9M5X

Cryo-EM structure of Arabidopsis thaliana MET1

Summary for 9M5X

• Entry DOI: 10.2210/pdb9m5x/pdb
• EMDB information: 63652
• Descriptor: DNA (cytosine-5)-methyltransferase 1, ZINC ION (2 entities in total)
• Functional Keywords: dna methylation, structural protein
• Biological source: Arabidopsis thaliana (thale cress)
• Total number of polymer chains: 1
• Total formula weight: 173179.85

Authors

Kikuchi, A.,Arita, K. (deposition date: 2025-03-06, release date: 2025-08-20, Last modification date: 2025-10-08)

Primary citation

Kikuchi, A.,Nishiyama, A.,Chiba, Y.,Nakanishi, M.,To, T.K.,Arita, K.
Cryo-EM reveals evolutionarily conserved and distinct structural features of plant CG maintenance methyltransferase MET1.
Nat Commun, 16:8524-8524, 2025

PubMed Abstract: DNA methylation is essential for genomic function and transposable element silencing. In plants, DNA methylation occurs in CG, CHG, and CHH contexts (where H = A, T, or C), with the maintenance of CG methylation mediated by the DNA methyltransferase MET1. The molecular mechanism by which MET1 maintains CG methylation, however, remains unclear. Here, we report cryogenic electron microscopy structures of Arabidopsis thaliana MET1. We find that the methyltransferase domain of MET1 specifically methylates hemimethylated DNA in vitro. The structure of MET1 bound to hemimethylated DNA reveals the activation mechanism of MET1 resembling that of mammalian DNMT1. Curiously, the structure of apo-MET1 shows an autoinhibitory state distinct from that of DNMT1, where the RFTS2 domain and the connecting linker inhibit DNA binding. The autoinhibition of MET1 is relieved upon binding of a potential activator, ubiquitinated histone H3. Taken together, our structural analysis demonstrates both conserved and distinct molecular mechanisms regulating CG maintenance methylation in plant and animal DNA methyltransferases.

PubMed: 41006297
DOI: 10.1038/s41467-025-63765-9

Experimental method

ELECTRON MICROSCOPY (3.21 Å)