To identify some of the structural features determining specific protease recognition of complement components C3 and C4, we used site-specific mutagenesis to construct mutants of murine C3 that are cleaved by the C4-specific Cis protease. Insertion of three amino acid residues corresponding to residues at the Cis cleavage site of human C4 into murine C3 at the analogous C3 convertase cleavage site was adequate to render the mutant protein susceptible to Cis cleavage. In addition, insertion of C3-specific residues at the same site or introduction of the C4-specific residues as substitutions rather than as an insertion also rendered the site susceptible to cleavage, but with 10-to 50-fold lower efficiencies, and insertion of even a single amino acid residue affected recognition by Cis. Finally, insertion of amino acid residues into mC3 partially inhibited cleavage by the alternative-pathway C3 convertase, with insertion of C3-or C4-specific residues giving about the same level of inhibition. A simple interpretation of these data is that Cis cleavage is dependent primarily on steric accessibility and on recognition of specific amino acid residues at the cleavage site, whereas C3 convertase cleavage is dependent primarily on specific interactions distal to the cleavage site, with only relatively weak, non-C3-specific interactions at the cleavage site itself.Complement components C3, C4, and C5 constitute a family of proteins that play central roles in complement activation and regulation. They share similar subunit structures, biosynthetic pathways, gene structures, and about 25% amino acid sequence identity; nevertheless they are quite distinct functionally and biochemically (reviewed in refs. 1 and 2).For example, while C3, C4, and C5 are activated by proteolytic cleavage at structurally analogous sites in their a subunits, with accompanying release of anaphylatoxins C3a, C4a, and C5a, proteolysis is carried out by three distinct proteases: C3 convertase, Cis, and C5 convertase, respectively. The two convertases are complex proteases assembled from multiple complement components; they share the same catalytic subunit (structurally and evolutionarily related C2a and Bb in the classical and alternative pathways, respectively) but differ in their noncatalytic subunits. The CIs protease, on the other hand, is a subunit of component C1 and is structurally distinct from C2 and B.What is the molecular basis for specific recognition of C3, C4, and C5? For all three proteins, cleavage occurs immediately after the sequence -Leu-Xaa-Arg-, where Xaa is Ala, Gln, or Gly. These residues are doubtless necessary for cleavage (3), but because of their similarity are unlikely to determine cleavage specificity. In aligning the amino acid sequences of mouse and human C3 (4, 5), C4 (6-8), and C5 (9, 10) near their respective proteolytic activation sites, we noticed that the best alignment requires the introduction of a gap, a few amino acid residues in length, into both the C3 and C5 sequences just downstream of the cleavage ...