Aspartyl proteases are a highly specific family of proteases - they tend to cleave dipeptide bonds that have hydrophobic residues as well as a beta-methylene group. Unlike the closely related serine proteases these proteases do not form a covalent intermediate during cleavage.
While a number of different mechanisms for aspartyl proteases have been proposed, the most widely accepted is a general acid-base mechanism involving coordination of a water molecule between the two highly-conserved aspartate residues. One aspartate activates the water by abstracting a proton, enabling the water to attack the carbonyl carbon of the substrate scissile bond, generating a tetrahedral oxyanion intermediate. Rearrangement of this intermediate leads to protonation of the scissile amide.
Read more about this topic: Aspartic Acid Proteases
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