We study an atomic quantum dot representing a single hyperfine “impurity” atom which is coherently coupled to two well-separated Bose-Einstein condensates, in the limit when the coupling between the dot and the condensates dominates the intercondensate tunneling coupling. It is demonstrated that the quantum dot by itself can induce large-amplitude Josephson-like oscillations of the particle imbalance between the condensates, which display a two-frequency behavior. For noninteracting condensates, we provide an approximate solution to the coupled nonlinear equations of motion which allows us to obtain these two frequencies analytically.