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.
14  structures 80  species 1  interaction 98  sequences 3  architectures

Family: BID (PF06393)

Summary: BH3 interacting domain (BID)

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 "BH3 interacting-domain death agonist". More...

BH3 interacting-domain death agonist Edit Wikipedia article

BID
BID protein 2bid.png
Available structures
PDB Ortholog search: PDBe RCSB
Identifiers
Aliases BID, Bid, 2700049M22Rik, AI875481, AU022477, FP497, BH3 interacting domain death agonist
External IDs MGI: 108093 HomoloGene: 923 GeneCards: BID
RNA expression pattern
PBB GE BID 211725 s at fs.png

PBB GE BID 204493 at fs.png
More reference expression data
Orthologs
Species Human Mouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_007544

RefSeq (protein)

NP_031570.2
NP_031570

Location (UCSC) Chr 22: 17.73 – 17.77 Mb Chr 6: 120.89 – 120.92 Mb
PubMed search [1] [2]
Wikidata
View/Edit Human View/Edit Mouse
BID
PDB 2bid EBI.jpg
human pro-apoptotic protein bid
Identifiers
Symbol BID
Pfam PF06393
InterPro IPR010479
SCOP 1ddb
SUPERFAMILY 1ddb
TCDB 1.A.21
OPM superfamily 42
OPM protein 2m5i

The BH3 interacting-domain death agonist, or BID, gene is a pro-apoptotic member of the Bcl-2 protein family.[3] Bcl-2 family members share one or more of the four characteristic domains of homology entitled the Bcl-2 homology (BH) domains (named BH1, BH2, BH3 and BH4), and can form hetero- or homodimers. Bcl-2 proteins act as anti- or pro-apoptotic regulators that are involved in a wide variety of cellular activities.

Interactions

BID is a pro-apoptotic Bcl-2 protein containing only the BH3 domain. In response to apoptotic signaling, BID interacts with another Bcl-2 family protein, Bax, leading to the insertion of Bax into organelle membranes, primarily the outer mitochondrial membrane. Bax is believed to interact with, and induce the opening of the mitochondrial voltage-dependent anion channel, VDAC. Alternatively, growing evidence suggest that activated Bax and/or Bak form an oligomeric pore, MAC in the outer membrane. This results in the release of cytochrome c and other pro-apoptotic factors (such as SMAC/DIABLO)[4] from the mitochondria, often referred to as mitochondrial outer membrane permeabilization, leading to activation of caspases. This defines BID as a direct activator of Bax, a role common to some of the pro-apoptotic Bcl-2 proteins containing only the BH3 domain.

The anti-apoptotic Bcl-2 proteins, including Bcl-2 itself, can bind BID and inhibit BID's ability to activate Bax. As a result, the anti-apoptotic Bcl-2 proteins may inhibit apoptosis by sequestering BID, leading to reduced Bax activation.

The expression of BID is upregulated by the tumor suppressor p53, and BID has been shown to be involved in p53-mediated apoptosis.[5] The p53 protein is a transcription factor that, when activated as part of the cell's response to stress, regulates many downstream target genes, including BID. However, p53 also has a transcription-independent role in apoptosis. In particular, p53 interacts with Bax, promoting Bax activation and the insertion of Bax into the mitochondrial membrane.

The BH3 interacting-domain death agonist has been shown to interact with:

Cleavage

Caspase-8 (as surface) cleavage of Bid (as ribbon) (visualization by Kosi Gramatikoff)

Several reports have demonstrated that caspase-8, and its substrate BID, are frequently activated in response to certain apoptotic stimuli in a death receptor-independent manner. N-hydroxy-L-arginine (NOHA), a stable intermediate product formed during the conversion of L-arginine to nitric oxide activates caspase-8.[14] Activation of caspase-8, and subsequent BID cleavage participate in cytochrome-c mediated apoptosis.[15] 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) mediated activation of caspase-9 via cytochrome-c release has been shown to result in the activation of caspase-8 and Bid cleavage.[16] Aspirin and Curcumin (diferuloylmethane) too activate caspase-8 to cleave and translocated Bid, induced a conformational change in and translocation of Bax and cytochrome-c release.[17][18]

