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20  structures 86  species 2  interactions 947  sequences 55  architectures

Family: DED (PF01335)

Summary: Death effector domain

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This is the Wikipedia entry entitled "Death effector domain". More...

Death effector domain Edit Wikipedia article

Death effector domain
PDB 1a1z EBI.jpg
structure of the FADD (Mort1) death-effector domain.[1]
Identifiers
Symbol DED
Pfam PF01335
InterPro IPR001875
SMART DED
PROSITE PS50168
SCOP 1a1z
SUPERFAMILY 1a1z
CDD cd00045

The death-effector domain (DED) is a protein interaction domain found to regulate a variety of cellular signalling pathways.[2] The DED domain is found in inactive procaspases (cysteine proteases) and proteins that regulate caspase activation in the apoptosis cascade such as FAS-associating death domain-containing protein (FADD). FADD recruits procaspase 8 and procaspase 10 into a death induced signaling complex (DISC). This recruitment is mediated by a homotypic interaction between the procaspase DED and a second DED that is death effector domain in an adaptor protein that is directly associated with activated TNF receptors. Complex formation allows proteolytic activation of procaspase into the active caspase form which results in the initiation of apoptosis (cell death). Structurally the DED domain are a subclass of protein motif known as the death fold and contains 6 alpha helices, that closely resemble the structure of the Death domain.

References[edit]

  1. ^ Eberstadt M, Huang B, Chen Z, et al. (April 1998). "NMR structure and mutagenesis of the FADD (Mort1) death-effector domain". Nature 392 (6679): 941–5. doi:10.1038/31972. PMID 9582077. 
  2. ^ Valmiki MG, Ramos JW (March 2009). "Death effector domain-containing proteins". Cell. Mol. Life Sci. 66 (5): 814–30. doi:10.1007/s00018-008-8489-0. PMID 18989622. 

External links[edit]

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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Literature references

  1. Eberstadt M, Huang B, Chen Z, Meadows RP, Ng SC, Zheng L, Lenardo MJ, Fesik SW; , Nature 1998;392:941-945.: NMR structure and mutagenesis of the FADD (Mort1) death-effector domain. PUBMED:9582077 EPMC:9582077


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001875

The death effector domain (DED) is a homotypic protein interaction module composed of a bundle of six alpha-helices. DED is related in sequence and structure to the death domain (DD, see INTERPRO) and the caspase recruitment domain (CARD, see INTERPRO), which work in similar pathways and show similar interaction properties [PUBMED:11504623]. The dimerisation of DED domains is mediated primarily by electrostatic interactions. DED domains can be found in isolation, or in combination with other domains. Domains associated with DED include: caspase catalytic domains (in caspase-8, -10), death domains (in FADD), nuclear localisation sequences (in DEDD), transmembrane domains (in Bap31 and Bar), nucleotide-binding domains (in Dap3), coiled-coil domains (in Hip and Hippi), SAM domains (in Bar), and E2-binding RING domains (in Bar) [PUBMED:15226512].

Several DED-containing proteins are involved in the regulation of apoptosis through their interactions with DED-containing caspases (INTERPRO), such as caspases 8 and 10 in humans, both of which contain tandem pairs of DEDs. There are many DED-containing modulators of apoptosis, which can either enhance or inhibit caspase activation [PUBMED:15173180].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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
(37)
Full
(947)
Representative proteomes NCBI
(826)
Meta
(0)
RP15
(158)
RP35
(186)
RP55
(257)
RP75
(419)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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Format an alignment

  Seed
(37)
Full
(947)
Representative proteomes NCBI
(826)
Meta
(0)
RP15
(158)
RP35
(186)
RP55
(257)
RP75
(419)
Alignment:
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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
(37)
Full
(947)
Representative proteomes NCBI
(826)
Meta
(0)
RP15
(158)
RP35
(186)
RP55
(257)
RP75
(419)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download    
Gzipped Download   Download   Download   Download   Download   Download   Download    

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: none
Type: Domain
Author: Bateman A, Finn RD
Number in seed: 37
Number in full: 947
Average length of the domain: 81.10 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 27.28 %

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 22.6 22.6
Trusted cut-off 22.6 22.6
Noise cut-off 22.5 22.5
Model length: 84
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 2 interactions for this family. More...

DED Death

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 DED domain has been found. There are 20 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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