TY - JOUR
T1 - The structure of DNA-bound human topoisomerase II alpha
T2 - Conformational mechanisms for coordinating inter-subunit interactions with DNA cleavage
AU - Wendorff, Timothy J.
AU - Schmidt, Bryan H.
AU - Heslop, Pauline
AU - Austin, Caroline A.
AU - Berger, James M.
N1 - Funding Information:
The authors would like to thank members of the Berger group for helpful discussions. This work was supported by a National Science Foundation graduate research fellowship to T.J.W. (DGE 1106400), an Leukaemia Lymphoma Research grant to C.A.A. (07038), and a National Cancer Institute-sponsored RO1 to J.M.B. (CA077373).
PY - 2012/12/7
Y1 - 2012/12/7
N2 - 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.
AB - 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.
KW - allostery
KW - chemotherapeutics
KW - double-strand DNA breaks
KW - protein-drug interactions
KW - type IIA topoisomerase
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U2 - 10.1016/j.jmb.2012.07.014
DO - 10.1016/j.jmb.2012.07.014
M3 - Article
C2 - 22841979
AN - SCOPUS:84869097457
SN - 0022-2836
VL - 424
SP - 109
EP - 124
JO - Journal of molecular biology
JF - Journal of molecular biology
IS - 3-4
ER -