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Review
. 2020 Oct 17;25(20):4769.
doi: 10.3390/molecules25204769.

Mechanism of Type IA Topoisomerases

Tumpa Dasgupta  1   2   3 , Shomita Ferdous  1   2   3 , Yuk-Ching Tse-Dinh  1   2
Affiliations
Review

Mechanism of Type IA Topoisomerases

Tumpa Dasgupta et al. Molecules. .

Abstract

Topoisomerases in the type IA subfamily can catalyze change in topology for both DNA and RNA substrates. A type IA topoisomerase may have been present in a last universal common ancestor (LUCA) with an RNA genome. Type IA topoisomerases have since evolved to catalyze the resolution of topological barriers encountered by genomes that require the passing of nucleic acid strand(s) through a break on a single DNA or RNA strand. Here, based on available structural and biochemical data, we discuss how a type IA topoisomerase may recognize and bind single-stranded DNA or RNA to initiate its required catalytic function. Active site residues assist in the nucleophilic attack of a phosphodiester bond between two nucleotides to form a covalent intermediate with a 5'-phosphotyrosine linkage to the cleaved nucleic acid. A divalent ion interaction helps to position the 3'-hydroxyl group at the precise location required for the cleaved phosphodiester bond to be rejoined following the passage of another nucleic acid strand through the break. In addition to type IA topoisomerase structures observed by X-ray crystallography, we now have evidence from biophysical studies for the dynamic conformations that are required for type IA topoisomerases to catalyze the change in the topology of the nucleic acid substrates.

Keywords: DNA supercoiling; RNA topology; decatenation; topoisomerase; type IA.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Some of the potential topological problems during the life cycle of a positive-sense single-stranded RNA virus that may require the RNA topoisomerase activity of human TOP3B. Genome circularization can be mediated by RNA–RNA interactions and proteins binding to the 5′ and 3′ ends. Decatenation of the catenated circular viral genome by TOP3B is required to remove blocks of (A) viral protein translation, (B) viral RNA transport and packaging. (C) When a translating ribosome or a helicase unwinds a duplex region in a viral RNA hairpin, and if the hairpin is bound to an immobile RNP or cellular matrix, the helical torsion will need to be relaxed by TOP3B. The figure is modified from a published version for potential TOP3B action on mRNA in [29].
Figure 2
Figure 2
Domain arrangement in E. coli topoisomerase I as seen in the crystal structure of the N-terminal core domains (PDB 1ECL) or full-length enzyme (PDB 4RUL). D1: amino acids 4–36, 81–157 colored in pink; D2: amino acids 216–278,405–472 colored in orange; D3: amino acids 279–404 colored in salmon; D4: amino acids 61–80,158–215,473–590 colored in blue; D5: amino acids 591–635 colored in magenta; D6: amino acids 636–706 colored in red; D7: amino acids 707–754 colored in cyan; D8: amino acids 755–795 colored in yellow; helix hairpin linker: amino acids 796–824 colored in gray; D9: amino acids 825–865 colored in green.
Figure 3
Figure 3
Type IA topoisomerase core domains interactions with the G-strand. (A) Active site of the M. tuberculosis topoisomerase I noncovalent complex (PDB 6CQ2) showing an interaction between the catalytic tyrosine and adjacent arginine with the scissile phosphate of the G-strand (in gold). A Mg2+ ion (in green) interacts with the scissile phosphate and TOPRIM acidic residues. (B) Structure of the E. coli topoisomerase I covalent complex (PDB 3PX7) showing the positioning of the G-strand by residues interacting with the G-strand backbone and a cytosine base (shown in the space-filling display) at a distance of four nucleotides from the phosphoryl tyrosine (PTR) formed from the cleavage of the G-strand. (C) Alignment of residues strictly conserved at the active site and type IA topoisomerases including bacterial topoisomerase I, reverse gyrase (RG) and topoisomerase III from prokaryotes and eukaryotes. Species represented include Ec: E. coli, Tm: Thermotoga maritima. Mt: Mycobacterium tuberculosis, Sm: Streptococcus mutans, Af: Archaeoglobus fulgidus, Sc: Saccharomyces cerevisiae, Hs: Homo sapiens. (D) Alignment of residues (shown in red) that are strictly conserved in type IA topoisomerases for interacting with the G-strand backbone. Residues conserved for the specific binding of a cytosine base 4 nucleotides upstream of the scissile phosphate are shown in blue.
Figure 4
Figure 4
Structural motifs found in the C-terminal domains of bacterial topoisomerase I. (A) The Topo_C_ZnRpt motif with the Zn(II) ion coordinated by four cysteines in E. coli topoisomerase I (from PDB 4RUL) and Topo_C_Rpt motif with conserved GxxGPY residues (in the space-filling display) in M. tuberculosis topoisomerase I (from PDB 5UJ1). (B) Comparison of ssDNA binding by the C-terminal domain of E. coli topoisomerase I and M. smegmatis topoisomerase I (from the Supplementary Information of [52]). Conserved aromatic residues from each C-terminal domain form π–π stackings with the nucleotide bases.
Figure 5
Figure 5
Model for the relaxation of supercoiled DNA by bacterial topoisomerase I based on the crystal structures of E. coli and Mycobacteria topoisomerase I. (i) Apo enzyme; (ii) C-terminal domains (green) bind ssDNA as T-strand (red); (iii) ssDNA or G-strand (yellow) binds the N-terminal domains (blue); (iv) Active site tyrosine (red circle) becomes accessible; (v) Cleavage of the G-strand and gate opening; (vi) Passage of T-strand inside the toroid; (vii) Gate closing and trapping of T-strand; (viii) Religation of the G-strand; (ix) Gate opening and release of dsDNA.
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