Summary: Beta defensin
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 "Beta defensin". More...
The Wikipedia text that you see displayed here is a download from Wikipedia. This means that the information we display is a copy of the information from the Wikipedia database. The button next to the article title ("Edit Wikipedia article") takes you to the edit page for the article directly within Wikipedia. You should be aware you are not editing our local copy of this information. Any changes that you make to the Wikipedia article will not be displayed here until we next download the article from Wikipedia. We currently download new content on a nightly basis.
Does Pfam agree with the content of the Wikipedia entry ?
Pfam has chosen to link families to Wikipedia articles. In some case we have created or edited these articles but in many other cases we have not made any direct contribution to the content of the article. The Wikipedia community does monitor edits to try to ensure that (a) the quality of article annotation increases, and (b) vandalism is very quickly dealt with. However, we would like to emphasise that Pfam does not curate the Wikipedia entries and we cannot guarantee the accuracy of the information on the Wikipedia page.
Editing Wikipedia articles
Before you edit for the first time
Wikipedia is a free, online encyclopedia. Although anyone can edit or contribute to an article, Wikipedia has some strong editing guidelines and policies, which promote the Wikipedia standard of style and etiquette. Your edits and contributions are more likely to be accepted (and remain) if they are in accordance with this policy.
You should take a few minutes to view the following pages:
How your contribution will be recorded
Anyone can edit a Wikipedia entry. You can do this either as a new user or you can register with Wikipedia and log on. When you click on the "Edit Wikipedia article" button, your browser will direct you to the edit page for this entry in Wikipedia. If you are a registered user and currently logged in, your changes will be recorded under your Wikipedia user name. However, if you are not a registered user or are not logged on, your changes will be logged under your computer's IP address. This has two main implications. Firstly, as a registered Wikipedia user your edits are more likely seen as valuable contribution (although all edits are open to community scrutiny regardless). Secondly, if you edit under an IP address you may be sharing this IP address with other users. If your IP address has previously been blocked (due to being flagged as a source of 'vandalism') your edits will also be blocked. You can find more information on this and creating a user account at Wikipedia.
If you have problems editing a particular page, contact us at firstname.lastname@example.org and we will try to help.
The community annotation is a new facility of the Pfam web site. If you have problems editing or experience problems with these pages please contact us.
Beta defensin Edit Wikipedia article
|SCOPe||1bnb / SUPFAM|
Defensins are 2-6 kDa, cationic, microbicidal peptides active against many Gram-negative and Gram-positive bacteria, fungi, and enveloped viruses, containing three pairs of intramolecular disulfide bonds. On the basis of their size and pattern of disulfide bonding, mammalian defensins are classified into alpha, beta and theta categories. Every mammalian species explored thus far has beta-defensins. In cows, as many as 13 beta-defensins exist in neutrophils. However, in other species, beta-defensins are more often produced by epithelial cells lining various organs (e.g. the epidermis, bronchial tree and genitourinary tract.
Human, rabbit and guinea-pig beta-defensins, as well as human beta-defensin-2 (hBD2), induce the activation and degranulation of mast cells, resulting in the release of histamine and prostaglandin D2.
Î²-defensins are coding for genes which impact the function of the innate immune system. These genes are responsible for production of antimicrobial peptides found in white blood cells such as macrophages, granulocytes and NK-cells, Î²-defensins are also found in epithelial cells. Single-nucleotide polymorphisms (SNPs) are found in genes coding for Î²-defensins. The presences of SNPs are lower in the coding regions compared to non-coding regions. The appearance of SNPs in the coding region will highly likely affecting the resistance against infections through changes in the protein sequences which will give rise to different biological functions.
Receptors such as toll-like receptors (TLR) and nod-like receptors (NLR) will activate the immune system by binding of ligands such as lipopolysaccharides and peptidoglycan. Toll-like receptors are expressed in intestinal epithelial cells  or antigen presenting cells (APCs) such as dendritic cells, B-lymphocytes and macrophages. When the receptors are activated a cascade reaction will take place and substances such as cytokines and antimicrobial peptides  will be released.
Î²-defensins are cationic and can therefore interact with the membrane of invading microbes, which are negative due to lipopolysaccharides (LPS) and lipoteichoic acid (LTA) found in the cell membrane. The peptides have higher affinity to the binding site compared to Ca2+ and Mg2+ ions. The peptides will therefore exchange place with those ions, thus affecting the stability of the membrane. The peptides have a greater size compared with the ions which cause changes in the membrane structure. Due to changes in the electric potential, peptides will pass across the membrane and thus aggregate into dimers. Pore complex will be created as a result of breaking the hydrogen bonds between the amino acids in the terminal end of the strands connecting defensins monomers. Formation of pore complex will cause membrane depolarization and cell lysis.
Defensins not only have the ability to strengthen the innate immune system but can also enhance the adaptive immune system by chemotaxis of monocytes, T-lymphocytes, dendritic cells and mast cells to the infection site. Defensins will also improve the capacity of macrophage phagocytosis.
