Chlorogenic acid (CGA) has been proved to be an activator of calcineurin (CN) in our previous research. In this study, the activation mechanism of CN by CGA was further explored. The results showed that although the purified CN was inactive in vitro if only Ca(2+)/calmodulin (CaM) existed without Mn(2+)/Ni(2+), CGA activated the inactive CN potently. It was found that CN's activity increased as the concentration of CGA increased and reached a plateau of 4- to 6-fold higher activity using p-nitrophenyl phosphate (pNPP) or phosphopeptide (32)P-RII as substrate. And the activation was CaM-dependent. Moreover, the fluorescent emission of CN had a 17 nm red shift in the presence of 128 muM CGA, and the quenching constant was 1.21x10(12) M(-1) . s(-1), which indicated that CGA bound to CN statically and changed its conformation. According to the kinetic analysis, CGA preferred to activate CN in a substrate noncompetitive manner. When Mn(2+) or Ni(2+) presented, CGA also activated CN with CaM-dependency by improving CN's affinity for Mn(2+) or Ni(2+). In addition, the inhibition of CN by Zn(2+) was partially eliminated by CGA chelation. Our findings suggested the activation of CN by CGA was in a CaM-dependent and substrate noncompetitive manner. This might provide the basis for the further study of CN-targeted activators.