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69  structures 80  species 1  interaction 464  sequences 4  architectures

Family: Defensin_beta (PF00711)

Summary: Beta defensin

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Beta defensin Edit Wikipedia article

Beta defensin
1ijv.gif
Identifiers
Symbol Defensin_beta
Pfam PF00711
InterPro IPR001855
SCOP 1bnb
SUPERFAMILY 1bnb
OPM superfamily 56
OPM protein 1ut3

Beta defensins are a family of mammalian defensins. The beta defensins are antimicrobial peptides implicated in the resistance of epithelial surfaces to microbial colonization.

Defensins are 2-6 kDa, cationic, microbicidal peptides active against many Gram-negative and Gram-positive bacteria, fungi, and enveloped viruses,[1] 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.[2]

Genes[edit]

β-defensins are coding for genes which impact the function of the innate immune system.[3] These genes are responsible for production of antimicrobial peptides found in white blood cells such as macrophages, granulocytes and NK-cells, β-defensins are also found in epithelial cells.[4] Single-nucleotide polymorphisms (SNPs) are found in genes coding for β-defensins.[5] The presences of SNPs are lower in the coding regions compared to non-coding regions.[5] 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.[5]

Initiation[edit]

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.[6] Toll-like receptors are expressed in antigen presenting cells (APCs) such as dendritic cells, B-lymphocytes and macrophages.[6] When the receptors are activated a cascade reaction will take place and substances such as cytokines and antimicrobial peptides will be released.[6]

Function[edit]

β-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.[1] The peptides have higher affinity to the binding site compared to Ca2+ and Mg2+ ions.[5] The peptides will therefore exchange place with those ions, thus affecting the stability of the membrane.[5] The peptides have a greater size compared with the ions which cause changes in the membrane structure.[5] Due to changes in the electric potential, peptides will pass across the membrane and thus aggregate into dimers.[7] 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.[7] Formation of pore complex will cause membrane depolarization and cell lysis.[5]

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.[5] Defensins will also improve the capacity of macrophage phagocytosis.[5]

Avian β-defensins[edit]

β-defensins are classified in three classes and Avian β-defensins constitute for one of the classes.[3] This division is based on Zhang’s classification and both the length, the homology of the peptides and the gene structure are factors affecting the classification.[7]

Avian β-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.[7]

Avian heterophiles lack protective oxidative mechanisms, such as superoxide and myeloperoxidase. Making non-oxidative mechanisms, such as lysosomes and cationic peptides, even more important.[7]

Evolution[edit]

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 β-defensins have existed for a long time.[7]Ostrich and other ratite species are related to Palaeognathiformes, which is the oldest order of birds living today.[8]

β-defensins genes are found in the genome of both ostrich and mammalians.[7] The genes coding for β-defensins could originate from genes which existed prior diversification of the avian and the mammalian line, which occurred for around 150 million years ago.[9]

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 β-defensins.[10]

Hoover et al. (2001) showed that the origin of defensins were molecules similar to β-defensins which are found today, by comparing the amino acids and structures of the origin of β-defensins with β-defensins from insects and α-defensins found in mammalians.[11] The β-defensins found in insects were actually more similar to the origin of defensins compared to α-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.[7]

The first human beta-defensin, HBD1, was discovered in 1995,[2] followed by the HBD2 in 1997.[12]

Human proteins containing this domain[edit]

DEFB1; DEFB103A; DEFB105A; DEFB105B; DEFB108B; DEFB109; DEFB110; DEFB111; DEFB114; DEFB130; DEFB136; DEFB4; SPAG11A;

References[edit]

