Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
50  structures 289  species 1  interaction 451  sequences 11  architectures

Family: Pilin (PF00114)

Summary: Pilin (bacterial filament)

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Pilin". More...

Pilin Edit Wikipedia article

Pilin (bacterial filament)
Pilin-2pil.png
Pilin protein from Neisseria gonorrhoeae, a parasitic bacterium that requires functional pili for pathogenesis.
Identifiers
Symbol Pilin
Pfam PF00114
InterPro IPR001082
PROSITE PDOC00342
SCOP 1paj
SUPERFAMILY 1paj
OPM superfamily 74
OPM protein 2hil

Pilin refers to a class of fibrous proteins that are found in pilus structures in bacteria. Bacterial pili are used in the exchange of genetic material during bacterial conjugation, while a shorter type of appendages also made up of pilin, called fimbriae, are used as a cell adhesion mechanism. Although not all bacteria have pili or fimbriae, bacterial pathogens often use their fimbriae to attach to host cells. In Gram-negative bacteria, where pili are more common, individual pilin molecules are linked by noncovalent protein-protein interactions, while Gram-positive bacteria often have polymerized pilin.[1]

Some pilin proteins are α+β proteins characterized by a very long N-terminal alpha helix. The assembly of these pili relies on interactions between the N-terminal helices of the individual monomers. The pilus structure sequesters the helices in the center of the fiber lining a central pore, while antiparallel beta sheets occupy the exterior of the fiber.[2] The exact mechanism of assembly of these pili from monomers is not known, although chaperone proteins have been identified for some types of pilin.[3] and specific amino acids required for proper pilus formation have been isolated.[4]

Development of molecular tools

Pili in Gram-positive bacteria contain spontaneously formed isopeptide bonds. These bonds provide enhanced mechanical[5] and proteolytic[6] stability to the pilin protein. Recently, the pilin protein from Streptococcus pyogenes has been split into two fragments to develop a new molecular tool called the isopeptag.[7] The isopeptag is a short peptide that can be attached to a protein of interest and can bind its binding partner through a spontaneously formed isopeptide bond. This new peptide tag can allow scientists to target and isolate their proteins of interest through a permanent covalent bond.

Role of ComP pilin in bacterial transformation

Genetic transformation is the process by which a recipient bacterial cell takes up DNA from a neighboring cell and integrates this DNA into the recipient’s genome by homologous recombination. In Neisseria meningitides, DNA transformation requires the presence of short DNA uptake sequences (DUSs) which are 9-10mers residing in coding regions of the donor DNA. Specific recognition of DUSs is mediated by a type IV pilin, ComP.[8][9] Menningococcal type IV pili bind DNA through the minor pilin ComP via an electropositive stripe that is predicted to be exposed on the filament's surface. ComP displays an exquisite binding preference for selective DUSs. The distribution of DUSs within the N. meningitides genome favors certain genes, suggesting that there is a bias for genes involved in genomic maintenance and repair.[10][11]

