Summary: PAAD/DAPIN/Pyrin domain
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This is the Wikipedia entry entitled "Pyrin domain". More...
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Pyrin domain Edit Wikipedia article
A pyrin domain is a protein domain and a subclass of protein motif known as the death fold; it allows a pyrin domain containing protein to interact with other proteins that contain a pyrin domain. It is also known as a PYD or PAAD/DAPIN domain, and is distantly evolutionarily related to the Death domain family of protein domains. Proteins containing a pyrin domain are frequently involved in biological processes called inflammation and apoptosis. Proteins that possess a pyrin domain include intracellular microbial sensors called NOD-like receptors, and proteins associated with their function, such as PYCARD and certain fish caspases.
- Fairbrother WJ, Gordon NC, Humke EW, et al. (September 2001). "The PYRIN domain: a member of the death domain-fold superfamily". Protein Sci. 10 (9): 1911–8. doi:10.1110/ps.13801. PMC . PMID 11514682.
- Staub E, Dahl E, Rosenthal A (February 2001). "The DAPIN family: a novel domain links apoptotic and interferon response proteins". Trends Biochem. Sci. 26 (2): 83–5. doi:10.1016/s0968-0004(00)01717-5. PMID 11166557.
- Pawłowski K, Pio F, Chu Z, Reed JC, Godzik A (February 2001). "PAAD - a new protein domain associated with apoptosis, cancer and autoimmune diseases". Trends Biochem. Sci. 26 (2): 85–7. doi:10.1016/s0968-0004(00)01729-1. PMID 11166558.
- Bertin J, DiStefano PS (December 2000). "The PYRIN domain: a novel motif found in apoptosis and inflammation proteins". Cell Death Differ. 7 (12): 1273–4. doi:10.1038/sj.cdd.4400774. PMID 11270363.
- Gumucio DL, Diaz A, Schaner P, et al. (2002). "Fire and ICE: the role of pyrin domain-containing proteins in inflammation and apoptosis". Clin. Exp. Rheumatol. 20 (4 Suppl 26): S45–53. PMID 12371636.
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PAAD/DAPIN/Pyrin domain Provide feedback
This domain is predicted to contain 6 alpha helices and to have the same fold as the PF00531 domain. This similarity may mean that this is a protein-protein interaction domain.
Martinon F, Hofmanndouble dagger K, Tschopp J; , Curr Biol 2001;11:118-120.: The pyrin domain: a possible member of the death domain-fold family implicated in apoptosis and inflammation. PUBMED:11250163 EPMC:11250163
Internal database links
|Similarity to PfamA using HHSearch:||DED|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR004020
The DAPIN (Domain in Apoptosis and INterferon response) domain is an 80-100- residue domain which is found in the N terminus of diverse vertebrate and vertebrate-specific viral proteins involved in apoptosis, cancer, inflammation, and immune response. The DAPIN domain can be found alone or in association with other domains [ PUBMED:1166557 , PUBMED:11166558 , PUBMED:11250163 ] like CARD, LRR, SPRY, Caspase or Zinc finger B-box. It has been proposed that the DAPIN domain might have an adaptor function, coupling apoptosis and immune disorders [ PUBMED:11166557 , PUBMED:11166558 , PUBMED:11250163 ]. It has been shown that the DAPIN domain is a protein-protein interaction domain capable of binding to other DAPIN domains [ PUBMED:11166557 ].
Secondary structure predictions have identified the DAPIN domain as mostly alpha-helical and it has been suggested that it could belong to the DEATH- domain-fold superfamily, which includes the CARD, the DEATH domain (DD) and the DEATH effector domain (DED) [ PUBMED:11166557 , PUBMED:11166558 , PUBMED:11250163 ].
The DAPIN domain has also been called pyrin domain, pyrin N-terminal homology domain (PYD) or PAAD (after the protein families pyrin, AIM, ASC death-domain- like) [ PUBMED:11166558 , PUBMED:11250163 ].
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
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The death domain superfamily is composed of three families: the death domain (DD); the death effector domain (DED) and the caspase recruitment domain (CARD). All of the members perform a pivotal role in signalling events that regulate apoptosis. Protein-protein interactions are mediated by self-self associations, in which CARD-CARD, DD-DD and DED-DED contacts are formed exclusively The three families possess remarkably similar structures, each comprising an antiparallel six helical bundle in the Greek Key topology. Structurally, the DD and CARD families are the most dissimilar. The former is comprised of two perpendicular three-helix bundles, whereas the latter CARD domain contains six helices that are almost parallel with each other. Interestingly, the interactions in CARD or DD containing heterodimers are quite different .
The clan contains the following 7 members:Atypical_Card CARD CARD_2 Death Death_2 DED PYRIN
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...
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:
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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.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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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.
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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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|Seed source:||Bateman A|
|Number in seed:||180|
|Number in full:||4792|
|Average length of the domain:||74.60 aa|
|Average identity of full alignment:||27 %|
|Average coverage of the sequence by the domain:||12.01 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||19|
|Download:||download the raw HMM for this family|
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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 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:
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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 PYRIN domain has been found. There are 132 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.