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

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.

• Authors: Timothy J Wendorff, Bryan H Schmidt, Pauline Heslop, Caroline A Austin, James M Berger
• Journal: Journal of molecular biology (J Mol Biol) Vol. 424 Issue 3-4 Pg. 109-24 (Dec 07 2012) ISSN: 1089-8638 [Electronic] Netherlands
• PMID: 22841979 (Publication Type: Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't, Research Support, U.S. Gov't, Non-P.H.S.)
• Copyright: Copyright © 2012 Elsevier Ltd. All rights reserved.

Chemical References

• Antigens, Neoplasm
• DNA-Binding Proteins
• Poly-ADP-Ribose Binding Proteins
• Protein Subunits
• DNA
• DNA Topoisomerases, Type II
• TOP2A protein, human

Topics

• Antigens, Neoplasm (chemistry, metabolism)
• Crystallography, X-Ray
• DNA (chemistry, metabolism)
• DNA Cleavage
• DNA Topoisomerases, Type II (chemistry, metabolism)
• DNA-Binding Proteins (chemistry, metabolism)
• Humans
• Models, Molecular
• Poly-ADP-Ribose Binding Proteins
• Protein Binding
• Protein Conformation
• Protein Subunits (chemistry, metabolism)