Asymmetric T-segment binding and gate dynamics govern the final stages of the type IIA topoisomerase catalytic cycle

Stevanović, Kristina (author), Herlah, Barbara (author), Pavlin, Matic (author), Perdih, Andrej (author)

Type IIA DNA topoisomerases are molecular nanomachines that alter DNA topology during essential cellular processes. The final steps of their catalytic cycle, after translocation of the transported (T-) segment into the C-gate, are still not fully understood. Here, we performed all-atom molecular dynamics simulations of several conformational states of Saccharomyces cerevisiae topoisomerase IIA, each with a T-segment inserted into the C-gate. Bound ATP and ADP nucleotides allosterically modulated the N-gate dynamics, likely stabilizing the dimer and preventing premature dissociation. The T-segment was asymmetrically bound and stabilized within the C-gate by positively charged residues, and this gate remained structurally rigid, highlighting its role as a retention site. The positioning of the T-segment in the C-gate allosterically influenced the G-segment to a straighter geometry that favors religation and release. Our simulations support coordinated release of DNA segments and point to a potentially important role for dynamic communication between the gates in the mechanism. These results provide new insights into the late stages of the catalytic cycle and highlight the intertwined roles of nucleotide binding, DNA topology and coupled protein domain dynamics in regulating this important enzyme.

• Language: English
• Keywords: type IIA DNA topoisomerase, T-segment, C-gate, catalytic cycle, molecular dynamics
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: FFA - Faculty of Pharmacy
• Publication status: Published
• Publication version: Version of Record
• Year: 2025
• Number of pages: 17 str.
• Numbering: Vol. 327, pt. 1, art. 147216
• PID: 20.500.12556/RUL-182652
• UDC: 577
• ISSN on article: 1879-0003
• DOI: 10.1016/j.ijbiomac.2025.147216
• COBISS.SI-ID: 249271555
• Publication date in RUL: 20.05.2026

Record is a part of a journal

• Title: International journal of biological macromolecules
• Shortened title: Int. j. biol. macromol.
• Publisher: Elsevier
• ISSN: 1879-0003
• COBISS.SI-ID: 23180805

Licences

• License: CC BY-NC-ND 4.0, Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
• Link: http://creativecommons.org/licenses/by-nc-nd/4.0/
• Description: The most restrictive Creative Commons license. This only allows people to download and share the work for no commercial gain and for no other purposes.

Secondary language

• Language: Slovenian
• Keywords: biokemija, topoizomeraza IIα, DNK, molekulska dinamika