InterPro domain: IPR036213

This group of cysteine peptidases belong to the MEROPS peptidase family C2 (calpain family, clan CA). A type example is calpain, which is an intracellular protease involved in many important cellular functions that are regulated by calcium [ 1 , 2 ]. The protein is a complex of 2 polypeptide chains (light and heavy), with eleven known active peptidases in humans and two non-peptidase homologues known as calpamodulin and androglobin [ 3 ]. These include a highly calcium-sensitive (i.e., micro-molar range) form known as mu-calpain, mu-CANP or calpain I; a form sensitive to calcium in the milli-molar range, known as m-calpain, m-CANP or calpain II; and a third form, known as p94, which is found in skeletal muscle only [ 4 ].

All forms have identical light but different heavy chains. Both mu- and m-calpain are heterodimers containing an identical 28kDa subunit and an 80kDa subunit that shares 55-65% sequence homology between the two proteases [ 5 , 6 ]. The crystallographic structure of m-calpain reveals six "domains" in the 80kDa subunit [ 6 , 7 ]:

1. A 19-amino acid NH2-terminal sequence;
2. Active site domain IIa;
3. Active site domain IIb. Domain 2 showslow levels of sequence similarity to papain; although the catalytic His hasnot been located by biochemical means, it is likely that calpain and papainare related [ 8 ].
4. Domain III;
5. An 18-amino acid extended sequence linking domain III to domain IV;
6. Domain IV, which resembles the penta EF-hand family of polypeptides, binds calcium and regulates activity [ 8 ]. Ca ²⁺ -binding causes a rearrangement of the protein backbone, the net effect of which is that a Trp side chain, which acts as a wedge between catalytic domains IIa and IIb in the apo state, moves away from the active site cleft allowing for the proper formation of the catalytic triad [ 8 ].

This superfamily describes domain III. Calpains are activated via rearrangement of the catalytic domain II induced by cooperative binding of Ca2+ to several sites of the molecule. A cluster of acidic residues in domain III, the acidic loop, has been proposed to function as part of an electrostatic switch in the activation process [ 9 ].

1. Tandemly reiterated negative enhancer-like elements regulate transcription of a human gene for the large subunit of calcium-dependent protease. J. Biol. Chem. 264, 6404-11
2. Structural basis for possible calcium-induced activation mechanisms of calpains. Biol. Chem. 382, 753-66
3. Calpains: an elaborate proteolytic system. Biochim. Biophys. Acta 1824, 224-36
4. Molecular cloning of a novel mammalian calcium-dependent protease distinct from both m- and mu-types. Specific expression of the mRNA in skeletal muscle. J. Biol. Chem. 264, 20106-11
5. Families of cysteine peptidases. Meth. Enzymol. 244, 461-86
6. Structure and physiological function of calpains. Biochem. J. 328 ( Pt 3), 721-32
7. The structure of calpain. J. Biochem. 129, 653-64
8. How calpain is activated by calcium. Nat. Struct. Biol. 9, 239-41
9. Electrostatic interactions of domain III stabilize the inactive conformation of mu-calpain. Biochem. J. 382, 607-17