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11  structures 60  species 0  interactions 767  sequences 56  architectures

Family: PYRIN (PF02758)

Summary: PAAD/DAPIN/Pyrin domain

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This is the Wikipedia entry entitled "Pyrin domain". More...

Pyrin domain Edit Wikipedia article

PAAD/DAPIN/Pyrin domain
PDB 1pn5 EBI.jpg
Identifiers
Symbol PAAD_DAPIN
Pfam PF02758
Pfam clan CL0041
InterPro IPR004020
PROSITE PS50824
SCOP 1pn5
SUPERFAMILY 1pn5
CDD cd08305

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.[1][2][3]Proteins containing a pyrin domain are frequently involved in biological processes called inflammation and apoptosis.[4][5] 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.

References[edit]

  1. ^ 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 2253208. PMID 11514682. 
  2. ^ 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. PMID 11166557. 
  3. ^ 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. PMID 11166558. 
  4. ^ 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. 
  5. ^ 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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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.

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.

Literature references

  1. Pawlowski K, Pio F, Chu Z, Reed JC, Godzik A; , Trends Biochem Sci 2001;26:85-87.: PAAD - a new protein domain associated with apoptosis, cancer and autoimmune diseases. PUBMED:11166558 EPMC:11166558

  2. Staub E, Dahl E, Rosenthal A; , Trends Biochem Sci 2001;26:83-85.: The DAPIN family: a novel domain links apoptotic and interferon response proteins. PUBMED:11166557 EPMC:11166557

  3. Aravind L, Dixit VM, Koonin EV; , Science 2001;291:1279-1284.: Apoptotic molecular machinery: vastly increased complexity in vertebrates revealed by genome comparisons. PUBMED:11181990 EPMC:11181990

  4. 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

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].

Domain organisation

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

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Pfam Clan

This family is a member of clan Death (CL0041), which contains the following 5 members:

CARD Death Death_2 DED PYRIN

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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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.

  Seed
(38)
Full
(767)
Representative proteomes NCBI
(774)
Meta
(1)
RP15
(23)
RP35
(69)
RP55
(115)
RP75
(298)
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Format an alignment

  Seed
(38)
Full
(767)
Representative proteomes NCBI
(774)
Meta
(1)
RP15
(23)
RP35
(69)
RP55
(115)
RP75
(298)
Alignment:
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Sequence:
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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.

  Seed
(38)
Full
(767)
Representative proteomes NCBI
(774)
Meta
(1)
RP15
(23)
RP35
(69)
RP55
(115)
RP75
(298)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

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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.

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: Bateman A
Previous IDs: PAAD_DAPIN;
Type: Domain
Author: Bateman A
Number in seed: 38
Number in full: 767
Average length of the domain: 81.90 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 11.69 %

HMM information View help on HMM parameters

HMM build commands:
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 22.4 22.4
Trusted cut-off 22.9 23.0
Noise cut-off 22.1 22.3
Model length: 83
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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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 PYRIN domain has been found. There are 11 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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