We found that the Mg-isocitrate complex is the true substrate for pine isocitrate lyase and that magnesium acts as a non-essential activator. Both the non-activated and the activated enzyme forms are catalytically active. Our model is consistent with the presence of two Mg-binding sites with different affinities: an activator site with high affinity in addition to the catalytic site with lower affinity. This may result in a complex, fine regulation of isocitrate lyase activity by magnesium. The affinity of the free enzyme for isocitrate is very low. Moreover, free isocitrate does not bind to the activated enzyme, nor it can yield a catalytically active form by binding to an enzyme species whose catalytic site has already been bound by magnesium.