Figure 1. The reactions carried out by topoisomerases. (a) Supercoiling/relaxation. (b) Catenation/decatenation. (c) Knotting/unknotting. Double-stranded DNA is represented as a solid tube.

Figure 2. Three-dimensional structures of topoisomerase fragments. The three-dimensional structures are represented as ribbons following the protein main chains. The active-site tyrosine residues (see text) are shown as yellow spheres, and monomer subunits of dimeric structures are coloured red and blue. (a) 67-kDa Escherichia coli topoisomerase I fragment. The domains are coloured arbitrarily to emphasize the two halves of the molecule. (b) 43 kDa N-terminal ATPase fragment of E. coli GyrB. The 5¢-adenylyl-,-imidodiphosphate (ADPNP) molecules are indicated in yellow. (c) 92-kDa fragment of Saccharomyces cerevisiae topoisomerase II. (d) 59-kDa N-terminal fragment of E. coli GyrA. The figures were generated using RasMol 2.6 from crystallographic coordinates described in Lima et al. (1994), Wigley et al. (1991), Berger et al. (1996) and Morais Cabral et al. (1997). The coordinates were acquired from the Protein Data Bank (Abola et al., 1987) apart from (b) which was acquired from DB Wigley (personal communication).

Figure 3. Alignment of the protein sequences of type II topoisomerases. Saccharomyces cerevisiae topoisomerase II and the two subunits of Escherichia coli DNA gyrase are aligned. The purple regions show no sequence similarity. The ‘insert’ region is present in a subset of GyrB sequences, but in no topoisomerase IIs. The active-site tyrosine residues are indicated by a Y, and the regions corresponding to the structures in Figure 1 are indicated as black bars.

Figure 4. Mechanistic models of topoisomerases. (a) Type IA topoisomerases. (b) Type IB topoisomerases (based on Stewart et al. (1998). (c) Type II topoisomerases. Separate domains or monomers are shown in red and blue, active-site tyrosines in yellow, and ATP as yellow ellipses. See text for mechanistic details.