Symmetry and chirality in topoisomerase II-DNA crossover recognition

Several experimental data support the notion that the recognition of DNA cr ossovers play an important role in the multiple functions of topoisomerase II. Here, a theoretical analysis of the possible modes of assembly of yeast topoisomerase II with right and left-handed tight DNA crossovers is perfor med, using the crystal coordinates of the docking partners. The DNA crossov ers are assumed to be clamped into the central hole of the enzyme. Taking i nto account the rules for building symmetric ternary complexes and the stru ctural constraints imposed by DNA-DNA and protein-DNA interactions, this an alysis shows that two geometric solutions could exist, depending on the chi rality of the DNA crossovers. In the first one, the two DNA segments are sy mmetrically recognized by the enzyme while each single double helix binds a symmetrically the protein dimer. In the second one, each double helix is sy mmetrically recognized by the protein around its dyad axis, while the two D NA segments have their own binding modes. The finding of potential DNA-bind ing domains which could interact with the crossovers provides structural su pports for each model. The structural similarity of a loop containing a clu ster of conserved basic residues pointing into the central hole of topoisom erase II and the second DNA-binding site of histone H5 which binds DNA cros sover is of particular interest. Each solution, which is consistent with di fferent sets of experimental data found in the literature, could either cor respond to different functions of the enzyme or different steps of the reac tion. This work provides structural insights for better understanding the r ole of chirality and symmetry in topoisomerase II-DNA crossover recognition , suggests testable experiments to further elucidate the structure of terna ry complexes, and raises new questions about the relationships between the mechanism of strand-passage and strand-exchange catalyzed by the enzyme. (C ) 1998 Academic Press.