  1. ^ a b White SH, Wimley WC, Selsted ME (August 1995). "Structure, function, and membrane integration of defensins". Curr. Opin. Struct. Biol. 5 (4): 521–7. doi:10.1016/0959-440X(95)80038-7. PMID 8528769. 
  2. ^ a b Bensch KW, Raida M, Mägert HJ, Schulz-Knappe P, Forssmann WG (July 1995). "hBD-1: a novel beta-defensin from human plasma". FEBS Lett. 368 (2): 331–5. doi:10.1016/0014-5793(95)00687-5. PMID 7628632. 
  3. ^ a b Hellgren O, Sheldon BC (July 2011). "Locus-specific protocol for nine different innate immune genes (antimicrobial peptides: β-defensins) across passerine bird species reveals within-species coding variation and a case of trans-species polymorphisms". Molecular Ecology Resources 11 (4): 686–692. doi:10.1111/j.1755-0998.2011.02995.x. 
  4. ^ Ganz T (September 2003). "Defensins: antimicrobial peptides of innate immunity". Nat. Rev. Immunol. 3 (9): 710–20. doi:10.1038/nri1180. PMID 12949495. 
  5. ^ a b c d e f g h i van Dijk A, Veldhuizen EJ, Haagsman HP (July 2008). "Avian defensins". Vet. Immunol. Immunopathol. 124 (1-2): 1–18. doi:10.1016/j.vetimm.2007.12.006. PMID 18313763. 
  6. ^ a b c Mogensen TH (April 2009). "Pathogen recognition and inflammatory signaling in innate immune defenses". Clin. Microbiol. Rev. 22 (2): 240–73, Table of Contents. doi:10.1128/CMR.00046-08. PMC 2668232. PMID 19366914. 
  7. ^ a b c d e f g h Sugiarto H, Yu PL (October 2004). "Avian antimicrobial peptides: the defense role of beta-defensins". Biochem. Biophys. Res. Commun. 323 (3): 721–7. doi:10.1016/j.bbrc.2004.08.162. PMID 15381059. 
  8. ^ Yu P-L, Choudhury SD, Ahrens K (January 2001). Biotechnology Letters 23 (3): 207–210. doi:10.1023/A:1005623806445. 
  9. ^ Hedges SB, Parker PH, Sibley CG, Kumar S (May 1996). "Continental breakup and the ordinal diversification of birds and mammals". Nature 381 (6579): 226–9. doi:10.1038/381226a0. PMID 8622763. 
  10. ^ 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. 
  11. ^ 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): 39021–6. doi:10.1074/jbc.M103830200. PMID 11486002. 
  12. ^ Harder J, Siebert R, Zhang Y, Matthiesen P, Christophers E, Schlegelberger B, Schröder JM (December 1997). "Mapping of the gene encoding human beta-defensin-2 (DEFB2) to chromosome region 8p22-p23.1". Genomics 46 (3): 472–5. doi:10.1006/geno.1997.5074. PMID 9441752. 

Further reading[edit]

  • Liu L, Zhao C, Heng HH, Ganz T (August 1997). "The human beta-defensin-1 and alpha-defensins are encoded by adjacent genes: two peptide families with differing disulfide topology share a common ancestry". Genomics 43 (3): 316–20. doi:10.1006/geno.1997.4801. PMID 9268634. 

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The beta defensins are antimicrobial peptides implicated in the resistance of epithelial surfaces to microbial colonisation [1].

Literature references

  1. Bensch KW, Raida M, Magert HJ, Schulz-Knappe P, Forssmann WG; , FEBS Lett 1995;368:331-335.: hBD-1: a novel beta-defensin from human plasma. PUBMED:7628632 EPMC:7628632

  2. Liu L, Zhao C, Heng HH, Ganz T; , Genomics 1997;43:316-320.: The human beta-defensin-1 and alpha-defensins are encoded by adjacent genes: two peptide families with differing disulfide topology share a common ancestry. PUBMED:9268634 EPMC:9268634


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001855

Defensins are 2-6 kDa, 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.

This entry represents a range of Beta defensins.

Gene Ontology

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Domain organisation

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Pfam Clan

This family is a member of clan Defensin (CL0075), which has the following description:

This clan includes diverse defensins as well as myotoxins.

The clan contains the following 7 members:

Defensin_1 Defensin_3 Defensin_4 Defensin_beta Defensin_beta_2 Defensin_big Toxin_4

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RP15
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RP75
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Seed source: Pfam-B_675 (release 2.1)
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 54
Number in full: 464
Average length of the domain: 34.50 aa
Average identity of full alignment: 32 %
Average coverage of the sequence by the domain: 54.72 %

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build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.0 21.0
Trusted cut-off 21.0 21.0
Noise cut-off 20.9 20.9
Model length: 36
Family (HMM) version: 14
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Interactions

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Defensin_beta

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 Defensin_beta domain has been found. There are 69 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.

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