References

  1. ^ Telford JL, Barocchi MA, Margarit I, Rappuoli R, Grandi G (2006). "Pili in gram-positive pathogens". Nat. Rev. Microbiol. 4 (7): 509–19. doi:10.1038/nrmicro1443. PMID 16778837. 
  2. ^ Forest KT, Tainer JA (1997). "Type-4 pilus-structure: outside to inside and top to bottom--a minireview". Gene. 192 (1): 165–9. doi:10.1016/s0378-1119(97)00008-5. PMID 9224887. 
  3. ^ Jones CH, Pinkner JS, Nicholes AV, Slonim LN, Abraham SN, Hultgren SJ (1993). "FimC is a periplasmic PapD-like chaperone that directs assembly of type 1 pili in bacteria". Proc. Natl. Acad. Sci. U.S.A. 90 (18): 8397–401. doi:10.1073/pnas.90.18.8397. PMC 47363Freely accessible. PMID 8104335. 
  4. ^ Mu XQ, Jiang ZG, Bullitt E (2005). "Localization of a critical interface for helical rod formation of bacterial adhesion P-pili". J. Mol. Biol. 346 (1): 13–20. doi:10.1016/j.jmb.2004.11.037. PMID 15663923. 
  5. ^ Alegre-Cebollada J, Badilla CL, Fernández JM (2010). "Isopeptide bonds block the mechanical extension of pili in pathogenic Streptococcus pyogenes". J. Biol. Chem. 285 (15): 11235–11242. doi:10.1074/jbc.M110.102962. PMC 2857001Freely accessible. PMID 20139067. 
  6. ^ Kang HJ, Coulibaly F, Clow F, Proft T, Baker EN (2007). "Stabilizing isopeptide bonds revealed in gram-positive bacterial pilus structure". Science. 318: 1625–1628. doi:10.1126/science.1145806. 
  7. ^ Zakeri B, Howarth M (2010). "Spontaneous intermolecular amide bond formation between side chains for irreversible peptide targeting". J. Am. Chem. Soc. 132 (13): 4526–7. doi:10.1021/ja910795a. PMID 20235501. 
  8. ^ Berry JL, Cehovin A, McDowell MA, Lea SM, Pelicic V (2013). "Functional analysis of the interdependence between DNA uptake sequence and its cognate ComP receptor during natural transformation in Neisseria species". PLoS Genet. 9 (12): e1004014. doi:10.1371/journal.pgen.1004014. PMC 3868556Freely accessible. PMID 24385921. 
  9. ^ Cehovin A, Simpson PJ, McDowell MA, Brown DR, Noschese R, Pallett M, Brady J, Baldwin GS, Lea SM, Matthews SJ, Pelicic V (2013). "Specific DNA recognition mediated by a type IV pilin". Proc. Natl. Acad. Sci. U.S.A. 110 (8): 3065–70. doi:10.1073/pnas.1218832110. PMC 3581936Freely accessible. PMID 23386723. 
  10. ^ Davidsen T, Rødland EA, Lagesen K, Seeberg E, Rognes T, Tønjum T (2004). "Biased distribution of DNA uptake sequences towards genome maintenance genes". Nucleic Acids Res. 32 (3): 1050–8. doi:10.1093/nar/gkh255. PMC 373393Freely accessible. PMID 14960717. 
  11. ^ Caugant DA, Maiden MC (2009). "Meningococcal carriage and disease--population biology and evolution". Vaccine. 27 Suppl 2: B64–70. doi:10.1016/j.vaccine.2009.04.061. PMC 2719693Freely accessible. PMID 19464092. 

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Pilin (bacterial filament) Provide feedback

Proteins with only the short N-terminal methylation site are not separated from the noise. The Prosite pattern detects those better.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001082

Pilin is a subunit of the pilus, a polar flexible filament, which consists of a single polypeptide chain arranged in a helical configuration of five subunits per turn. Gram-negative bacteria produce pilin which is characterised by the presence of a very short leader peptide of 6 to 7 residues, followed by a methylated N-terminal phenylalanine residue and by a highly conserved sequence of about 24 hydrophobic residues, of the NMePhe type pilin [PUBMED:2898203, PUBMED:3118043].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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

Loading domain graphics...

Pfam Clan

This family is a member of clan Pilus (CL0327), which has the following description:

This is a clan contains bacterial pilus subunits and proteins involved in secretion. Pili proteins enable the transfer of plasmid between bacteria. The families in this clan adopt an alpha helical structure which is packed against a beta sheet [2-3].

The clan contains the following 11 members:

Bundlin ComP_DUS Pilin Pilin_GH Pilin_PilX PilS T2SSG T2SSI T2SSJ TcpA YadA_anchor

Alignments

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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

View options

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.

  Seed
(141)
Full
(451)
Representative proteomes UniProt
(3078)
NCBI
(7014)
Meta
(90)
RP15
(100)
RP35
(321)
RP55
(625)
RP75
(1147)
Jalview View  View  View  View  View  View  View  View  View 
HTML View  View               
PP/heatmap 1 View               

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(141)
Full
(451)
Representative proteomes UniProt
(3078)
NCBI
(7014)
Meta
(90)
RP15
(100)
RP35
(321)
RP55
(625)
RP75
(1147)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(141)
Full
(451)
Representative proteomes UniProt
(3078)
NCBI
(7014)
Meta
(90)
RP15
(100)
RP35
(321)
RP55
(625)
RP75
(1147)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download   Download  

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

HMM logo

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...

Trees

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.

Note: You can also download the data file for the tree.

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: Prosite
Previous IDs: pilin;
Type: Domain
Author: Sonnhammer ELL
Number in seed: 141
Number in full: 451
Average length of the domain: 112.20 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 66.40 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.8 21.8
Trusted cut-off 21.8 21.8
Noise cut-off 21.7 21.7
Model length: 109
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

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

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Interactions

There is 1 interaction for this family. More...

Pilin

Structures

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 Pilin domain has been found. There are 50 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 seqence.

Loading structure mapping...