PROSITE documentation PDOC00128

Eukaryotic and viral aspartyl proteases signature and profiles

Aspartyl proteases (APs), also known as acid proteases, (EC 3.4.23.-) are a widely distributed family of proteolytic enzymes [1,2,3,4,5] known to exist in vertebrates, fungi, plants, retroviruses and some plant viruses. APs use an Asp dyad to hydrolyze peptide bonds.

APs found in eukaryotic cells are α/β monomers composed of two asymmetric lobes, with the catalytic Asp dyad located at the lobe interface and a flap made up of a β-hairpin covering the peptide substrates ("pepsin-like" proteases) (see <PDB:1FKN>). Each of the lobes provides a catalytic Asp residue, positioned within the hallmark motif Asp-Thr/Set-Gly, to the active site. Eukaryotic APs form peptidase family A1 of clan AA [E1]. Currently known eukaryotic APs are:

• Vertebrate gastric pepsins A and C (also known as gastricsin).
• Vertebrate chymosin (rennin), involved in digestion and used for making cheese.
• Vertebrate lysosomal cathepsins D (EC 3.4.23.5) and E (EC 3.4.23.34).
• Mammalian renin (EC 3.4.23.15) whose function is to generate angiotensin I from angiotensinogen in the plasma.
• Fungal proteases such as aspergillopepsin A (EC 3.4.23.18), candidapepsin (EC 3.4.23.24), mucoropepsin (EC 3.4.23.23) (mucor rennin), endothiapepsin (EC 3.4.23.22), polyporopepsin (EC 3.4.23.29), and rhizopuspepsin (EC 3.4.23.21).
• Yeast saccharopepsin (EC 3.4.23.25) (proteinase A) (gene PEP4). PEP4 is implicated in posttranslational regulation of vacuolar hydrolases.
• Yeast barrierpepsin (EC 3.4.23.35) (gene BAR1); a protease that cleaves α-factor and thus acts as an antagonist of the mating pheromone.
• Fission yeast sxa1 which is involved in degrading or processing the mating pheromones.

Most retroviruses and some plant viruses, such as badnaviruses, encode for APs which are β homodimers (see <PDB:1A30>), where the aspartates are located on two loops at the monomer interface and where two β-hairpins cover the active site. In most retroviruses, the protease is encoded as a segment of a polyprotein which is cleaved during the maturation process of the virus. It is generally part of the pol polyprotein and, more rarely, of the gag polyprotein. Retroviral APs form peptidase family A2 of clan AA [E2].

Despite the structural differences and the low sequence identity, it is believed that the eukaryotic and retroviral protease families are evolutionarily related since, in both folds, the cleavage site loops are homologous, the Asp dyad is located at an interface region, and the viral subunits are structurally similar to the N-terminal lobes of the eukaryotic family enzymes. Conservation of the sequence around the two aspartates of eukaryotic APs and around the single active site of the viral proteases allows us to develop a single signature pattern for both groups of protease. A profile was developed to specifically detect viral aspartyl proteases, which are missed by the pattern. Another profile is directed against the eukaryotic peptidase family A1 catalytic domain.