6PCM

Crystal Structure of Mycobacterium smegmatis Topoisomerase I with ssDNA bound to both N- and C-terminal domains

Summary for 6PCM

• Entry DOI: 10.2210/pdb6pcm/pdb
• Descriptor: DNA topoisomerase 1, DNA (5'-D(P*AP*GP*TP*GP*AP*GP*CP*GP*AP*GP*CP*TP*TP*CP*CP*GP*CP*TP*TP*GP*AP*CP*TP*T)-3'), SULFATE ION (3 entities in total)
• Functional Keywords: topoisomerase i, ss dna binding, n-terminal domain, c-terminal domain, isomerase-dna complex, isomerase/dna
• Biological source: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155); More
• Total number of polymer chains: 4
• Total formula weight: 202624.23

Authors

Tan, K.,Cao, N.,Tse-Dinh, Y.C. (deposition date: 2019-06-17, release date: 2020-03-25, Last modification date: 2023-10-11)

Primary citation

Cao, N.,Tan, K.,Zuo, X.,Annamalai, T.,Tse-Dinh, Y.C.
Mechanistic insights from structure of Mycobacterium smegmatis topoisomerase I with ssDNA bound to both N- and C-terminal domains.
Nucleic Acids Res., 48:4448-4462, 2020

PubMed 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.

PubMed: 32232337
DOI: 10.1093/nar/gkaa201

Experimental method

X-RAY DIFFRACTION (3.107 Å)