Calcium vector protein target (CaVPT), a 26-kDa endogenous target of calcium vector protein from Amphioxus (CaVP), contains three distinct regions: a N-terminal Pro-Ala-Lys-rich motif, segment 36-50 displaying sequence similarity to the calmodulin-binding site in neuromodulin and neurogranin where they are designated as the IQ domain; and two immunoglobulin-like folds. The phosphorylation by protein kinase C of Ser-43 in the IQ domain drastically decreases the affinity of CaVPT for CaVP and CaVP protects CaVPT from phosphorylation. Phosphorylation by the catalytic subunit of cyclic AMP-dependent protein kinase has a similar effect, but in addition to Ser-43 four other phosphorylated sites were identified. Removal of the Pro-Ala-Lys-rich region and the IQ domain in CaVPT by trypsin leads to the loss of binding to CaVP, whereas the chymotryptic fragment, containing these regions and first immunoglobulin-like domain, retained the ability to interact with CaVP. A synthetic IQ domain alone interacts strongly with calmodulin, but not with CaVP. Two main conclusions can be drawn from this study: 1) the regulation of interaction between CaVP and CaVPT is very similar to the mechanism observed in the complex between neuromodulin or neurogranin and calmodulin; 2) in spite of this similarity the entire CaVP-binding site is not restricted to the IQ domain; in addition the Pro-Ala-Lys-rich motif may be necessary for high affinity binding to CaVP.