Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
24  structures 72  species 3  interactions 859  sequences 62  architectures

Family: DED (PF01335)

Summary: Death effector domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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, just in eukaryota cells, 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(DD)

Structure

Tertiary structure of DED in FADD protein

The DED is a subfamily of the superfamily DD (other recogniazable domains in this superfamily are: caspase‐recruitment domain (CARD), pyrin domain (PYD) and death domain (DD)). The subfamilies resemble structurally one another, all of them (and DED in particular) are composed of a bundle of 6 alpha-helices, but they diverge in the surface features.

The hole primary structure of this proteic domain hasn't been consensually described yet; some studies have shown that it contains 2-184 residues and that both extreme terminuses residues haven't been able to be observed by now. Depending on some amino acids, which confer the solubility and aggregation to DED, it has been able to differentiate DED's in different proteins, such as of caspase-8 and MC159.The secondary structure, as said, is built by 6 alpha-helices.

Its tertiary structure has been described as product of the crystallization of the caspase 8 in Homo-Sapiens species, The method that has been used to describe the structure is X-RAY difraccion and the resolution abotained is 2,2A.[3] DEDs in this protein can be found showing an asimetric unit dimer; its interaface contains two hydrogen bonding networks, that appear as a filamentus structure for both DEDs in caspase-8.

DED's function is in part due to its structure; as far as it is known, the homotypic interactions that activate caspase that will iniciate apoptosis are mediated by asimetrical surface contacts betweeen partners (like DED1 and DED2 in caspase-8 case).[4] The residues that form the surfaces are typically charged amino acids; but it is also known that a short hidrophofobic patch can also be observed on the interactive surface of the domain.

Function

DED domain is best known for its role in apoptosis. However, DED-containing proteins are also involved in other cellular processes so that they control both life and death cell decisions.

Extrinsic apoptosis

[5] Apoptosis is a controlled and programmed cell death that confers advantages during an organism lifecycle. The extrinsic pathway is directed by a family of proteases which become active in response to death stimuli. To know the role of DEDs in this process is important to observe the formation of the multiprotein death-including signalling complex (DISC).

DR4, TRAIL-R2 and CD95 are death receptors (members of TNF receptor superfamily) which interact together using their intracellular death domains (DDs). The DD of FADD, a protein containing a DED, can then interact with these DDs described. Here the function of FADD DED is to create a stabilized structure by self-associating FADD.

Molecular assembly of FADD forming DED chain-like structure. Each FADD molecule is shown in a different color.

[6] These interactions are defined by helices α1/α4 and α2/α3: residues Ser1, Val6, His9, Leu43, Asp44 and Glu51 from α1/α4 are in contact with Thr21, Phe25, Lys33, Arg34, Glu37 and Glu51 from α2/α3 of the second molecule. Each interaction involves an area of 1062 Å2 and contributions from hydrophobic side chains, hydrogen bonding and salt bridges. The final homodimer has a structure oriented so that each subunit has the 2 interaction sites.

Procaspase-8, also a DED-containing protein, has affinity for the FADD DED. It’s for that reason that they are recruited to FADD as monomers via their DEDs. These interaction is defined by α1/α4 of procapase-8 DED-A and FADD DED α2/α3 or α1/α4 of FADD DED and α2/α5 of procapase-8 DED-B. Porcapase-8 DED-B interacts with FADD and DED-A mediates capase-8 chain formation, or vice versa. However, in both cases the interaction leads to create a dimmer between procaspases, which generates a conformational change. This dimerization is essential to create the active site; a p12 subunit is liberated and it is subsequently processed to the small p10 subunit. The two molecules of procapase-8 are associated with these p10 subunits creating an active protease-8 cell death.[7][8]

When two procaspase-8 are recruited to the DISC, their caspase domains undergo conformational changes with the consequent liberation of P12 subunit which is processed to the small P10 catalytic subunit. The intermediate capspase-8 breaks in the region between DED and P18 subunit. The two molecules of the two caspase-8 intermediates associate with the two P10 subunits to form the active protease.

