We have prepared full-length Drosophila and human topoisomerase II and 
truncation constructs containing the amino-terminal ATPase domain, and we have 
analyzed their biochemical properties. The ATPase activity of the truncation 
proteins, similar to that of the full-length proteins, is greatly stimulated by 
the presence of DNA. This activity of the truncation proteins is also sensitive 
to the inhibition by the drug bisdioxopiperazine, ICRF-193, albeit at a much 
lower level than the full-length protein. Therefore, bisdioxopiperazine can 
directly interact with the NH(2)-terminal ATPase domain, but the drug-enzyme 
interaction may involve other domains as well. The ATPase activity of the ATPase 
domain protein showed a quadratic dependence on enzyme concentration, suggesting 
that dimerization of the NH(2)-terminal domain is a rate-limiting step. Using 
both protein cross-linking and sedimentation equilibrium analysis, we showed 
that the ATPase domain exists as a monomer in the absence of cofactors but can 
readily dimerize in the presence of a nonhydrolyzable analog of ATP, 
5'-adenylyl-beta,gamma-imidodiphosphate. More interestingly, both ATP and ADP 
can also promote protein dimerization. This result thus suggests that the 
protein clamp, mediated through the dimerization of ATPase domain, remains 
closed after ATP hydrolysis and opens upon the dissociation of ADP.