Structural aspects of activation pathways of aspartic protease zymogens and viral 3C protease precursors

The three-dimensional structures of the inactive protein precursors (zymoge ns) of the serine, cysteine, aspartic, and metalloprotease classes of prote olytic enzymes are known. Comparisons of these structures with those of the mature, active proteases reveal that, in general, the preformed, active co nformations of the residues involved in catalysis are rendered sterically i naccessible to substrates by the residues of the zymogens' N-terminal exten sions or prosegments. The prosegments interact in nonsubstrate-like fashion s with the residues of the active sites in most of the cases. The gastric a spartic proteases have a well-characterized zymogen conversion pathway. Str uctures of human progastricsin, the inactive intermediate 2, and active hum an pepsin are known and have been used to define the conversion pathway. Th e structure of the zymogen precursor of plasmepsin II, the malarial asparti c protease, shows a new twist on the mode of inactivation used by the gastr ic zymogens; The prosegment of proplasmepsin disrupts the active conformati on of the two catalytic aspartic acid residues by inducing a major reorient ation of the two domains of the mature protease. The picornaviral 2A and 3C proteases have a chymotrypsin-like tertiary structure but with a cysteine nucleophile. These enzymes cleave themselves from the viral polyprotein in cis (intramolecular cleavage) and carry out trans cleavages of other scissi le peptides important for the virus life cycle. Although the structure of t he precursor viral polyprotein is unknown, it probably resembles the organi zation of the proenzymes of the bacterial serine proteases, subtilisin, and alpha-lytic protease. Cleavage of the prosegment is known to occur in cis for these precursor molecules.