Protease

Proteases are a class of proteins that break down other proteins. They are also called proteolytic enzymes.

Proteases are classified by the amino acids or ligands that catalyze the hydrolysis reaction. For example, serine proteases contain a serine in the active site. The serine is helped by a neighboring histidine and aspartic acid. This combination is called the catalytic triad, and is conserved in all serine proteases. Serine proteases work in a two step fashion; first, they form a covalent intermediate with the protein to be cleaved; in the second step, water comes in and releases the second half of the cleaved protein.

Serine proteases include a number of digestive enzymes, including Trypsin, Chymotrypsin, and Elastase. While they all contain the same catalytic triad, they differ in where they cleave proteins. This specificity is due to a binding pocket that contains different functional groups. Chymotrypsin prefers a large hydrophobic residue; its pocket is large and contains hydrophobic residues. Trypsin is specific for positively charged residues, and contains a negative amino acid at the bottom of the pocket. Elastase prefers a small neutral residue; it has a very small pocket.

Another class of protease is aspartate proteases. This family includes HIV protease. HIV produces its proteins as one long chain; HIV protease cleaves the long protein into functional units. Aspartate proteases include two aspartate residues in the active site, which increase the reactivity of an active site water molecule to directly cleave the substrate protein.

A third class of proteases are metalloproteases such as carboxypeptidase. Carboxypeptidases remove the C terminal amino acids from proteins. The active site contains a zinc, which is bound to the protein