InterPro domain: IPR034161

Aspartyl proteases (APs), also known as acid proteases, ([intenz:3.4.23.-]) are a widely distributed family of proteolytic enzymes [ 1 , 2 , 3 , 4 , 5 , 6 ] 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 alpha/beta monomers composed of two asymmetric lobes ("bilobed"). Each of the lobes provides a catalytic Asp residue, positioned within the hallmark motif Asp-Thr/Ser-Gly, to the active site. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The enzymes specifically cleave bonds in peptides which have at least six residues in length with hydrophobic residues in both the P1 and P1' positions. The active site is located at the groove formed by the two lobes, with an extended loop projecting over the cleft to form an 11-residue flap, which encloses substrates and inhibitors in the active site. Specificity is determined by nearest-neighbour hydrophobic residues surrounding the catalytic aspartates, and by three residues in the flap. The enzymes are mostly secreted from cells as inactive proenzymes that activate autocatalytically at acidic pH. Eukaryotic APs form peptidase family A1 of clan AA.

This entry represents a domain found in aspartic endopeptidases from plants including nepenthesin (MEROPS identifier A01.040), a digestive enzyme from the pitcher of the carnivorous pitcher plant Nepenthes [ 7 ]; CDR1 endopeptidase (=Constitutive Disease Resistance 1; MEROPS identifier A01.069) from the Arabidopsis apoplast involved in disease resistance signalling and which is not inhibited by pepstatin [ 8 ]; PCS1 peptidase (MEROPS identifier A01.074) which is important for protecting cells from apoptosis during embryo development [ 9 ]; and S5 peptidases (MEROPS identifier A01.086), which exist as homo- and hetero- dimers and formation of heterodimers leads to embryo-sac abortion resulting in sterility [ 10 ]. Proteins containing this domain belong to the aspartic peptidase A1 family (peptidase family A1, subfamily A1B).

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2. The structure and function of the aspartic proteinases. Biochemistry 19, 189-215
3. Structural and evolutionary relationships between retroviral and eucaryotic aspartic proteinases. Essays Biochem. 30, 4663-71
4. Evolutionarily conserved functional mechanics across pepsin-like and retroviral aspartic proteases. Genome Biol Evol 127, 3734-42
5. Extensive expansion of A1 family aspartic proteinases in fungi revealed by evolutionary analyses of 107 complete eukaryotic proteomes. Acta Crystallogr F Struct Biol Commun 6, 1480-94
6. The aspartic proteases. J. Am. Chem. Soc. 210, 5-22
7. Crystallization of nepenthesin I using a low-pH crystallization screen. J. Biol. Chem. 72, 24-8
8. Characterization of recombinant CDR1, an Arabidopsis aspartic proteinase involved in disease resistance. EMBO Rep. 282, 31358-65
9. An Arabidopsis aspartic protease functions as an anti-cell-death component in reproduction and embryogenesis. Plant Physiol. 6, 282-8
10. Molecular basis underlying the S5-dependent reproductive isolation and compatibility of indica/japonica rice hybrids. null 158, 1319-28