Prepilin type IV endopeptidase, peptidase domain (IPR000045)

Short name: Prepilin_IV_endopep_pep

Overlapping homologous superfamilies


Domain relationships



This group of aspartic endopeptidases belong to MEROPS peptidase family A24 (type IV prepilin peptidase family). The family is divided into two subfamilies: subfamily A24A includes the type IV prepilin peptidase from bacteria and subfamily A24B includes the preflagellin peptidase from archaea. Peptidases in the family are also known as "GXGD membrane proteases" because of the common motif that includes one of the two active site residues [PMID: 21765428].

Bacteria produce a number of protein precursors that undergo post-translational methylation and proteolysis prior to secretion as active proteins. Type IV prepilin leader peptidases are enzymes that mediate this type of post-translational modification. Type IV pilin is a protein found on the surface of Pseudomonas aeruginosa, Neisseria gonorrhoeae and other Gram-negative pathogens. Pilin subunits attach the infecting organism to the surface of host epithelial cells. They are synthesised as prepilin subunits, which differ from mature pilin by virtue of containing a 6-8 residue leader peptide consisting of charged amino acids. Mature type IV pilins also contain a methylated N-terminal phenylalanine residue.

The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second post-translational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [PMID: 9224881].

In type IV prepilin peptidase, the two active-site Asp residues occur in the motifs Xaa-Xaa-Asp-Xaa-Xbb-Xcc-Xcc-Xcc-Xaa-Pro and Xaa-Gly-Xcc-Gly-Asp-Xaa-Lys-Xaa-Xaa-Xaa (where Xaa is hydrophobic, Xbb is charged and Xcc is any amino acid).

Some archaea possess a flagellum that contains a flagellin protein. Flagellin is synthesized as a precursor with a positively charged leader peptide. This leader peptide is removed by prepilin peptidase before flagellin is incorporated into the filament [PMID: 14622420]. The tertiary structure of the preflagellin peptidase from Methanococcus maripaludis has been solved, and shows a bundle of six helices. The active site residues are far apart on transmembrane helices 1 and 4, which implies that a conformational change is required to activate the peptidase [PMID: 21765428].

This entry represents the peptidase domain from the prepilin type IV endopeptidases [PMID: 10625704]. It can be found on its own, or in the case of the bifunctional enzymes, next to a methylation domain.

Aspartic peptidases, also known as aspartyl proteases ([intenz:3.4.23.-]), are widely distributed proteolytic enzymes [PMID: 6795036, PMID: 2194475, PMID: 1851433] 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 [PMID: 8439290].

  • 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) [PMID: 2682266]. 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 [PMID: 4912600].
  • 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) [PMID: 10497172]. 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 [PMID: 21765428]. The active site aspartic acids are located within a large cavity in the membrane into which water can gain access [PMID: 23254940].
  • 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 [PMID: 10331925, PMID: 10864493].
  • 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 [PMID: 11566868].
  • 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 [PMID: 21751400].

GO terms

Biological Process

No terms assigned in this category.

Molecular Function

GO:0004190 aspartic-type endopeptidase activity

Cellular Component

GO:0016020 membrane

Contributing signatures

Signatures from InterPro member databases are used to construct an entry.