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.
0  structures 0  species 2  interactions 0  sequences 0  architectures

Family: Bcl-2_3 (PF15286)

Summary: Apoptosis regulator M11, B cell 2 leukaemia/lymphoma like

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 "Bcl-2 family". More...

Bcl-2 family Edit Wikipedia article

Apoptosis regulator proteins, Bcl-2 family
PDB 1maz EBI.jpg
Structure of human Bcl-xL, an inhibitor of programmed cell death.[1]
Identifiers
Symbol Bcl-2
Pfam PF00452
InterPro IPR000712
SMART SM00337
PROSITE PDOC00829
SCOP 1maz
SUPERFAMILY 1maz
OPM superfamily 42
OPM protein 2l5b
Bcl-2 homology region 4
PDB 1af3 EBI.jpg
rat bcl-xl an apoptosis inhibitory protein
Identifiers
Symbol BH4
Pfam PF02180
InterPro IPR003093
SMART BH4
SCOP 1af3
SUPERFAMILY 1af3
TCDB 1.A.21

The Bcl-2 Family (TC# 1.A.21) consists of apoptosis regulator Bcl-2 and its homologues.[2] These proteins govern mitochondrial outer membrane permeabilization (MOMP) and can be either pro-apoptotic (Bax, BAD, Bak and Bok among others) or anti-apoptotic (including Bcl-2 proper, Bcl-xL, and Bcl-w, among an assortment of others). There are a total of 25 genes in the Bcl-2 family known to date.

Function

Overview of signal transduction pathways involved in apoptosis.

Active cell suicide (apoptosis) is induced by events such as growth factor withdrawal and toxins. It is controlled by regulators, which have either an inhibitory effect on programmed cell death (anti-apoptotic) or block the protective effect of inhibitors (pro-apoptotic).[3][4] Many viruses have found a way of countering defensive apoptosis by encoding their own anti-apoptosis genes preventing their target-cells from dying too soon.

Bcl-x is a dominant regulator of programmed cell death in mammalian cells.[5][6] The long form (Bcl-x(L), displays cell death repressor activity, but the short isoform (Bcl-x(S)) and the β-isoform (Bcl-xβ) promote cell death. Bcl-x(L), Bcl-x(S) and Bcl-xβ are three isoforms derived by alternative RNA splicing.

There are a number of theories concerning how the Bcl-2 gene family exert their pro- or anti-apoptotic effect. An important one states that this is achieved by activation or inactivation of an inner mitochondrial permeability transition pore, which is involved in the regulation of matrix Ca2+, pH, and voltage. It is also thought that some Bcl-2 family proteins can induce (pro-apoptotic members) or inhibit (anti-apoptotic members) the release of cytochrome c into the cytosol which, once there, activates caspase-9 and caspase-3, leading to apoptosis. Although Zamzami et al. suggest that the release of cytochrome c is indirectly mediated by the PT pore on the inner mitochondrial membrane,[7] strong evidence suggest an earlier implication of the MAC pore on the outer membrane.[8][9]

Another theory suggests that Rho proteins play a role in Bcl-2, Mcl-1 and Bid activation. Rho inhibition reduces the expression of anti-apoptotic Bcl-2 and Mcl-1 proteins and increases protein levels of pro-apoptotic Bid but had no effect on Bax or FLIP levels. Rho inhibition induces caspase-9 and caspase-3-dependent apoptosis of cultured human endothelial cells.[10]

Site of action

These proteins are localized to the outer mitochondrial membrane of the animal cell where they are thought to form a complex with the voltage-dependent anion channel porin (VDAC). Interaction of Bcl-2 with VDAC1 or with peptides derived from VDAC3 protects against cell death by inhibiting cytochrome c release. A direct interaction of Bcl-2 with bilayer-reconstituted purified VDAC was demonstrated, with Bcl-2 decreasing channel conductance.[11]

Within the mitochondria are apoptogenic factors (cytochrome c, Smac/Diablo homolog, Omi) that if released activate the executioners of apoptosis, the caspases.[12] Depending on their function, once activated, Bcl-2 proteins either promote the release of these factors, or keep them sequestered in the mitochondria. Whereas the activated pro-apoptotic Bak and/or Bax would form MAC and mediate the release of cytochrome c, the anti-apoptotic Bcl-2 would block it, possibly through inhibition of Bax and/or Bak.[13]

Proteins of the Bcl-2 family are also present in the perinuclear envelope and are widely distributed in many body tissues. Their ability to form oligomeric pores in artificial lipid bilayers has been documented but the physiological significance of pore formation is not clear. Each of these proteins has distinctive properties, including some degree of ion selectivity.[14]

Transport reaction

The generalized transport reaction proposed for membrane-embedded, oligomeric Bcl-2 family members is:

cytochrome c (mitochondrial intermembrane space) ⇌ cytochrome c (cytoplasm)

Structure

Fig: D. Domains of the Bcl-2 family[15]

The Bcl-2 family has a general structure that consists of a hydrophobic helix surrounded by amphipathic helices. Many members of the family have transmembrane domains.

