Substrate-mediated proton relay mechanism for the religation reaction in topoisomerase II

Abstract

The DNA religation reaction of yeast type II topoisomerase (topo II) was investigated to elucidate its metal-dependent general acid/base catalysis. Quantum mechanical/molecular mechanical calculations were performed for the topo II religation reaction, and the proton transfer pathway was examined. We found a substrate-mediated proton transfer of the topo II religation reaction, which involves the 3′ OH nucleophile, the reactive phosphate, water, Arg781, and Tyr782. Metal A stabilizes the transition states, which is consistent with a two-metal mechanism in topo II. This pathway may be required for the cleavage/religation reaction of topo IA and II and will provide a general explanation for the catalytic mechanism in the topo IA and II.

Keywords:

• topoisomerase II
• QM/MM study
• proton transfer
• catalytic mechanism
• DNA religation

Acknowledgments

This research has been supported by (1) “Interdisciplinary Computational Science Program” in Center for Computational Sciences, University of Tsukuba, (2) “Initiative on Promotion of Supercomputing for Young Researchers” in Supercomputing Division, Information Technology Center, The University of Tokyo, and (3) the Supercomputer Center, Institute for Solid State Physics, University of Tokyo. We also deeply appreciate EPCC and EPSRC for providing us with HECToR computer resources to help our early recovery from the Great East Japan Earthquake disaster in 2011.