InterPro domain: IPR018061

Aspartic peptidases, also known as aspartyl proteases ([intenz:3.4.23.-]), are widely distributed proteolytic enzymes [ 1 , 2 , 3 ] known to exist in vertebrates, fungi, plants, protozoa, bacteria, archaea, retroviruses and some plant viruses. All known aspartic peptidases are endopeptidases. A water molecule, activated by two aspartic acid residues, acts as the nucleophile in catalysis. Aspartic peptidases can be grouped into five clans, each of which shows a unique structural fold [ 4 ].

• Peptidases in clan AA are either bilobed (family A1 or the pepsin family) or are a homodimer (all other families in the clan, including retropepsin from HIV-1/AIDS) [ 5 ]. Each lobe consists of a single domain with a closed beta-barrel and each lobe contributes one Asp to form the active site. Most peptidases in the clan are inhibited by the naturally occurring small-molecule inhibitor pepstatin [ 6 ].
• Clan AC contains the single family A8: the signal peptidase 2 family. Members of the family are found in all bacteria. Signal peptidase 2 processes the premurein precursor, removing the signal peptide. The peptidase has four transmembrane domains and the active site is on the periplasmic side of the cell membrane. Cleavage occurs on the amino side of a cysteine where the thiol group has been substituted by a diacylglyceryl group. Site-directed mutagenesis has identified two essential aspartic acid residues which occur in the motifs GNXXDRX and FNXAD (where X is a hydrophobic residue) [ 7 ]. No tertiary structures have been solved for any member of the family, but because of the intramembrane location, the structure is assumed not to be pepsin-like.
• Clan AD contains two families of transmembrane endopeptidases: A22 and A24. These are also known as "GXGD peptidases" because of a common GXGD motif which includes one of the pair of catalytic aspartic acid residues. Structures are known for members of both families and show a unique, common fold with up to nine transmembrane regions [ 8 ]. The active site aspartic acids are located within a large cavity in the membrane into which water can gain access [ 9 ].
• Clan AE contains two families, A25 and A31. Tertiary structures have been solved for members of both families and show a common fold consisting of an alpha-beta-alpha sandwich, in which the beta sheet is five stranded [ 10 , 11 ].
• Clan AF contains the single family A26. Members of the clan are membrane-proteins with a unique fold. Homologues are known only from bacteria. The structure of omptin (also known as OmpT) shows a cylindrical barrel containing ten beta strands inserted in the membrane with the active site residues on the outer surface [ 12 ].
• There are two families of aspartic peptidases for which neither structure nor active site residues are known and these are not assigned to clans. Family A5 includes thermopsin, an endopeptidase found only in thermophilic archaea. Family A36 contains sporulation factor SpoIIGA, which is known to process and activate sigma factor E, one of the transcription factors that controls sporulation in bacteria [ 13 ].

This group of aspartic peptidases belong to the peptidase clan AA. The clan includes the single domain aspartic proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses) which are active as homodimers. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin [ 14 , 14 ].

Family A2 includes the peptidase (retropepsin, EC 3.4.23.16) from the human immunodeficiency virus and other retroviruses. In most retroviruses, the peptidase is encoded as a segment of a polyprotein (usually the pol polyprotein, which includes the peptidase, a reverse transcriptase, RNase H and an integrase, but occassionally the gag polyprotein) which it cleaves during viral maturation to release individual proteins. Some retrotransposon polyproteins also contain a homologous, retropepsin-like peptidase which is also a member of family A2.

Family A3 includes peptidases from the double-stranded DNA plant viruses known as badnaviruses or pararetroviruses. The viral genome includes genes (ORFs IV and V) that encodes polyproteins. The ORF V polyprotein contains the peptidase and a reverse transcriptase. The peptidase processes the ORF IV polyprotein, which includes the viral coat protein [ 15 ].

Family A9 includes peptidases from spumaretroviruses, and the peptidase is a component of either the gag and pol polyprotein, which is processes [ 16 ]. The structure has been solved for the peptidase from simian foamy virus and shows a retropepsin-like fold [ 17 ].

Family A11 includes polyprotein-processing peptidases from retrotransposons such as the copia transposon from Drosophila melanogaster . No tertiary structure has been solved for any member of the family, and family A11 is included in clan AA on the basis of the similar motif around the active site Asp.

Family A28 includes the yeast DNA-damage inducible protein 1 which is a component of the DNA repair pathway. The tertiary structure shows a retropepsin-like fold [ 18 ]. This peptidase is not a component of a polyprotein.

Family A32 includes the bacterial PerP peptidase which converts the transmembrane factor PodJ from a form that recruits proteins for pilus formation, to a truncated form that recruits proteins for stalk formation. This converts the bacterium from a motile form to the sessile form found in biofilms [ 19 ].

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