PNAS Plus: Intrinsic evolutionary constraints on protease structure, enzyme acylation, and the identity of the catalytic triad
The structure-function relationship of proteases is central to our understanding of biochemistry. Nature has evolved at least 23 independent solutions to this problem, using an acylation mechanism. We examined the structures of these proteases, using a new framework to characterize the geometric relationships within each active site. This analysis revealed the orientation of the base determines the stereochemistry of catalysis and elucidated why threonine does not substitute for serine in the catalytic triad. These observations explain how the absolute stereostructures of natural protease inhibitors prevent off-target inhibition and serve as boundary conditions to enzyme design.