Structural basis of the interaction between Topoisomerase IIIβ and the TDRD3 auxiliary factor

Topoisomerase III beta (TOP3 beta) is a DNA/RNA topoisomerase that has been implicated in epigenetic or translational control of gene expression. In cells, TOP3 beta co-exists with its specific auxiliary factor, TDRD3. TDRD3 serves as a scaffold protein to recruit TOP3 beta to its DNA/RNA substrates accumulating in specific cellular sites such as methylated chromatins or neural stress granules. Here we report the crystal structures of the catalytic domain of TOP3 beta, the DUF1767-OB-fold domains of TDRD3 and their complex at 3.44 angstrom, 1.62 angstrom an 3.6 angstrom resolutions, respectively. The toroidal-shaped catalytic domain of TOP3 beta binds the OB-fold domain of TDRD3. The TDRD3 OB-fold domain harbors the insertion loop, which is protruding from the core structure. Both the insertion loop and core region interact with TOP3 beta. Our pull-down binding assays showed that hydrophobic characters of the core surface and the amino-and carboxy-terminal regions of the insertion loop are essential for the interaction. Furthermore, by comparison with the structure of the homologous Topoisomerase IIIa (TOP3 alpha)-RMI1 complex, we identified Arg96, Val109, Phe139 and the short insertion loop of TDRD3 as the critical structural elements for the specific interaction with TOP3 beta to avoid the non-cognate interaction with TOP3 alpha.