SNAP-annotated 5mC-DNA-protein interactions: PDB entry 9v4p

PDB-id

9v4p; DSSR-derived features in text and JSON formats; DNAproDB

Class

gene regulation-DNA

Method

cryo-EM (2.34 Å)

Summary

cryo-EM structure of a. thaliana met1(610-1534) bound covalently to a hemi-mcpg DNA

Reference

Zhang Z, Li W, Liu Y, Chi C, Nan J, Wang C, Zhu Y, Zhao J, Xue Y, Li Y, Wang P, Zhai J, Du J (2025): "Structural insights into plant DNA CG methylation maintenance by MET1." Plant Cell, 37. doi: 10.1093/plcell/koaf244.

Abstract

DNA methylation plays critical roles in eukaryotic gene silencing, genome defense, and the suppression of transposable elements. During DNA replication, DNA methylation is diluted and must therefore be restored through maintenance DNA methylation. In plants, in addition to symmetric CG methylation, non-CG methylation is also abundant, with the maintenance of each DNA methylation pattern employing different pathways. Here, we investigate the molecular basis of CG maintenance methylation by plant METHYLTRANSFERASE 1 (MET1), an ortholog of mammalian DNA Methyltransferase 1 (DNMT1). The cryogenic electron microscopy structure of full-length Arabidopsis (Arabidopsis thaliana) MET1 reveals a unique autoinhibitory mechanism that is distinct from that of DNMT1. The structure of the MET1 catalytic domain in complex with hemimethylated substrate DNA suggests specific recognition of hemimethylated CG DNA and reveals the catalytic mechanism. Overall, our study illuminates the molecular basis of MET1 autoinhibition and its preference for hemimethylated DNA substrates.

• The contacts include paired nucleotides (mostly a G in Watson-Crick G-C pairing) and amino-acids within a 4.5-Å distance cutoff to base atoms of 5mC.
• The structure is oriented in the base reference frame of 5mC, allowing for easy comparison and direct superimposition between entries.
• The black sphere (•) denotes the 5-methyl carbon atom in 5mC.