Summary for clan AA

Summary Alignment Structure Literature
Clan type peptidaseA01.001 - pepsin A (Homo sapiens), MEROPS Accession MER0000885 (peptidase unit: 63-388); PDB accession 1PSO
HistoryBiochem.J. 290:205-218 (1993)
DescriptionWater nucleophile; water bound by two Asp from monomer or dimer; all endopeptidases, from eukaryote organisms, some bacteria and viruses or virus-like organisms
Contents of clanPeptidase clan AA contains endopeptidases.
EvidencePepsin A (A01.001) is the type peptidase of clan AA, and the structure of retropepsin (A02.001) resembles that of one of the structural domains of pepsin. A sequence motif that contains the active site Asp residues can be recognised in all the families of the clan. This is Xaa-Xaa-Asp-Xbb-Gly-Xcc, where a Xaa is hydrophobic, Xbb is Thr or Ser, and Xcc is Ser, Thr or Ala (see the Alignment). Histoaspartic peptidase (A01.043) in family A1 has one Asp replaced by His.
Catalytic mechanismActivity is dependent upon two aspartic residues, which support a water molecule that is the nucleophile in catalysis. Accordingly, the peptidases of clan AA are termed 'water nucleophile' peptidases in MEROPS. The catalytic mechanism has been reviewed by James (2004).
Peptidase activityAll the peptidases in clan AA are endopeptidases, and the great majority have pH optima at acidic pH. Hydrophobic residues are commonly preferred near the scissile bond.
Protein foldTertiary structures have been determined for members of families A1 (for example pepsin A, Fujinaga et al., 1995) and A2 (Jaskolski et al., 1991). Peptidases in family A1 are all-beta proteins consisting of two similar beta barrel domains, each of which contributes one active site Asp. Each domain contains two psi-loops, which are parallel beta strands that resemble the Greek letter psi. One of the psi-loops contains the active site Asp and a second conserved "hydrophobic-hydrophobic-Gly" motif (Castillo et al., 1999). The barrel domains are believed to be derived from a very ancient duplication event. The N-terminal barrel is partially open and carries a beta hairpin loop known as the 'flap' which carries residues important for specificity, especially Tyr137, that interact with the substrate and are part of the S1 subsite. The C-terminal barrel is closed. In family A2, the protein consists of a single beta barrel domain and to form an active peptidase dimerization must occur, producing a structure very similar to that of pepsin, except that the flap is not present.
EvolutionClan AA is unusual in being unknown from all but a few prokaryotic organisms, and may have arisen in an early eukaryote. The prokaryote homologues may have arisen by lateral transfer of a eukaryote gene.
Homologous non-peptidase familiesThe beta barrel domain, also known as a double-psi beta barrel (because the domain contains two psi-loops), has been in several families of proteins that are not peptidases, including the enzymes dimethylsulfoxide reductase, formate dehydrogenase H, endoglucanase V and the plant defense protein barwin. A circular permutation of the secondary structure elements has occurred in the aspartic proteinases (Castillo et al., 1999).
Activation mechanismMost of the peptidases in family A1 have proenzymes that are activated by cleavage of the propeptide, like pepsin (A01.001: Sielecki et al., 1991). The peptidases in the other families are encoded in the polyproteins of viruses and transposons, and they become active only when two monomers assemble to form the catalytically active dimer (Ingr et al., 2003).
Other databases PFAMCL0129


Family Family Type Peptidase Structure
A1 pepsin A (Homo sapiens) Yes
A2 HIV-1 retropepsin (human immunodeficiency virus 1) Yes
A3 cauliflower mosaic virus-type peptidase (cauliflower mosaic virus) -
A9 spumapepsin (human spumaretrovirus) Yes
A11 Copia transposon peptidase (Drosophila melanogaster) -
A28 DNA-damage inducible protein 1 (Saccharomyces cerevisiae) Yes
A32 PerP peptidase ({Caulobacter} sp.) (Caulobacter crescentus) -

Distribution of clan AA among Kingdoms of Organisms