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6  structures 131  species 0  interactions 321  sequences 43  architectures

Family: Pertactin (PF03212)

Summary: Pertactin

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No Pfam abstract.

Literature references

  1. Emsley P, Charles IG, Fairweather NF, Isaacs NW; , Nature 1996;381:90-92.: Structure of Bordetella pertussis virulence factor P.69 pertactin. PUBMED:8609998 EPMC:8609998

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004899

Bordetella pertussis is a Gram-negative, aerobic coccobacillus that causes pertussis (whooping cough), especially in young children [ PUBMED:2542937 ]. Once present in the lungs, the bacterium attaches to ciliated pulmonary epithelial cells via a collection of outer membrane proteins, all of which are virulence factors.

Pertactin, or P69 protein, is one of these virulence factors. Pertactin and filamentous haemagglutinin have been identified as Bordetella adhesins [ PUBMED:1527510 ]. Both proteins contain an arg-gly-asp (RGD) motif that promotes binding to integrins, known to be important in cell mobility and development. The production of most Bordetella virulence factors (including pertactin) is controlled by a two-component signal transduction system, comprising the BvgA regulator and the BvgS sensor [ PUBMED:10943406 ]. Pertactin shares a high level of similarity with other Bordetella adhesins, such as BrkA. The protein is first produced as a 93kDa precursor. Upon secretion into the extracellular environment, a 30kDa domain at the C terminus remains in the outer membrane, while the mature 60.4kDa pertactin molecule is released [ PUBMED:8609998 ].

The crystal structure of mature pertactin has been determined to 2.5A resolution by means of X-ray diffraction. The fold is characterised by a 16-stranded parallel beta-helix, with a V-shaped cross-section. Several between-strand amino-acid repeats form internal and external ladders. The helical structure is interrupted by several protruding loops that contain motifs associated with the activity of the protein. One such sequence - [GGXXP]5 - appears directly after the RGD motif, and may mediate interaction with epithelial cells. The C-terminal region of P.69 pertactin contains a [PQP]5 motif loop, which contains the major immunoprotective epitope [ PUBMED:8609998 ].

The superfamily also includes immunoglobulin A1 protease and adhesion penetration protein HAP.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...


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

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_2005 (release 6.5)
Previous IDs: none
Type: Repeat
Sequence Ontology: SO:0001068
Author: Mifsud W
Number in seed: 8
Number in full: 321
Average length of the domain: 118.30 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 10.63 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.3 21.3
Trusted cut-off 21.3 21.3
Noise cut-off 21.1 21.1
Model length: 121
Family (HMM) version: 16
Download: download the raw HMM for this family

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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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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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 Pertactin domain has been found. There are 6 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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
P33924 View 3D Structure Click here
P52143 View 3D Structure Click here
P76017 View 3D Structure Click here
P77199 View 3D Structure Click here
P77552 View 3D Structure Click here