The HIV protease is a C2-symmetric homodimeric enzyme consisting of two 99 amino acid monomers. Each monomer contributes an aspartic acid residue that is essential for catalysis, Asp-25 and Asp-25´. The HIV protease has the sequence Asp-Thr-Gly, which is conserved among other mammalian aspartic protease enzymes. An extended beta-sheet region on the monomers, known as the flap, constitutes in part the substrate binding site with the two aspartyl residues lying on the bottom of a hydrophobic cavity. Each flexible flap contains three characteristic regions: side chains that extend outward (Met46, Phe53), hydrophobic chains extending inward (Ile47, Ile54), and a glycine rich region (Gly48, 49, 51, 52). Ile50 remains at the tip of the turn and when the enzyme is unliganded a water molecule makes hydrogen bonds to the backbone of Ile50 on each monomer.
HIV proteases catalyze the hydrolysis of peptide bonds with high sequence selectivity and catalytic proficiency. The mechanism of the HIV protease shares many features with the rest of the aspartic protease family although the full detailed mechanism of this enzyme is not fully understood. The water molecule seems to play a role in the opening and closing of the flaps as well as increasing the affinity between enzyme and substrate. The aspartyl residues are involved in the hydrolysis of the peptide bonds. The preferred cleavage site for this enzyme is the N-terminal side of proline residues, especially between phenylalanine and proline or tyrosine and proline.