Troponin C (TnC) from amphioxus (Protochordate) was purified and its primary structure determined. Unlike the case of vertebrates and other invertebrates, amphioxus TnC is found in the soluble fraction after extractions at physiological ionic strength in the presence of Ca2+. Edman sequencing combined with mass spectroscopy indicate that the protein contains 163 amino acid residues. It possesses an acetylated N-terminus (although a small percentage has a free Ser N-terminus) and either epsilon-N-methyllysine or epsilon-N-dimethyllysine in position 20. It displays about 50% sequence identity with vertebrate skeletal-muscle and cardiac-muscle TnC, 44% with TnC of sea squirt, also a Protochordate, and 30% with other invertebrate TnC. Like vertebrate TnC, amphioxus TnC contains a N-terminal alpha-helix plus the usual four ancestral Ca(2+)-binding regions, but analysis of the sequence suggests that the fourth site is not functional. Flow dialysis shows that amphioxus TnC binds three Ca2+ with the mean apparent affinity constant K' of 3.4 +/- 1.5 10(5) M-1. No cooperativity exists between the sites, and the presence of up to 10 mM Mg2+ does not influence the Ca(2+)-binding isotherm, indicating that the metal-binding sites are Ca(2+)-specific at physiological Mg2+ concentrations. It forms a Ca(2+)-dependent, 1:1 complex with melittin and rabbit or crayfish troponin I (TnI). Amphioxus TnC possesses one Trp residue in position 151 and one at the C-terminus. Trp fluorescence suggests that one or both residues are solvent-exposed in the metal-free form and efficiently shielded in the Ca2+ form. Although Mg2+ has no effect on the Ca2+ binding, the Trp fluorescence is influenced by millimolar Mg2+, suggesting the presence of one or more independent Mg(2+)-binding site(s). A phylogenetic analysis clearly shows that amphioxus TnC is positioned on the branch of the Chordates, but at a distance from the vertebrate TnC. Its place on the phylogenetic tree is in accordance with the consensus evolutionary phylogeny.