Pseudomonas aeruginosa myovirus KZ has a 270-kb genome within a T72؍ icosahedral capsid that contains a large, unusual, and structurally well-defined protein cylindrical inner body (IB) spanning its interior. Proteolysis forms a pivotal stage in KZ head and IB morphogenesis, with the protease gp175 cleaving at least 19 of 49 different head proteins, including the major capsid protein and five major structural IB proteins. Here we show that the purified mature form of gp175 is active and cleaves purified IB structural proteins gp93 and gp89. Expression vector synthesis and purification of the zymogen/precursor yielded an active, mature-length protease, showing independent C-terminal gp175 self-cleavage autoactivation. Mutation of either the predicted catalytic serine or histidine inactivated mature gp175, supporting its classification as a serine protease and representing the first such direct biochemical demonstration with purified protease and substrate proteins for any phage protease. These mutations also blocked self-cleavage of the precursor while allowing intermolecular gp175 processing. To confirm the cleavage specificity of gp175, we mutated three cleavage sites in gp93, which blocked proteolysis at these sites. The N-terminal propeptide of gp93 was shown to undergo more extensive proteolysis than previously identified. We found that proteolysis in gp93 progressed from the N to C terminus, while blocking cleavage sites slowed but did not eliminate downstream proteolysis. These findings were shown by informatics to be relevant to the head morphogenesis of numbers of other related IB-containing giant phages as well as to T4 and herpesviruses, which have homologous proteases.T he giant myovirus KZ, which is infective for Pseudomonas aeruginosa, is a member of the KZ-related phages that currently incorporate two genera, the KZ-like phages (KZ, PA3, and 2012-1) and the more distantly related EL-like phages (EL and OBP) (1-3). These phages are distributed widely geographically and are of interest because those infective for pathogens have been used for phage therapy (4) and/or have potential for further biocontrol applications (5-8). These phages are also a curiosity, as they are remarkably complex, both at the genome and structural levels, with large virions comprised of a Tϭ27 capsid or head (9) and contractile tail that ends in an elaborate baseplate (10, 11). The complexity of the virion is reflected in the numbers of different proteins, Ͼ60 different proteins, with nearly 50 different proteins present in the head alone, possibly the highest number for any known group of viruses (12)(13)(14). A remarkable feature of the KZ-related phages is that within the head there is a large, protein cylinder called an inner body (IB) around which the DNA is tightly spooled (15). The structure of the KZ IB was recently solved, revealing it to be approximately 24 by 105 nm and tilted at an angle of approximately 22°relative to the portal axis (16). Its structure is also regular, with an apparent 6-fold symmetry in some ...