Protein phosphatase 2A (PP2A) represents a family of multimeric serine/threonine phosphatases with pleiotropic roles in signal transduction. We previously described the functional analysis of two Ca(2+)-binding EF-hands in the PR72/B'' class of regulatory PP2A subunits. Now we report partial degradation of PR72/B"alpha2 and PR130/B"alpha1 into a 45-48kDa proteolysis-resistant fragment ('PR45') by the Ca(2+)-dependent protease m-calpain. This limited proteolysis is dependent on EF-hand integrity, independent of two PEST-domains, and highly specific as PP2A(C), PR65/A and representatives of PR55/B and PR61/B' subunit families are calpain-resistant. PR45 was also generated in staurosporine-induced apoptotic MCF7 cells in a calpain-dependent way. Calpain treatment weakens the PR72-core enzyme interaction, activates basal PP2A(T72) phosphatase activity and dramatically increases its sensitivity for and activation by polycations. This unique property can be exploited in a specific biochemical assay for these holoenzymes. We propose local calpain action in vivo may constitute a novel regulatory mechanism of these holoenzymes.