7UBU

Crystal structure of ZMET2 in complex with hemimethylated CAG DNA and a histone H3Kc9me2 peptide

Summary for 7UBU

• Entry DOI: 10.2210/pdb7ubu/pdb
• Descriptor: DNA (cytosine-5)-methyltransferase 1, Histone H3.2, 5MC SSDNA, ... (6 entities in total)
• Functional Keywords: dna methyltransferase, complex, dna binding protein, transferase, transferase-dna complex, transferase/dna
• Biological source: Zea mays; More
• Total number of polymer chains: 5
• Total formula weight: 105970.65

Authors

Fang, J.,Song, J. (deposition date: 2022-03-15, release date: 2022-06-08, Last modification date: 2024-10-23)

Primary citation

Fang, J.,Jiang, J.,Leichter, S.M.,Liu, J.,Biswal, M.,Khudaverdyan, N.,Zhong, X.,Song, J.
Mechanistic basis for maintenance of CHG DNA methylation in plants.
Nat Commun, 13:3877-3877, 2022

PubMed Abstract: DNA methylation is an evolutionarily conserved epigenetic mechanism essential for transposon silencing and heterochromatin assembly. In plants, DNA methylation widely occurs in the CG, CHG, and CHH (H = A, C, or T) contexts, with the maintenance of CHG methylation mediated by CMT3 chromomethylase. However, how CMT3 interacts with the chromatin environment for faithful maintenance of CHG methylation is unclear. Here we report structure-function characterization of the H3K9me2-directed maintenance of CHG methylation by CMT3 and its Zea mays ortholog ZMET2. Base-specific interactions and DNA deformation coordinately underpin the substrate specificity of CMT3 and ZMET2, while a bivalent readout of H3K9me2 and H3K18 allosterically stimulates substrate binding. Disruption of the interaction with DNA or H3K9me2/H3K18 led to loss of CMT3/ZMET2 activity in vitro and impairment of genome-wide CHG methylation in vivo. Together, our study uncovers how the intricate interplay of CMT3, repressive histone marks, and DNA sequence mediates heterochromatic CHG methylation.

PubMed: 35790763
DOI: 10.1038/s41467-022-31627-3

Experimental method

X-RAY DIFFRACTION (2.39 Å)