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136  structures 36  species 1  interaction 174  sequences 2  architectures

Family: Defensin_1 (PF00323)

Summary: Mammalian defensin

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This is the Wikipedia entry entitled "Alpha defensin". More...

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No Pfam abstract.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006081

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. Alpha-defensins, which have been identified in humans, monkeys and several rodent species, are particularly abundant in neutrophils, certain macrophage populations and Paneth cells of the small intestine.

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 synthesized as propeptides which may be relevant to this process.

Human neutrophil-derived alpha-defensins (HNPs) are capable of enhancing phagocytosis by mouse macrophages. HNP1-3 have been reported to increase the production of tumor necrosis factor (TNF) and IL-1, while decreasing the production of IL-10 by monocytes. Increased levels of proinflammatory factors (e.g. IL-1, TNF, histamine and prostaglandin D2) and suppressed levels of IL-10 at the site of microbial infection are likely to amplify local inflammatory responses. This might be further reinforced by the capacity of some human and rabbit alpha-defensins to inhibit the production of immunosuppressive glucocorticoids by competing for the binding of adrenocorticotropic hormone to its receptor. Moreover, human alpha-defensins can enhance or suppress the activation of the classical pathway of complement in vitro by binding to solid-phase or fluid-phase complement C1q, respectively. The capacity of defensins to enhance phagocytosis, promote neutrophil recruitment, enhance the production of proinflammatory cytokines, suppress anti-inflammatory mediators and regulate complement activation argues that defensins upregulate innate host inflammatory defences against microbial invasion.

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 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

Alignments

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(39)
Full
(174)
Representative proteomes UniProt
(224)
NCBI
(422)
Meta
(0)
RP15
(33)
RP35
(36)
RP55
(50)
RP75
(85)
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  Seed
(39)
Full
(174)
Representative proteomes UniProt
(224)
NCBI
(422)
Meta
(0)
RP15
(33)
RP35
(36)
RP55
(50)
RP75
(85)
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  Seed
(39)
Full
(174)
Representative proteomes UniProt
(224)
NCBI
(422)
Meta
(0)
RP15
(33)
RP35
(36)
RP55
(50)
RP75
(85)
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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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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.

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Curation and family details

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Seed source: Prosite
Previous IDs: defensins;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD
Number in seed: 39
Number in full: 174
Average length of the domain: 28.90 aa
Average identity of full alignment: 45 %
Average coverage of the sequence by the domain: 31.37 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.4 21.4
Trusted cut-off 21.4 21.4
Noise cut-off 20.8 21.2
Model length: 29
Family (HMM) version: 20
Download: download the raw HMM for this family

Species distribution

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

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Interactions

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

Defensin_1

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_1 domain has been found. There are 136 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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