See also

References

  1. ^ "Human PubMed Reference:". 
  2. ^ "Mouse PubMed Reference:". 
  3. ^ Wang K, Yin XM, Chao DT, Milliman CL, Korsmeyer SJ (1996). "BID: a novel BH3 domain-only death agonist". Genes Dev. 10 (22): 2859–69. PMID 8918887. doi:10.1101/gad.10.22.2859. 
  4. ^ Weinberg, Robert A. (2007). The biology of cancer. New York: Taylor & Francis. p. 341. ISBN 0-8153-4076-1. 
  5. ^ Sax JK, Fei P, Murphy ME, Bernhard E, Korsmeyer SJ, El-Deiry WS (2002). "BID regulation by p53 contributes to chemosensitivity". Nat. Cell Biol. 4 (11): 842–9. PMID 12402042. doi:10.1038/ncb866. 
  6. ^ Liu Y, Bertram CC, Shi Q, Zinkel SS (2011). "Proapoptotic Bid mediates the Atr-directed DNA damage response to replicative stress". Cell Death Differ. 18 (5): 841–52. PMC 3074003Freely accessible. PMID 21113148. doi:10.1038/cdd.2010.151. 
  7. ^ a b Chen L, Willis SN, Wei A, Smith BJ, Fletcher JI, Hinds MG, Colman PM, Day CL, Adams JM, Huang DC (2005). "Differential targeting of prosurvival Bcl-2 proteins by their BH3-only ligands allows complementary apoptotic function". Mol. Cell. 17 (3): 393–403. PMID 15694340. doi:10.1016/j.molcel.2004.12.030. 
  8. ^ Real PJ, Cao Y, Wang R, Nikolovska-Coleska Z, Sanz-Ortiz J, Wang S, Fernandez-Luna JL (2004). "Breast cancer cells can evade apoptosis-mediated selective killing by a novel small molecule inhibitor of Bcl-2". Cancer Res. 64 (21): 7947–53. PMID 15520201. doi:10.1158/0008-5472.CAN-04-0945. 
  9. ^ a b Guo Y, Srinivasula SM, Druilhe A, Fernandes-Alnemri T, Alnemri ES (2002). "Caspase-2 induces apoptosis by releasing proapoptotic proteins from mitochondria". J. Biol. Chem. 277 (16): 13430–7. PMID 11832478. doi:10.1074/jbc.M108029200. 
  10. ^ Paroni G, Henderson C, Schneider C, Brancolini C (2001). "Caspase-2-induced apoptosis is dependent on caspase-9, but its processing during UV- or tumor necrosis factor-dependent cell death requires caspase-3". J. Biol. Chem. 276 (24): 21907–15. PMID 11399776. doi:10.1074/jbc.M011565200. 
  11. ^ Gajate C, Mollinedo F (2005). "Cytoskeleton-mediated death receptor and ligand concentration in lipid rafts forms apoptosis-promoting clusters in cancer chemotherapy". J. Biol. Chem. 280 (12): 11641–7. PMID 15659383. doi:10.1074/jbc.M411781200. 
  12. ^ Weng C, Li Y, Xu D, Shi Y, Tang H (2005). "Specific cleavage of Mcl-1 by caspase-3 in tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)-induced apoptosis in Jurkat leukemia T cells". J. Biol. Chem. 280 (11): 10491–500. PMID 15637055. doi:10.1074/jbc.M412819200. 
  13. ^ Liu Y, Vaithiyalingam S, Shi Q, Chazin WJ, Zinkel SS (2011). "BID binds to replication protein A and stimulates ATR function following replicative stress". Mol. Cell. Biol. 31 (21): 4298–309. PMC 3209332Freely accessible. PMID 21859891. doi:10.1128/MCB.05737-11. 
  14. ^ Singh R, Pervin S, Chaudhuri G (2002). "Caspase-8-mediated BID cleavage and release of mitochondrial cytochrome c during Nomega-hydroxy-L-arginine-induced apoptosis in MDA-MB-468 cells. Antagonistic effects of L-ornithine". J. Biol. Chem. 277 (40): 37630–6. PMID 12145284. doi:10.1074/jbc.M203648200. 
  15. ^ Tang D, Lahti JM, Kidd VJ (2000). "Caspase-8 activation and bid cleavage contribute to MCF7 cellular execution in a caspase-3-dependent manner during staurosporine-mediated apoptosis". J. Biol. Chem. 275 (13): 9303–7. PMID 10734071. doi:10.1074/jbc.275.13.9303. 
  16. ^ Viswanath V, Wu Y, Boonplueang R, Chen S, Stevenson FF, Yantiri F, Yang L, Beal MF, Andersen JK (2001). "Caspase-9 activation results in downstream caspase-8 activation and bid cleavage in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-induced Parkinson's disease". J. Neurosci. 21 (24): 9519–28. PMID 11739563. 
  17. ^ Gu Q, Wang JD, Xia HH, Lin MC, He H, Zou B, Tu SP, Yang Y, Liu XG, Lam SK, Wong WM, Chan AO, Yuen MF, Kung HF, Wong BC (2005). "Activation of the caspase-8/Bid and Bax pathways in aspirin-induced apoptosis in gastric cancer". Carcinogenesis. 26 (3): 541–6. PMID 15579484. doi:10.1093/carcin/bgh345. 
  18. ^ Anto RJ, Mukhopadhyay A, Denning K, Aggarwal BB (2002). "Curcumin (diferuloylmethane) induces apoptosis through activation of caspase-8, BID cleavage and cytochrome c release: its suppression by ectopic expression of Bcl-2 and Bcl-xl". Carcinogenesis. 23 (1): 143–50. PMID 11756235. doi:10.1093/carcin/23.1.143. 