Necroptosis

[9] During the creation of the DISC procaspase-8 can also heterodimerise with another DED-containing protein known as FLIPL. FLIPL’s pseudo-caspase has two tandem DEDs that are very similar to the N-terminus of capase-8, but in which there is an important mutation in the active site (cysteine to tyrosine).

This heterodimeration done between their DEDs prevents from the normal homodimeration so that the pseudo-caspase is unable to activate the apoptotic cascade. FLIPL ’s pseudo-caspase is more efficient at inducing the conformational change. However, FLIPL hasn’t enough enzymatic activity so that cleavage between the DEDs and p18 it’s not possible. In consequence it’s impossible to create the active protease cell death.[10]

Procaspase-8 can also heterodimerise with FLIPS, also a DED containing protein. In this case heterodimerisation directly fails to activate procaspase-8 as the initial conformational change cannot take place in procaspase-8’s caspase domain.[10]

When FLIP is highly expressed, it creates an heterodimer with procaspase-8 at the DISC via interactions between their DEDs and those of FADD. The pseudo-caspase domain of FLIPL is able to induce the conformational change in procaspase-8’s caspase domain that is necessary to create its active site. The heterodimer is processed between the p18 and p12 subunits of both proteins, but is unable to be further processed owing to FLIPL’s lack of enzymatic activity, and this heterodimer is unable to activate apoptosis.

This is how DED can also inhibit the apoptosis cascade, and the consequence is necroptosis.

The DED protein family

DED-containing proteins

Caspase-8 and caspase-10

[11] Caspases are cysteine proteases responsible for dismantling off the cell during apoptosis.

These proteins are zymogens and become active after their cleavage at specific sites within the molecule.

Structure:

  • Death Effector Domain (DED) and a Caspase Recruitment Domain (CARD) that are englobed in a structure called pro-domain, which is located at the N-terminus
  • Catalytic protease domain at the C-terminus.

There are two groups of proteases:

  • Effector caspases: induce the biggest part of the morphological changes that occur during apoptosis.
  • Initiator caspases: responsible for the activation of effector caspases. These caspases are activated through oligomerization and cleavage that make the protein functional.

The two tandem DEDs in the pro-domain of caspase induce the protein-protein interactions with other proteins like the FADD.

Studying caspases is important since they don’t only control apoptosis but also inhibit it, depending on the necessity of the cell. Scientists find that they are a mechanism that can regulate cell life and is important for cancer therapies.

FLICE-like inhibitory proteins (FLIPs)

FLICE-like inhibitory proteins (FLIPs) are cell inhibitors capable of stopping the death receptors’ signal, which cause cell apoptosis.

The first FLIPs that were identified were expressed by γ-herpes viruses so they were called v-FLIPs. These v-FLIPs were able to associate with the receptor in the death-inducing signaling complex (DISC), blocking that way the CD95-mediated apoptosis.

[12]vFLIPs predominantly contain two sequential DEDs, which are highly homologous to the N-terminus of caspase-8.

[10] The cellular homologues of v-FLIPs are generally expressed in two forms:

  • c-FLIPS (short): it contains only the amino-terminal tandem DEDs followed by a short carboxy-terminal section. Its structure is similar to the viral FLIPs.
  • c-FLIPL (long): it consists of not only the tandem DEDs, but also a protease-like domain (homologous to caspase-8) in which different important for protease activity amino acids are mutated, including the active site cysteine.

[12] Both forms of c-FLIP are draft to the CD95 DISC, where they heterodimerize with caspase-8. c-FLIP has been involved in signaling alternative pathways, connecting the CD95 receptor to the NF-κB, JNK and MAPK pathways.

PEA-15/PED

PEA-15 (Phosphoprotein Enriched in Astrocytes-15 kDa) also known as PED (Phosphoprotein Enriched in Diabetes) is a DED-containing protein with pleiotropic effects.

PED is a small, non-catalytic, protein consisting of an N-terminal death-effector domain (DED) and a C-terminal tail with irregular structure.[13] PED/PEA-15 interacts with various types of proteins with and without DEDs, and its specificity of joining these proteins is mediated by the phosphorylation on two serine residues on the C-terminal tail:

[13] PEA-15 works as an antiapoptotic DED protein in several signaling cascades. In TNF α-, CD95- and TRAIL-mediated pathways, PEA-15 acts binding and disrupting FADD and caspase-8 interactions.

