9JOR

structure of phage T4 topoisomerase II central domain bound with DNA

Summary for 9JOR

• Entry DOI: 10.2210/pdb9jor/pdb
• EMDB information: 61683
• Descriptor: DNA topoisomerase medium subunit, DNA topoisomerase large subunit,DNA topoisomerase small subunit, DNA (5'-D(P*TP*GP*TP*GP*TP*GP*TP*AP*TP*AP*TP*AP*TP*AP*CP*AP*CP*AP*TP*AP*TP*AP*TP*A)-3'), ... (5 entities in total)
• Functional Keywords: topoisomerase ii, isomerase
• Biological source: Escherichia phage T4 (Bacteriophage T4); More
• Total number of polymer chains: 6
• Total formula weight: 273758.88

Authors

Chen, Y.T.,Xin, Y.H. (deposition date: 2024-09-25, release date: 2025-10-22, Last modification date: 2026-04-15)

Primary citation

Xin, Y.,Xian, R.,Liu, C.,Zhang, O.,Rao, Z.,Li, X.,Chen, Y.
Direct trapping of the transport-segment DNA by the central domain of type IIA topoisomerases.
Sci Adv, 11:eadw2839-eadw2839, 2025

PubMed Abstract: Type IIA topoisomerases modulate DNA topology by coordinating the cleavage of gate-segment DNA and the passage of transport-segment DNA-a mechanism conserved across species and essential for diverse cellular processes. While gate-segment interactions have been extensively studied, direct structural evidence of transport-segment capture has remained elusive, limiting our understanding of the full catalytic cycle. Here, we present a cryo-electron microscopy structure of the T4 bacteriophage topoisomerase II with a transport-segment DNA bound directly to its central domain. The structure reveals conformational rearrangements in the central domain that accommodate the transport-segment DNA, suggesting an alternative sequence of events in which the enzyme sliding along the loosely bound religated gate segment may precede transport-segment passage through the coiled-coil gate. Supported by mutational and biochemical assays, our findings provide previously unidentified mechanistic insights and open potential avenues for the development of next-generation type IIA topoisomerase inhibitors.

PubMed: 41406217
DOI: 10.1126/sciadv.adw2839

Experimental method

ELECTRON MICROSCOPY (3.09 Å)