Î²-defensins are classified in three classes and Avian Î²-defensins constitute for one of the classes. This division is based on Zhangâ€™s classification and both the length, the homology of the peptides and the gene structure are factors affecting the classification.
Avian Î²-defensins are separated in avian heterophiles and non-heterophiles. Avian heterophiles can be divided into two sub-classes, depending on the number of present homologous residues in the genome.
Ostriches have a genome containing the gene coding for the antimicrobial peptide, Ostricacin-1. The presence of this peptide indicate that the genes coding for Î²-defensins have existed for a long time. Ostrich and other ratite species are related to Palaeognathiformes, which is the oldest order of birds living today.
Î²-defensins genes are found in the genome of both ostrich and mammalians. The genes coding for Î²-defensins could originate from genes which existed prior diversification of the avian and the mammalian line, which occurred for around 150 million years ago.
The fact that alpha and theta defensins are absence in older vertebrates, like birds and fishes, indicates that defensins must have evolved from the same ancestral gene coding for Î²-defensins.
Hoover et al. (2001) showed that the origin of defensins were molecules similar to Î²-defensins which are found today, by comparing the amino acids and structures of the origin of Î²-defensins with Î²-defensins from insects and Î±-defensins found in mammalians. The Î²-defensins found in insects were actually more similar to the origin of defensins compared to Î±-defensins found in mammalians. The insects lines have been around for a longer time compared to mammalian lines, which suggest that the ancestor of the genes coding for defensins have existed for a long time.
The first beta-defensin discovered was Tracheal Antimicrobial Peptide, found in the bovine airway in 1991. The first human beta-defensin, HBD1, was discovered in 1995, followed by the HBD2 in 1997.
Human proteins containing this domain
- White SH, Wimley WC, Selsted ME (August 1995). "Structure, function, and membrane integration of defensins". Curr. Opin. Struct. Biol. 5 (4): 521â€“7. doi:10.1016/0959-440X(95)80038-7. PMID 8528769.
- Bensch KW, Raida M, MÃ¤gert HJ, Schulz-Knappe P, Forssmann WG (July 1995). "hBD-1: a novel beta-defensin from human plasma". FEBS Lett. 368 (2): 331â€“5. doi:10.1016/0014-5793(95)00687-5. PMID 7628632.
- Hellgren O, Sheldon BC (July 2011). "Locus-specific protocol for nine different innate immune genes (antimicrobial peptides: Î²-defensins) across passerine bird species reveals within-species coding variation and a case of trans-species polymorphisms". Molecular Ecology Resources. 11 (4): 686â€“692. doi:10.1111/j.1755-0998.2011.02995.x.
- Ganz T (September 2003). "Defensins: antimicrobial peptides of innate immunity". Nat. Rev. Immunol. 3 (9): 710â€“20. doi:10.1038/nri1180. PMID 12949495.
- van Dijk A, Veldhuizen EJ, Haagsman HP (July 2008). "Avian defensins". Vet. Immunol. Immunopathol. 124 (1â€“2): 1â€“18. doi:10.1016/j.vetimm.2007.12.006. PMID 18313763.
- Mogensen TH (April 2009). "Pathogen recognition and inflammatory signaling in innate immune defenses". Clin. Microbiol. Rev. 22 (2): 240â€“73, Table of Contents. doi:10.1128/CMR.00046-08. PMC 2668232. PMID 19366914.
- Abreu MT (February 2010). "Toll-like receptor signalling in the intestinal epithelium: how bacterial recognition shapes intestinal function". Nat. Rev. Immunol. 10 (2): 131â€“44. doi:10.1038/nri2707. PMID 20098461.
- Vora P, Youdim A, Thomas LS, Fukata M, Tesfay SY, Lukasek K, Michelsen KS, Wada A, Hirayama T, Arditi M, Abreu MT (November 2004). "Beta-defensin-2 expression is regulated by TLR signaling in intestinal epithelial cells". J. Immunol. 173 (9): 5398â€“405. doi:10.4049/jimmunol.173.9.5398. PMID 15494486.
- Sugiarto H, Yu PL (October 2004). "Avian antimicrobial peptides: the defense role of beta-defensins". Biochem. Biophys. Res. Commun. 323 (3): 721â€“7. doi:10.1016/j.bbrc.2004.08.162. PMID 15381059.
- Yu P-L, Choudhury SD, Ahrens K (January 2001). "Purification and characterization of the antimicrobial peptide, ostricacin". Biotechnology Letters. 23 (3): 207â€“210. doi:10.1023/A:1005623806445.
- Hedges SB, Parker PH, Sibley CG, Kumar S (May 1996). "Continental breakup and the ordinal diversification of birds and mammals". Nature. 381 (6579): 226â€“9. doi:10.1038/381226a0. PMID 8622763.
