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2  structures 5518  species 0  interactions 8718  sequences 14  architectures

Family: Peptidase_A24 (PF01478)

Summary: Type IV leader peptidase family

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Type IV leader peptidase family Provide feedback

Peptidase A24, or the prepilin peptidase as it is also known, processes the N-terminus of the prepilins [1]. The processing is essential for the correct formation of the pseudopili of type IV bacterial protein secretion. The enzyme is found across eubacteria and archaea [2].

Literature references

  1. LaPointe CF, Taylor RK; , J Biol Chem 2000;275:1502-1510.: The type 4 prepilin peptidases comprise a novel family of aspartic acid proteases. PUBMED:10625704 EPMC:10625704

  2. Albers SV, Szabo Z, Driessen AJ; , J Bacteriol 2003;185:3918-3925.: Archaeal homolog of bacterial type IV prepilin signal peptidases with broad substrate specificity. PUBMED:12813086 EPMC:12813086

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000045

Aspartic peptidases, also known as aspartyl proteases ([intenz:3.4.23.-]), are widely distributed proteolytic enzymes [ PUBMED:6795036 , PUBMED:2194475 , PUBMED: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 [ PUBMED: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) [ PUBMED: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 [ PUBMED: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) [ PUBMED: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 [ PUBMED:21765428 ]. The active site aspartic acids are located within a large cavity in the membrane into which water can gain access [ PUBMED: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 [ PUBMED:10331925 , PUBMED: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 [ PUBMED: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 [ PUBMED:21751400 ].

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 [ PUBMED: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 [ PUBMED: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 [ PUBMED: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 [ PUBMED:21765428 ].

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

Gene Ontology

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Domain organisation

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Pfam Clan

This family is a member of clan Peptidase_AD (CL0130), which has the following description:

Members of this clan are peptidases that are integral membrane proteins. The catalytic aspartate is in the conserved GXGD motif.

The clan contains the following 4 members:

Peptidase_A22B Peptidase_A24 Presenilin SPP


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This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

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Curation View help on the curation process

Seed source: Yeats C
Previous IDs: Peptidase_C20;
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A , Yeats C
Number in seed: 72
Number in full: 8718
Average length of the domain: 111.60 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 49.70 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.5 26.5
Trusted cut-off 26.5 26.5
Noise cut-off 26.4 26.4
Model length: 107
Family (HMM) version: 21
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Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Peptidase_A24 domain has been found. There are 2 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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