 1060 (2014)
PMID: 24855943 DOI: 10.1016/j.cell.2014.03.056

Abstact

DNA methylation is a conserved epigenetic gene-regulation mechanism. DOMAINS REARRANGED METHYLTRANSFERASE (DRM) is a key de novo methyltransferase in plants, but how DRM acts mechanistically is poorly understood. Here, we report the crystal structure of the methyltransferase domain of tobacco DRM (NtDRM) and reveal a molecular basis for its rearranged structure. NtDRM forms a functional homodimer critical for catalytic activity. We also show that Arabidopsis DRM2 exists in complex with the small interfering RNA (siRNA) effector ARGONAUTE4 (AGO4) and preferentially methylates one DNA strand, likely the strand acting as the template for RNA polymerase V-mediated noncoding RNA transcripts. This strand-biased DNA methylation is also positively correlated with strand-biased siRNA accumulation. These data suggest a model in which DRM2 is guided to target loci by AGO4-siRNA and involves base-pairing of associated siRNAs with nascent RNA transcripts.

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Primary Citation of related structures