The structure of DNA-bound human topoisomerase II alpha: Conformational mechanisms for coordinating inter-subunit interactions with DNA cleavage

Timothy J. Wendorff, Bryan H. Schmidt, Pauline Heslop, Caroline A. Austin, James M. Berger

Research output: Contribution to journalArticlepeer-review

Abstract

Type II topoisomerases are required for the management of DNA superhelicity and chromosome segregation, and serve as frontline targets for a variety of small-molecule therapeutics. To better understand how these enzymes act in both contexts, we determined the 2.9-Å-resolution structure of the DNA cleavage core of human topoisomerase IIα (TOP2A) bound to a doubly nicked, 30-bp duplex oligonucleotide. In accord with prior biochemical and structural studies, TOP2A significantly bends its DNA substrate using a bipartite, nucleolytic center formed at an N-terminal dimerization interface of the cleavage core. However, the protein also adopts a global conformation in which the second of its two inter-protomer contact points, one at the C-terminus, has separated. This finding, together with comparative structural analyses, reveals that the principal site of DNA engagement undergoes highly quantized conformational transitions between distinct binding, cleavage, and drug-inhibited states that correlate with the control of subunit-subunit interactions. Additional consideration of our TOP2A model in light of an etoposide-inhibited complex of human topoisomerase IIβ (TOP2B) suggests possible modification points for developing paralog-specific inhibitors to overcome the tendency of topoisomerase II-targeting chemotherapeutics to generate secondary malignancies.

Original languageEnglish (US)
Pages (from-to)109-124
Number of pages16
JournalJournal of molecular biology
Volume424
Issue number3-4
DOIs
StatePublished - Dec 7 2012
Externally publishedYes

Keywords

  • allostery
  • chemotherapeutics
  • double-strand DNA breaks
  • protein-drug interactions
  • type IIA topoisomerase

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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