Serine proteases are enzymes that catalyze the hydrolysis of peptide bonds. In each case, the enzymes have a serine residue that plays a critical role in the catalysis. The enzymes cuts preferentially in distinct sites (Table 5.4). The active site regions of all of the serine proteases have a number of common factors. For example, an aspartate residue, a histidine residue, and a serine residue are always clustered about the active site depression. Such a structure for chymotrypsin is shown in Figure 11.11. Also, a "pocket" is always located close to the active site serine. The shape and charge of the "pocket," however, vary between different serine proteases (Figure 11.12). Thus, it is the nature of the pocket that gives a serine protease its specificity. For example, in chymotrypsin, the pocket is wide and lined with hydrophobic residues to accommodate a hydrophobic side chain, such as phenylalanine.

The catalytic mechanism of chymotrypsin, a serine protease is shown in Figure 11.13. These steps include the following:

1. Polypeptide substrate binding.

2. Proton transfer from Ser to His. The substrate forms a tetrahedral transition state with the enzyme.

3. Proton transfer to the C-terminal fragment, which is released by cleavage of the C-N bond. The N-terminal peptide is bound through acyl linkage to serine.

4. A water molecule binds to the enzyme in place of the departed polypeptide.

5. The water molecule transfers its proton to His 57. Again, a tetrahedral transition state is formed.

6. The second peptide fragment is released. The acyl bond is cleaved, the proton is tranferred from His back to Ser, and the enzyme returns to its initial state.

A key to the mechanism of serine protease catalysis lies in the stability of the two tetrahedral intermediate states, which are very similar to the essential transition states. They appear to be stabilized by hydrogen bonds from backbone amino protons from residues Ser 195 and Gly 193 to one of the oxygens in the tetrahedral complex (the carbonyl oxygen of the substrate). The hydrogen bonding can occur only with formation of the tetrahedral state and thus stabilizes the intermediates.

Both triose phosphate isomerase and serine proteases have a histidine and an acidic residue in their active site. Histidine is very common in active sites, because it readily accepts or donates protons at physiological pH.

1. Serine Proteases (from SCOP)