Pertactin is localized on the outer membrane of B. pertussis and is one of the virulence factors believed to contribute to the disease state of whooping cough, an acute respiratory disease of children. As the precursor protein, P.93 pertactin has been identified as an autotransporter (AT). It is translocated across the inner membrane (IM), and then it is secreted across the outer membrane (OM) with its C-terminal porin domain forming a pore through which the P.69 passenger domain is transported out of the cell. During this secretion process, P.69 pertactin is cleaved from the porin domain by either an unidentified OM protease, or an autocatalytic mechanism. In this study, we investigated possible candidates of the cleavage site and we found that when S602 was mutated to alanine, the proteolysis occuring at the OM was obviously impaired. Besides we also found different effects of this mutation to the proteolytic process occuring at the OM in different cell strains of E. coli cells, which suggested it was unlikely that this proteolysis occuring at the OM was autocatalytic.