A Molecular Dynamics simulation of the Deinococcus radiodurans topoisomerase IB crystallized in absence of DNA has been carried out. The protein stably maintains its initial conformation with the N- and C-terminal domains slightly oscillating around their initial positions, being their relative orientations stabilized by two inter-domain interactions, Arg4:Glu228 and Glu63:Arg91. A charge perturbation has then been introduced to destabilize the protein from its local minimum. The simulation carried out after the destabilization permits the two domains to change their relative orientation and to move one from the other, acting as independent units that fully maintain their intrinsic secondary and tertiary structure. The orientational rearrangement occurs because of the presence of a hinge, Gln93, located in a segment connecting the N- and C-terminal domains. Despite the large amplitude of motion the active site remains preformed with an orientation similar to that found in the crystal structure. Comparison with a similar study previously carried out on the human enzyme reveals the presence of structural common features between the two enzymes.