Structural basis of profactor D activation: from a highly flexible zymogento a novel self-inhibited serine protease, complement factor D

The crystal structure of profactor D, determined at 2.1 Angstrom resolution with an R-free and an R-factor of 25.1 and 20.4%, respectively, displays h ighly flexible or disordered conformation for five regions: N-22, 71-76, 14 3-152, 187-193 and 215-223 A comparison with the structure of its mature se rine protease, complement factor D, revealed major conformational changes i n the similar regions. Comparisons with the zymogen-active enzyme pairs of chymotrypsinogen, trypsinogen and prethrombin-2 showed a similar distributi on of the flexible regions. However, profactor D is the most flexible of th e four, and its mature enzyme displays inactive, self-inhibited active site conformation. Examination of the surface properties of the N-terminus-bind ing pocket indicates that Ile16 may play the initial positioning role for t he N-terminus, and Leu17 probably also helps in inducing the required confo rmational changes. This process, perhaps shared by most chymotrypsinogen-li ke zymogens, is followed by a factor D-unique step, the re-orientation of a n external Arg218 to an internal position for salt-bridging with Asp189, le ading to the generation of the self-inhibited factor D.