Aspartyl proteases catalytic mechanism

The carboxyl proteases are so called because they have two catalytically essential aspartate residues. They were formerly called acid proteases because most of them are active at low pH. The best-known member of the family is pepsin, which has the distinction of being the first enzyme to be named (in 1825, by T. Schwann). Other members are chymosin (rennin) cathepsin D Rhizopus-pepsin (from Rhizopus chinensis) penicillinopepsin (from Penicillium janthinel-lum) the enzyme from Endothia parasitica and renin, which is involved in the regulation of blood pressure. These constitute a homologous family, and all have an Mr of about 35 000. The aspartyl proteases have been thrown into prominence by the discovery of a retroviral subfamily, including one from HIV that is the target of therapy for AIDS. These are homodimers of subunits of about 100 residues.156,157 All the aspartyl proteases contain the two essential aspartyl residues. Their reaction mechanism is the most obscure of all the proteases, and there are no simple chemical models for guidance. 

Figure 1. Schematic representation of the relationships between proposed catalytic and inhibitory mechanisms. A. Postulated general acid-general base catalyzed mechanism for substrate hydrolysis by an aspartyl protease. The water molecule indicated is extensively hydrogen bonded to both aspartic acid residues plus other sites in the active site (see Reference 16 for details). Hydrogen bonds to water are omitted here. B. Kinetic events associated with the inhibition of pepsin by pepstatin. The pro-S hydroxyl group of statine displaces the enzyme immobilized water molecule shown in Figure lA. Variable aspartyl sequence numbers refer to penicillopepsin (pepsin, Rhizopus pepsin), respectively.

Figure 14 Profiling of aspartyl protease activity, (a) Catalytic mechanism of aspartyl proteases that cleave peptide bonds via activation of a water molecule, (b) A hydroxyethylene dipeptide isostere-based probe binds tightly to the active site and gets covalently attached via UV irradiation.

Proteins can be modified by a group of peptide hydrolyses (peptidases) commonly called proteases (or proteinoses). Based on their ability to hydrolyze specific proteins, proteases are classified as collagenase, keratinase, elastase, etc. On the basis of the pH range over which they are active, they are classified as either acidic, neutral, or alkaline. However, according to their mechanism of action, the Enzyme Commission classifies proteases into the four distinct classes of serine, cysteine, aspartyl, and metalloproteases. Serine proteases, for example, always contain serine residue at their catalytic center, which is essential for the action of proteolysis. 

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