Structures of Type IIB Topoisomerases
The organization of type IIB topoisomerases are similar to that of type IIAs, except that all type IIBs have two genes and form heterodimers. One gene, termed topo VI-B (since it resembles gyrB), contains the ATPase domain, a H2TH domain, and the transducer domain. The second gene, termed topo VI-A, contains the WHD and the Toprim domain.
The ATPase domain of topo VI B was solved in multiple nucleotide states (Corbett and Berger, EMBO J 2003). It closely resembles that of the GHKL domain of topo II and MutL and shows that the nucleotide state (ADP versus ATP) effects the orientation of the transducer domain (pdb ID= 1MU5 and 1MX0).
The structure of topo VI-A was solved by Bergerat et al. (Nature 1997), showing that the HTH and Toprim fold had a novel conformation compared with that of topo IIA.
A recent structure of the topo VI A/B complex was solved, showing an open and closed conformation, two states that are predicted in the two-gate mechanism (see below). These structures, of which one is an X-ray crystal structure and the other is a Small-Angle X-ray Scattering (SAXS) reconstruction, show that the ATPase domain can be either open or closed (Corbett, Benedetti, Berger Nature Structure Molecular Biology, 2007, PDB ID = 2Q2E).
Read more about this topic: Type II Topoisomerase
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