PROSITE documentation PDOC50990
Peptidase family C39 domain profile


ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily which uses the hydrolysis of ATP to energize diverse biological import and export systems (see <PDOC00185>). ABC transporters are constituted at least of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD) (see <PDOC00364>). These regions can be found on the same protein (mostly bacterial exporters and eukaryotes) or on two different ones (mostly bacterial importers) [1,2,3]. Nevertheless, in a wide range of ABC exporters, an additional protease domain of about 130 amino acid residues is found to be fused to the TMD and the NBD. This domain is a maturation protease for certain peptide bacteriocins, namely those containing the double glycine leader motif. These include class II bacteriocins of Gram-positive and Gram-negative bacteria, as well as some of the lantibiotics, the CSPs (competence stimulating peptide) and peptides pheromones. The proteolytic domain reside in the N-terminal region of the protein. It is a thiol peptidase and belongs to the C39 peptidase family [E1].

Thus all bacteriocin precursors containing double-glycine-type leader peptides are processed and export concomitantly by a proteolytic domain residing in the N-termini of their dedicated ABC transporter. It appears that this kind of processing is more efficient [4,5]. It results in cleavage and translocation of both peptides simultaneously, probably by processing the signal peptide and exporting the resulting mature lantibiotic. A number of the proteins are classified as non-peptidase homologues as they either have been found experimentally to be without peptidase activity, or to lack amino acid residues that are believed to be essential for the catalytic activity. Even though these domains have lost their proteolytic properties they still serve as substrate-recognition domains [6].

All different types of transporters containing an ABC peptidase domain are listed below (references are only provided for recently characterized proteins) [E2].

  • Lantibiotic exporter: hemolysin/bacteriocin (cylB).
  • Micrococin B17 exporter (mcbF).
  • Peptide-2 exporter: competence factor (comA/comB).
  • Protein-1 exporter: hemolysin (hlyB).
  • Protein-2 exporter: colicin V(cvaB).
  • Pediocin exporter (pedD).

The profile does not recognize other ABC proteases involved in complex export, which seem to be serine proteases. These are not fused to the TMD- NBD, and seem not to be evolutionnary related to this kind of fused proteases.

Last update:

May 2004 / First entry.


Technical section

PROSITE method (with tools and information) covered by this documentation:

PEPTIDASE_C39, PS50990; Peptidase family C39 domain profile  (MATRIX)


1AuthorsHolland I.B. Cole S.P.C. Kuchler K. Higgins C.F.
Source(In) ABC proteins from bacteria to man, Academic Press, San Diego, (2003).

2AuthorsHolland I.B. Blight M.A.
SourceJ. Mol. Biol. 293:381-399(1999).

3AuthorsSaurin W. Hofnung M. Dassa E.
TitleGetting in or out: early segregation between importers and exporters in the evolution of ATP-binding cassette (ABC) transporters.
SourceJ. Mol. Evol. 48:22-41(1999).
PubMed ID9873074

4AuthorsMichiels J. Dirix G. Vanderleyden J. Xi C.
TitleProcessing and export of peptide pheromones and bacteriocins in Gram-negative bacteria.
SourceTrends Microbiol. 9:164-168(2001).
PubMed ID11286880

5AuthorsVenema K. Kok J. Marugg J.D. Toonen M.Y. Ledeboer A.M. Venema G. Chikindas M.L.
TitleFunctional analysis of the pediocin operon of Pediococcus acidilactici PAC1.0: PedB is the immunity protein and PedD is the precursor processing enzyme.
SourceMol. Microbiol. 17:515-522(1995).
PubMed ID8559070

6AuthorsHavarstein L.S. Diep D.B. Nes I.F.
TitleA family of bacteriocin ABC transporters carry out proteolytic processing of their substrates concomitant with export.
SourceMol. Microbiol. 16:229-240(1995).
PubMed ID7565085



PROSITE is copyrighted by the SIB Swiss Institute of Bioinformatics and distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives (CC BY-NC-ND 4.0) License, see prosite_license.html.


View entry in original PROSITE document format
View entry in raw text format (no links)