9O7O

CryoEM structure of M. mazei topoisomerase VI(A-E342Q)-minicircle DNA complex in asymmetric state

Summary for 9O7O

• Entry DOI: 10.2210/pdb9o7o/pdb
• EMDB information: 70206
• Descriptor: Type 2 DNA topoisomerase 6 subunit A, Type 2 DNA topoisomerase 6 subunit B, Minicircle DNA (arbitrary model sequence), ... (6 entities in total)
• Functional Keywords: toprim, ghkl, minicircle dna, spo11, isomerase-dna complex, isomerase/dna
• Biological source: Methanosarcina mazei Go1; More
• Total number of polymer chains: 6
• Total formula weight: 268831.74

Authors

Richman, D.E.,Berger, J.M. (deposition date: 2025-04-15, release date: 2026-02-25, Last modification date: 2026-03-04)

Primary citation

Richman, D.E.,Wendorff, T.J.,Rashid, F.,Beck, C.,Yan, Q.,Johnson, H.R.,Eckerty, R.A.,Fogg, J.M.,Baker, M.L.,Zechiedrich, L.,Berger, J.M.
Supercoiled DNA recognition and cleavage control in topoisomerase VI.
Nat Commun, 2026

PubMed Abstract: Type II topoisomerases modulate DNA supercoiling and resolve chromosome entanglements. Type IIB topoisomerases, exemplified by DNA topoisomerase VI (Top6), are used by plants and archaea to support endoreduplication and cell proliferation, respectively; homologs of Top6 further serve to initiate meiotic recombination in eukaryotes and constitute the nuclease portion of MksBEFG/Wadjet/Gabija bacterial defense systems. To understand how such factors act upon DNA, we determine structures of Top6 bound to supercoiled minicircles in cleaved and uncleaved states using single-particle electron cryo-microscopy. The structures show that Top6 binds a curved 74 bp region of the supercoiled minicircle DNA and that it cuts at a distinct deformability motif, explaining its preference for supercoiled substrates and highlighting the role of DNA plasticity in cleavage site selection. Dynamic protein-DNA interactions and an unanticipated tension sensor help recognize bent DNA and couple ATPase disposition to cleavage state activation. Our observations explain how DNA recognition and cleavage by type II topoisomerases are regulated by interdependent structural changes in DNA and the enzyme.

PubMed: 41698922
DOI: 10.1038/s41467-026-69491-0

Experimental method

ELECTRON MICROSCOPY (2.7 Å)