Factor D is a glycosylated protein composed of a single 24,000 Da polypeptide chain. It is an essential component of the alternative pathway of complement activation. Its only known function is to cleave and activate factor B when factor B is bound to C3b or a C3b-like protein such as C3(H2O) or CVF. Factor D is a serine protease that circulates as a mature protease, but it exhibits a highly restricted specificity and it appears to be substrate activated. Factor D cleaves factor B bound to C3b between Arg233 and Lys234 causing the release of the Ba fragment (33,000 Da) and leaving the 60,000 Bb fragment bound to C3b. The C3b,Bb complex is called a C3 or C5 convertase because it converts these proteins to their active forms by cleaving off the small peptides C3a and C5a, respectively (Law, S.K.A. and Reid, K.B.M. (1995); Morikis, D. and Lambris, J.D. (2005)).
A unique feature of the alternative pathway is the ability of C3b,Bb to amplify itself on the surface of a complement-activating target particle. This enzyme cleaves C3 producing metastable C3b which can attach to the cell near the initial C3b. Each C3b deposited can bind factor B which is activated by factor D forming another C3/C5 convertase. Thus, factor D is a required component for alternative pathway amplification and the concentration of factor D is rate limiting. This amplification mechanism of the alternative pathway can deposit 2,000,000 C3b molecules on a yeast cell or 30,000 C3b on a single bacterial cell 10-15 min after they come in contact with blood. These numbers represent a monolayer of covalently attached opsonins (C3b, iC3b and C3d) which are ligands for phagocytic immune cells. The numbers of C3b and C5b-9 deposited far exceed those produced by the classical or lectin pathway due to the factor B-containing convertase and its ability to amplify itself and spread across the surface of a target.
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