Figure 2.

A model for the organization of the gyrase tetramer and the mechanism of strand passage. (a) The nucleotide-free conformation is shown, consisting of the 59-kDa domain of GyrA [green-blue (35)], the 43-kDa domain of GyrB [purple (36)] and the B′ subdomain of yeast topo II [red (10)], their relative positions suggested by electron microscopy observations (37). The structure of the 33-kDa domain is unknown; a representation is given here (yellow). The conformation of the bound DNA is shown here to be symmetrical. However, hydroxyl radical experiments show a preference for the protection of one of the DNA arms (12). Such protection must be the result of differences in the flexibility of the two arms and suggests that DNA structure plays a role in determining which of the two arms is captured by the ATP-operated clamp. (b) The conformation of the enzyme–DNA complex when the T segment is before the DNA gate. (c) The enzyme–DNA complex when the T segment is beyond the DNA gate. The conformational changes that are depicted to take place on nucleotide binding are discussed in the text. In the gate-open conformation, the structure of the 59-kDa domain has been substituted with that of the A′ subdomain of yeast topo II (10). In the nucleotide-bound complex (complexes b and c), the DNA gate is shown in the open state merely to illustrate the opening of the gate to allow strand passage. At equilibrium, this gate may be predominantly in the closed state, as suggested by the cleavage experiments in Fig. 3.