Structural Biochemistry/Enzyme/Aspartyl Proteases

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Aspartyl proteases are one of the eukaryotic protease enzymes that catalyze peptide substrates using aspartate residue. It is usually in an acidic pH range which is inhibited by pepstatin. Some examples of the aspartyl proteases are pepsins, cathepsins, and renins. It exists in vertebrates, plants, plant viruses, and retroviruses. It has a sequence of Asp- Thr- Gly. It is usually represented as monomeric enzymes with twofold symmetry and has a tertiary structure with an N-terminal and a C-terminal.


On the active sites of aspartyl proteases, there are aspartic acid residues that work together to promote a water molecule to attack the peptide bond. One of the aspartic acid residues (left on the diagram, deprotonated form) will activate the water molecule by attracting the hydrogen atom of water. The other aspartic acid (right on the diagram, protonated form) residue will polarize the carbonyl group on the peptide making it easier to attack. One of the aspartic acids usually has a lower pKa value.

Aspartyl Protease Mechanism

Renin, an enzyme that supports the regulation of blood pressure, is an important member of this class of enzyme (Berg, 7th Edition)

Common type of aspartyl protease[edit]

Renin is a proteolytic enzyme synthesized, stored and secreted by the juxtaglomerular cells of the kidney; it plays a role in regulation of blood pressure by catalyzing the conversion of the plasma glycoprotein angiotensinogen to angiotensin I. This, in turn, is converted to angiotensin II by an enzyme that is present in relatively high concentrations in the lung. Angiotensin II is one of the most potent vasoconstrictors known, and also is a powerful stimulus of aldosterone secretion. Pepsin is a digestive enzyme found in gastric juice that catalyzes the breakdown of protein to peptides. Pepsin is one of three protein-degrading or proteolytic enzymes in the digestive system; the other two being chymotrypsin and trypsin. The three enzymes work together to break proteins down into peptides and amino acids, which can be readily absorbed by the intestinal lining. Pepsin is most effective in cleaving the bonds of phenylalanine, tryptophan, and tyrosine.

The HIV protease is an example of the aspartyl protease. This protease is a dimer which consists of identical subunits. As a member of the aspartyl protease family, it contains two aspartic acid residues symmetrically located at the bottom of the binding pocket. The function of this protease is to cleave the domain of the viral protein into their dynamic forms. Those forms spread the virus. This process can be stopped by using HIV protease inhibitors, which attack the HIV protease, bind to it, and prevent cleavage of the domain. An example of an HIV protease inhibitor is Indinavir. Indinavir is used to treat HIV infection and AIDS and is one of the most successfully used protease inhibitors in medicine.

Lopinavir is also one of the HIV protease inhibitors. The structure of HIV-1 protease with Lopinavir is shown. The hydroxyl group acts as a transition analog, mimicking the oxygen of the tetrahedral intermediate. The benzyl group, positioned next to the hydroxyl group, helps to properly position the drug in the active site.

HIV-1 protease complexed with Lopinavir