Afg3p, a mitochondrial ATP-dependent metalloprotease, is involved in degradation of mitochondrially-encoded Cox1, Cox3, Cob, Su6, Su8 and Su9 subunits of the inner membrane complexes III, IV and V.

The yeast AFG3 gene encodes an ATP-dependent metalloprotease belonging to a subgroup of the AAA-family. This protease has been suggested to be essential for a metal- and ATP-dependent breakdown of incompletely mitochondrially synthesized polypeptides in the inner membrane, a process proposed to be important for mitochondrial function (Pajic et al. (1994) FEBS Lett. 353, 201-206). Here, we confirm the proteolytic activity by site-directed mutagenesis and demonstrate that the proteins Cox1, Cox3, Cob, Su6, Su8 and Su9 are substrates of Afg3p. Surprisingly, this proteolytic activity is not required for respiratory function and thus presumably also not essential for mitochondrial biogenesis.