9V4P

Cryo-EM structure of A. thaliana MET1(610-1534) bound covalently to a hemi-mCpG DNA

Summary for 9V4P

• Entry DOI: 10.2210/pdb9v4p/pdb
• EMDB information: 64782
• Descriptor: DNA (5'-D(*TP*AP*A*TP*GP*AP*CP*AP*TP*AP*(5CM)P*GP*AP*TP*CP*CP*AP*AP*TP*C)-3'), DNA (5'-D(*GP*AP*TP*TP*GP*GP*AP*TP*(C49)P*GP*TP*AP*TP*GP*TP*CP*AP*TP*TP*A)-3'), DNA (cytosine-5)-methyltransferase 1, ... (6 entities in total)
• Functional Keywords: dna methylation, met1, cryo-em structure, epigenetic regulation, gene regulation/dna, gene regulation-dna complex
• Biological source: Arabidopsis thaliana (thale cress); More
• Total number of polymer chains: 3
• Total formula weight: 116466.55

Authors

Zhang, Z.,Li, W.,Liu, Y.,Du, J. (deposition date: 2025-05-24, release date: 2025-11-26)

Primary citation

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.
Structural insights into plant DNA CG methylation maintenance by MET1.
Plant Cell, 37:-, 2025

PubMed 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.

PubMed: 41082561
DOI: 10.1093/plcell/koaf244

Experimental method

ELECTRON MICROSCOPY (2.34 Å)