4ONJ

Crystal structure of the catalytic domain of ntDRM

Summary for 4ONJ

• Entry DOI: 10.2210/pdb4onj/pdb
• Related: 4ONQ
• Descriptor: DNA methyltransferase, SINEFUNGIN (2 entities in total)
• Functional Keywords: dna methyltransferase, transferase-transferase inhibitor complex, transferase/transferase inhibitor
• Biological source: Nicotiana tabacum (tobacco)
• Total number of polymer chains: 2
• Total formula weight: 81779.28

Authors

Du, J.,Patel, D.J. (deposition date: 2014-01-28, release date: 2014-06-04, Last modification date: 2024-02-28)

Primary citation

Zhong, X.,Du, J.,Hale, C.J.,Gallego-Bartolome, J.,Feng, S.,Vashisht, A.A.,Chory, J.,Wohlschlegel, J.A.,Patel, D.J.,Jacobsen, S.E.
Molecular Mechanism of Action of Plant DRM De Novo DNA Methyltransferases.
Cell(Cambridge,Mass.), 157:1050-1060, 2014

PubMed Abstract: 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.

PubMed: 24855943
DOI: 10.1016/j.cell.2014.03.056

Experimental method

X-RAY DIFFRACTION (2.807 Å)