Crystal structure of calpain‐3 penta‐ EF ‐hand ( PEF ) domain – a homodimerized PEF family member with calcium bound at the fifth EF ‐hand

Calpains are Ca 2+ dependent intracellular cysteine proteases that cleave a wide range of protein substrates to help implement Ca 2+ signaling in the cell. The major isoforms of this enzyme family, calpain‐1 and calpain‐2, are heterodimers of a large and a small subunit, with the main dimer interface being formed through their C‐terminal penta‐ EF hand ( PEF ) domains. Calpain‐3, or p94, is a skeletal muscle‐specific isoform that is genetically linked to limb‐girdle muscular dystrophy. Biophysical and modeling studies with the PEF domain of calpain‐3 support the suggestion that full‐length calpain‐3 exists as a homodimer. Here, we report the crystallization of calpain‐3′s PEF domain and its crystal structure in the presence of Ca 2+ , which provides evidence for the homodimer architecture of calpain‐3 and supports the molecular model that places a protease core at either end of the elongated dimer. Unlike other calpain PEF domain structures, the calpain‐3 PEF domain contains a Ca 2+ bound at the EF 5‐hand used for homodimer association. Three of the four Ca 2+ ‐binding EF ‐hands of the PEF domains are concentrated near the protease core, and have the potential to radically change the local charge within the dimer during Ca 2+ signaling. Examination of the homodimer interface shows that there would be steric clashes if the calpain‐3 large subunit were to try to pair with a calpain small subunit. Database Structural data are available in the Protein Data Bank database under accession number 4OKH .Structured digital abstract Calpain-3  and  Calpain-3   bind  by  x-ray crystallography  ( View interaction )