Mechanistic insights from structure of Mycobacterium smegmatis topoisomerase I with ssDNA bound to both N- and C-terminal domains

Authors

Nan Cao, Department of Chemistry and Biochemistry, Florida International UniversityFollow
Kemin Tan, Structural Biology Center, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory
Xiaobing Zuo, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory
Thirunavukkarasu Annamalai, Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.Follow
Yuk-Ching Tse-Dinh, Department of Chemistry and Biochemistry, Florida International UniversityFollow

Date of this Version

5-7-2020

Document Type

Article

Rights

default

Abstract

Type IA topoisomerases interact with G-strand and T-strand ssDNA to regulate DNA topology. However, simultaneous binding of two ssDNA segments to a type IA topoisomerase has not been observed previously. We report here the crystal structure of a type IA topoisomerase with ssDNA segments bound in opposite polarity to the N- and C-terminal domains. Titration of small ssDNA oligonucleotides to Mycobacterium smegmatis topoisomerase I with progressive C-terminal deletions showed that the C-terminal region has higher affinity for ssDNA than the N-terminal active site. This allows the C-terminal domains to capture one strand of underwound negatively supercoiled DNA substrate first and position the N-terminal domains to bind and cleave the opposite strand in the relaxation reaction. Efficiency of negative supercoiling relaxation increases with the number of domains that bind ssDNA primarily with conserved aromatic residues and possibly with assistance from polar/basic residues. A comparison of bacterial topoisomerase I structures showed that a conserved transesterification unit (N-terminal toroid structure) for cutting and rejoining of a ssDNA strand can be combined with two different types of C-terminal ssDNA binding domains to form diverse bacterial topoisomerase I enzymes that are highly efficient in their physiological role of preventing excess negative supercoiling in the genome.

DOI

10.1093/nar/gkaa201

Identifier

32232337

Comments

(C) The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 License.

Recommended Citation

Cao N, Tan K, Zuo X, Annamalai T, Tse-Dinh YC. Mechanistic insights from structure of Mycobacterium smegmatis topoisomerase I with ssDNA bound to both N- and C-terminal domains. Nucleic Acids Res. 2020 May 7;48(8):4448-4462. doi: 10.1093/nar/gkaa201. PMID: 32232337; PMCID: PMC7192597.