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.

BH3 interacting domain (BID) Provide feedback

BID is a member of the BCL-2 superfamily of proteins are key regulators of programmed cell death, hence this family is related to PF00452 . BID is a pro-apoptotic member of the Bcl-2 superfamily and as such posses the ability to target intracellular membranes and contains the BH3 death domain. The activity of BID is regulated by a Caspase 8-mediated cleavage event, exposing the BH3 domain and significantly changing the surface charge and hydrophobicity, which causes a change of cellular localisation [1].

Literature references

  1. McDonnell JM, Fushman D, Milliman CL, Korsmeyer SJ, Cowburn D; , Cell 1999;96:625-634.: Solution structure of the proapoptotic molecule BID: a structural basis for apoptotic agonists and antagonists. PUBMED:10089878 EPMC:10089878


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR010479

Bcl-2 proteins are central regulators of caspase activation, and play a key role in cell death by regulating the integrity of the mitochondrial and endoplasmic reticulum (ER) membranes [PUBMED:12631689]. At least 20 Bcl-2 proteins have been reported in mammals, and several others have been identified in viruses. Bcl-2 family proteins fall roughly into three subtypes, which either promote cell survival (anti-apoptotic) or trigger cell death (pro-apoptotic). All members contain at least one of four conserved motifs, termed Bcl-2 Homology (BH) domains. Bcl-2 subfamily proteins, which contain at least BH1 and BH2, promote cell survival by inhibiting the adapters needed for the activation of caspases.

Pro-apoptotic members potentially exert their effects by displacing the adapters from the pro-survival proteins; these proteins belong either to the Bax subfamily, which contain BH1-BH3, or to the BH3 subfamily, which mostly only feature BH3 [PUBMED:9735050]. Thus, the balance between antagonistic family members is believed to play a role in determining cell fate. Members of the wider Bcl-2 family, which also includes Bcl-x, Bcl-w and Mcl-1, are described by their similarity to Bcl-2 protein, a member of the pro-survival Bcl-2 subfamily [PUBMED:9735050]. Full-length Bcl-2 proteins feature all four BH domains, seven alpha-helices, and a C-terminal hydrophobic motif that targets the protein to the outer mitochondrial membrane, ER and nuclear envelope.

BID is a member of the Bcl-2 superfamily of proteins that are key regulators of programmed cell death, hence this family is related to the Apoptosis regulator Bcl-2 protein BH domain. BID is a pro-apoptotic member of the Bcl-2 superfamily and as such posses the ability to target intracellular membranes and contains the BH3 death domain. The activity of BID is regulated by a Caspase 8-mediated cleavage event, exposing the BH3 domain and significantly changing the surface charge and hydrophobicity, which causes a change of cellular localisation [PUBMED:10089878].

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 BCLiA (CL0551), which has the following description:

This superfamily is characterised by families of proteins that inhibit apoptosis, They are regulated by all BH3-only proteins to promote apoptosis.

The clan contains the following 5 members:

APG6 Atg14 Bcl-2 Bcl-2_3 BID

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
(16)
Full
(98)
Representative proteomes UniProt
(138)
NCBI
(360)
Meta
(0)
RP15
(8)
RP35
(21)
RP55
(60)
RP75
(86)
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
(16)
Full
(98)
Representative proteomes UniProt
(138)
NCBI
(360)
Meta
(0)
RP15
(8)
RP35
(21)
RP55
(60)
RP75
(86)
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
(16)
Full
(98)
Representative proteomes UniProt
(138)
NCBI
(360)
Meta
(0)
RP15
(8)
RP35
(21)
RP55
(60)
RP75
(86)
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: Pfam-B_16321 (release 9.0)
Previous IDs: none
Type: Domain
Author: Finn RD
Number in seed: 16
Number in full: 98
Average length of the domain: 168.40 aa
Average identity of full alignment: 47 %
Average coverage of the sequence by the domain: 81.57 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 37.7 32.2
Noise cut-off 23.3 23.1
Model length: 191
Family (HMM) version: 10
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 is 1 interaction for this family. More...

Bcl-2

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 BID domain has been found. There are 14 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...