[10] Besides apoptosis, PEA-15 inhibits the insulin-mediated glucose transport in muscle cells, so a high level expression of PEA-15's mRNA has been associated to diabetes mellitus type II.

DEDD/DEDD2

Death effector domain containing DNA binding (DEDD). Shows DNA binding capacity, localized in the nucleoli in overexpression where it associates with a molecule called DEDAF (DED-associated factor) that potentiates apoptosis. In addition it blocks RNA polymerase I transcription by binding to the DNA.

DEDD2 (FLAME-3) is a DEDD homologue that shares a 48.5% of the amino acidic sequence. It is noted to interact with c-FLIP and DEDD and to have an important role in polymerase II-dependent transcription repression.

Proteins with a DED-related domain

HIP-1 and HIPPI

Huntingtin interacting protein-1 (HIP-1) is a protein that interacts with huntingtin (Htt), another protein that when is mutated (with expanded polyglutamine repeats) forms protein aggregates in the brain of patients with Huntington’s disease (HD).

[14] HIP-1 contains a pseudo death effector domain (pDED), that’s why the overexpression of HIP-1 induces apoptosis in several cells as DED proteins do. This type of apoptosis depends on the pDED of the HIP-1, and it consists in the activation of caspase-3, an enzyme that is reduced when wild-type Htt is expressed, that fact suggests that HIP-1 cooperates with Htt in the pathomechanism of Huntington’s disease.

[10] By yeast two-hybrid screening, HIP-1 has shown to interact with a protein of 419 amino acids called HIPPI (HIP-1 protein interactor). Succeeding experiments have revealed that the presence of HIPPI determines the HIP-1-induced apoptosis.

FLASH

FLICE-associated huge protein. Contains a similar domain to DED, but the homology is very weak and its function is still unclear.

Therapeutically exploiting DED

[7] DED complexes have been shown to function at crucial steps controlling life and death cell processes. This knowledge is particularly useful in therapy because there are so many pathologies related with an abnormal control of the cell life.

The absence of apoptosis is feature of cancer. In some cases the gene encoding procaspase-8 is silenced by methylation, so it is necessary to activate the gene using epigenetic treatments to have active protease. In other cases there is an overexpression of FLIP, the anti-apoptotic molecule that prevents from the formation of the active caspase. In this case there are some anti-cancer agents that downregulate FLIP expression.

However, the abnormal apoptosis it is not exclusive from cancer, there are other pathologies such as inflammation and neurodegenerative diseases than can also be treated with these kind oh therapeutics.

