In the central nervous system, a large amount of chelatable Zn(2+) is sequestered in presynaptic vesicles of certain glutamatergic nerve terminals. The exo-endocytotic cycle of synaptic vesicles is strictly linked to the small GTPase Rab3A. Metallothionein-3 (Zn(7)MT-3) has been proposed to be involved in the intracellular trafficking of Zn(2+) in zinc-containing neurons, but its role in this process is not understood. By using affinity precipitation and surface plasmon resonance analysis, we show that Zn(7)MT-3 binds reversibly to Rab3A.GDP (K(D) = 2.6 microM), but not to Rab3A.GTP. The binding of Zn(7)MT-3 to Rab3A.GDP is specific as no binding was observed with the metal-free form of MT-3. Mutational studies of Rab3A mapped the interaction site to the effector binding site of the protein. This location is further supported by the kinetics of GDP exchange, which was found to be unaffected by binding of Zn(7)MT-3 to Rab3A.GDP. The interaction of Zn(7)MT-3 with Rab3A indicates that Zn(7)MT-3 is not merely a cellular Zn(2+) buffer, but actively participates in synaptic vesicle trafficking upstream of vesicle fusion.