Complete primary structure for the zymogen of human complement factor B

The entire amino acid sequence of complement factor B has been established combining both protein and DNA sequencing strategies. The zymogen consists of 739 amino acids, has four asparagine-linked carbohydrate sites, and has independently disulfide-bonded NH2- and COOH-terminal regions. The catalytic subunit, Bb, is a unique serine protease containing 259 amino acids that are not integral to any of the classical serine proteases. It is proposed that this region of the Bb fragment functions as a cofactor-binding domain for C3b. The Ba fragment was found to contain three regions of internal sequence homology which were unrelated to the “kringle” regions of prothrombin and plasminogen and which suggest an independent evolution for the B genome. Sequence alignment of the active site of B to the serine proteases was made using the three-dimensional structures of chymotrypsin and trypsin as molecular models. Three stretches within the hypothetical model for B contrast markedly with all known serine proteases in both amino acid sequences and predicted configuration. It is suggested that these “altered” regions contribute at least in part to the formation of the catalytic region of the C3 convertase.