References

  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. 
  3. ^ Shen, Chen; Yue, Hong; Pei, Jianwen; Guo, Xiaomin; Wang, Tao; Quan, Jun-Min (2015). "Crystal structure of the death effector domains of caspase-8". Biochemical and Biophysical Research Communications. 463 (3): 297–302. doi:10.1016/j.bbrc.2015.05.054. ISSN 0006-291X. PMID 26003730. 
  4. ^ "Structures, Domains and Function in Cell Death". 
  5. ^ Elmore, Susan (2007). "Apoptosis: A Review of Programmed Cell Death". Toxicologic Pathology. 35 (4): 495–516. doi:10.1080/01926230701320337. ISSN 1533-1601. PMC 2117903Freely accessible. PMID 17562483. 
  6. ^ Singh, Nitu; Hassan, Ali; Bose, Kakoli (2015). "Molecular basis of death effector domain chain assembly and its role in caspase-8 activation". The FASEB Journal. 30 (1): 186–200. doi:10.1096/fj.15-272997. ISSN 1530-6860. PMID 26370846. 
  7. ^ a b Riley, JS; Malik, A; Holohan, C; Longley, DB (2015). "DED or alive: assembly and regulation of the death effector domain complexes". Cell Death and Disease. 6 (8): e1866. doi:10.1038/cddis.2015.213. ISSN 2041-4889. PMC 4558505Freely accessible. PMID 26313917. 
  8. ^ Yao, Zhan; Duan, Shanshan; Hou, Dezhi; Heese, Klaus; Wu, Mian (2007). "Death effector domain DEDa, a self‐cleaved product of caspase‐8/Mch5, translocates to the nucleus by binding to ERK1/2 and upregulates procaspase‐8 expression via a p53‐dependent mechanism". The EMBO Journal. 26 (4): 1068–1080. doi:10.1038/sj.emboj.7601571. ISSN 1460-2075. PMC 1852837Freely accessible. PMID 17290218. 
  9. ^ Lee, Eun-Woo; Seo, Jinho; Jeong, Manhyung; Lee, Sangsik; Song, Jaewhan (2012). "The roles of FADD in extrinsic apoptosis and necroptosis". BMB Reports. 45 (9): 496–508. doi:10.5483/BMBRep.2012.45.9.186. ISSN 1976-670X. PMID 23010170. 
  10. ^ a b c d e Barnhart, Bryan C; Lee, Justine C; Alappat, Elizabeth C; Peter, Marcus E (2003). "The death effector domain protein family". Oncogene. 22 (53): 8634–8644. doi:10.1038/sj.onc.1207103. ISSN 0950-9232. PMID 14634625. 
  11. ^ Schleich, K.; Buchbinder, J. H.; Pietkiewicz, S.; Kähne, T.; Warnken, U.; Öztürk, S.; Schnölzer, M.; Naumann, M.; Krammer, P. H. (2016-04-01). "Molecular architecture of the DED chains at the DISC: regulation of procaspase-8 activation by short DED proteins c-FLIP and procaspase-8 prodomain". Cell Death & Differentiation. 23 (4): 681–694. doi:10.1038/cdd.2015.137. ISSN 1350-9047. PMC 4986640Freely accessible. PMID 26494467. 
  12. ^ a b Yu, JW; Shi, Y (2008). "FLIP and the death effector domain family". Oncogene. 27 (48): 6216–6227. doi:10.1038/onc.2008.29. ISSN 0950-9232. PMID 18931689. 
  13. ^ a b Twomey, Edward C; Cordasco, Dana F; Wei, Yufeng (2012). "Profound conformational changes of PED/PEA-15 in ERK2 complex revealed by NMR backbone dynamics". Biochimica et biophysica acta. Proteins and proteomics. 1824 (12): 1382–1393. doi:10.1016/j.bbapap.2012.07.001. ISSN 1570-9639. PMID 22820249. 
  14. ^ Bhattacharyya, Nitai P; Banerjee, Manisha; Majumder, Pritha (2008). "Huntington's disease: roles of huntingtin-interacting protein 1 (HIP-1) and its molecular partner HIPPI in the regulation of apoptosis and transcription". The FEBS Journal. 275 (17): 4271–4279. doi:10.1111/j.1742-4658.2008.06563.x. ISSN 1742-464X. PMID 18637945. 

External links

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

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.

Death effector domain Provide feedback

No Pfam abstract.

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


Internal database links

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...

Loading domain graphics...

Pfam Clan

This family is a member of clan Death (CL0041), which has the following description:

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 [1].

The clan contains the following 6 members:

CARD CARD_2 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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

View options

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
(223)
Full
(859)
Representative proteomes UniProt
(1458)
NCBI
(3110)
Meta
(0)
RP15
(224)
RP35
(326)
RP55
(552)
RP75
(720)
Jalview View  View  View  View  View  View  View  View   
HTML View  View               
PP/heatmap 1 View               

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(223)
Full
(859)
Representative proteomes UniProt
(1458)
NCBI
(3110)
Meta
(0)
RP15
(224)
RP35
(326)
RP55
(552)
RP75
(720)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(223)
Full
(859)
Representative proteomes UniProt
(1458)
NCBI
(3110)
Meta
(0)
RP15
(224)
RP35
(326)
RP55
(552)
RP75
(720)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download    
Gzipped Download   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.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

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: 223
Number in full: 859
Average length of the domain: 80.30 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 24.79 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 35.1 35.1
Trusted cut-off 35.2 35.1
Noise cut-off 35.0 34.9
Model length: 82
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

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

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

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.

Interactions

There are 3 interactions for this family. More...

Death Pkinase DED

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 24 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.

Loading structure mapping...