- Semple CA, Rolfe M, Dorin JR (2003). "Duplication and selection in the evolution of primate beta-defensin genes". Genome Biol. 4 (5): R31. doi:10.1186/gb-2003-4-5-r31. PMC 156587. PMID 12734011.
- Hoover DM, Chertov O, Lubkowski J (October 2001). "The structure of human beta-defensin-1: new insights into structural properties of beta-defensins". J. Biol. Chem. 276 (42): 39021â€“6. doi:10.1074/jbc.M103830200. PMID 11486002.
- Diamond, G.; Zasloff, M.; Eck, H.; Brasseur, M.; Maloy, W.; Bevins, C. (1991). "Tracheal antimicrobial peptide, a novel cysteine-rich peptide from mammalian tracheal mucosa: Peptide isolation and cloning of a cDNA". Proc. Natl. Acad. Sci. USA. 88: 3952â€“3956. doi:10.1073/pnas.88.9.3952. PMC 51571. PMID 2023943.
- Harder J, Siebert R, Zhang Y, Matthiesen P, Christophers E, Schlegelberger B, SchrÃ¶der JM (December 1997). "Mapping of the gene encoding human beta-defensin-2 (DEFB2) to chromosome region 8p22-p23.1". Genomics. 46 (3): 472â€“5. doi:10.1006/geno.1997.5074. PMID 9441752.
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.
Beta defensin Provide feedback
The beta defensins are antimicrobial peptides implicated in the resistance of epithelial surfaces to microbial colonisation .
Internal database links
|Similarity to PfamA using HHSearch:||Defensin_beta|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR025933
The beta defensins are antimicrobial peptides implicated in the resistance of epithelial surfaces to microbial colonisation [PUBMED:7628632].
Defensins are 2-6kDa, cationic, microbicidal peptides active against many Gram-negative and Gram-positive bacteria, fungi, and enveloped viruses [PUBMED:8528769], containing three pairs of intramolecular disulphide bonds. On the basis of their size and pattern of disulphide bonding, mammalian defensins are classified into alpha, beta and theta categories. Every mammalian species explored thus far has beta-defensins. In cows, as many as 13 beta-defensins exist in neutrophils. However, in other species, beta-defensins are more often produced by epithelial cells lining various organs (e.g. the epidermis, bronchial tree and genitourinary tract).
Defensins are produced constitutively and/or in response to microbial products or proinflammatory cytokines. Some defensins are also called corticostatins (CS) because they inhibit corticotropin-stimulated corticosteroid production. The mechanism(s) by which microorganisms are killed and/or inactivated by defensins is not understood completely. However, it is generally believed that killing is a consequence of disruption of the microbial membrane. The polar topology of defensins, with spatially separated charged and hydrophobic regions, allows them to insert themselves into the phospholipid membranes so that their hydrophobic regions are buried within the lipid membrane interior and their charged (mostly cationic) regions interact with anionic phospholipid head groups and water. Subsequently, some defensins can aggregate to form `channel-like' pores; others might bind to and cover the microbial membrane in a `carpet-like' manner. The net outcome is the disruption of membrane integrity and function, which ultimately leads to the lysis of microorganisms. Some defensins are synthesised as propeptides which may be relevant to this process.
Human, rabbit and guinea-pig beta-defensins, as well as human beta-defensin-2 (hBD2), induce the activation and degranulation of mast cells, resulting in the release of histamine and prostaglandin D2.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||extracellular region (GO:0005576)|
|Biological process||innate immune response (GO:0045087)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- a link to the page in the Pfam site showing information about the sequence that the graphic describes
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Note that you can see the family page for a particular domain by clicking on the graphic. You can also choose to see all sequences which have a given architecture by clicking on the Show link in each row.
Finally, because some families can be found in a very large number of architectures, we load only the first fifty architectures by default. If you want to see more architectures, click the button at the bottom of the page to load the next set.
Loading domain graphics...
This clan includes diverse defensins as well as myotoxins.
The clan contains the following 15 members:DEFB136 Defensin_1 Defensin_3 Defensin_4 Defensin_beta Defensin_beta_2 Defensin_big Defensin_int Defensin_RK-1 Inhibitor_I68 Laterosporulin Meleagrin Myotoxins Pelovaterin Toxin_4
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...
There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- a Java applet developed at the University of Dundee. You will need Java installed before running jalview
- an HTML page showing the whole alignment.Please note: full Pfam alignments can be very large. These HTML views are extremely large and often cause problems for browsers. Please use either jalview or the Pfam viewer if you have trouble viewing the HTML version
- an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.
You can download (or view in your browser) a text representation of a Pfam alignment in various formats:
You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.
You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.
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.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
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.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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...
If you find these logos useful in your own work, please consider citing the following article:
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.
|Number in seed:||95|
|Number in full:||1074|
|Average length of the domain:||30.50 aa|
|Average identity of full alignment:||36 %|
|Average coverage of the sequence by the domain:||36.32 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||7|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
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.
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 Defensin_beta_2 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.
Loading structure mapping...