Bcl-x(L) is 233 amino acyl residues (aas) long and exhibits a single very hydrophobic putative transmembrane α-helical segment (residues 210-226) when in the membrane. Homologues of Bcl-x include the Bax (rat; 192 aas) and Bak (mouse; 208 aas) proteins, which also influence apoptosis. The high resolution structure of the monomeric soluble form of human Bcl-x(L) has been determined by both x-ray crystallography and NMR.[16]

The structure consists of two central primarily hydrophobic α-helices surrounded by amphipathic helices. The arrangement of the α-helices in Bcl-X(L) resembles that for diphtheria toxin and the colicins. Diphtheria toxin forms a transmembrane pore and translocates the toxic catalytic domain into the animal cell cytoplasm. The colicins similarly form pores in lipid bilayers. Structural homology therefore suggests that Bcl-2 family members that contain the BH1 and BH2 domains (Bcl-X(L) Bcl-2 and Bax) function similarly.

Domains

The members of the Bcl-2 family share one or more of the four characteristic domains of homology entitled the Bcl-2 homology (BH) domains (named BH1, BH2, BH3 and BH4) (see the figure D on the left). The BH domains are known to be crucial for function, as deletion of these domains via molecular cloning affects survival/apoptosis rates. The anti-apoptotic Bcl-2 proteins, such as Bcl-2 and Bcl-xL, conserve all four BH domains. The BH domains also serve to subdivide the pro-apoptotic Bcl-2 proteins into those with several BH domains (e.g. Bax and Bak) or those proteins that have only the BH3 domain (e.g. Bim Bid and BAD).

All proteins belonging to the Bcl-2 family[17] contain either a BH1, BH2, BH3 or BH4 domain. All anti-apoptotic proteins contain BH1 and BH2 domains, some of them contain an additional N-terminal BH4 domain (Bcl-2, Bcl-x(L) and Bcl-w), which is also seen in some pro-apoptotic proteins like Bcl-x(S), Diva, Bok-L and Bok-S. On the other hand, all pro-apoptotic proteins contain a BH3 domain necessary for dimerization with other proteins of Bcl-2 family and crucial for their killing activity, some of them also contain BH1 and BH2 domains (Bax and Bak). The BH3 domain is also present in some anti-apoptotic protein, such as Bcl-2 or Bcl-x(L). The three functionally important Bcl-2 homology regions (BH1, BH2 and BH3) are in close spatial proximity. They form an elongated cleft that may provide the binding site for other Bcl-2 family members.

BH3-only family

The BH3-only subset of the Bcl-2 family of proteins contain only a single BH3-domain. The BH3-only members play a key role in promoting apoptosis. The BH3-only family members are Bim, Bid, BAD and others. Various apoptotic stimuli induce expression and/or activation of specific BH3-only family members, which translocate to the mitochondria and initiate Bax/Bak-dependent apoptosis.[18]

Examples

Proteins that are known to contain these domains include vertebrate Bcl-2 (alpha and beta isoforms) and Bcl-x (isoforms Bcl-x(L) and Bcl-x(S)); mammalian proteins Bax and Bak; mouse protein Bid; Xenopus laevis proteins Xr1 and Xr11; human induced myeloid leukemia cell differentiation protein MCL1 and Caenorhabditis elegans protein ced-9.

Human genes encoding proteins that belong to this family include:

See also

References

  1. ^ Muchmore SW, Sattler M, Liang H, et al. (May 1996). "X-ray and NMR structure of human Bcl-xL, an inhibitor of programmed cell death". Nature. 381 (6580): 335–41. doi:10.1038/381335a0. PMID 8692274. 
  2. ^ Adams, J. M.; Cory, S. (1998-08-28). "The Bcl-2 protein family: arbiters of cell survival". Science (New York, N.Y.). 281 (5381): 1322–1326. ISSN 0036-8075. PMID 9735050. 
  3. ^ Vaux DL (1993). "A boom time for necrobiology". Curr. Biol. 3 (12): 877–878. doi:10.1016/0960-9822(93)90223-B. PMID 15335822. 
  4. ^ Milliman CL, Korsmeyer SJ, Wang K, Yin XM, Chao DT (1996). "BID: a novel BH3 domain-only death agonist". Genes Dev. 10 (22): 2859–2869. doi:10.1101/gad.10.22.2859. PMID 8918887. 
  5. ^ Boise, L. H.; González-García, M.; Postema, C. E.; Ding, L.; Lindsten, T.; Turka, L. A.; Mao, X.; Nuñez, G.; Thompson, C. B. (1993-08-27). "bcl-x, a bcl-2-related gene that functions as a dominant regulator of apoptotic cell death". Cell. 74 (4): 597–608. ISSN 0092-8674. PMID 8358789. 
  6. ^ Tsujimoto, Y.; Shimizu, S. (2000-01-21). "Bcl-2 family: life-or-death switch". FEBS letters. 466 (1): 6–10. ISSN 0014-5793. PMID 10648802. 
  7. ^ Zamzami N, Brenner C, Marzo I, Susin SA, Kroemer G (April 1998). "Subcellular and submitochondrial mode of action of Bcl-2-like oncoproteins". Oncogene. 16 (17): 2265–82. doi:10.1038/sj.onc.1201989. PMID 9619836. 
  8. ^ Kinnally KW, Antonsson B (May 2007). "A tale of two mitochondrial channels, MAC and PTP, in apoptosis". Apoptosis. 12 (5): 857–68. doi:10.1007/s10495-007-0722-z. PMID 17294079. 
  9. ^ Martinez-Caballero S, Dejean LM, Jonas EA, Kinnally KW (June 2005). "The role of the mitochondrial apoptosis induced channel MAC in cytochrome c release". J. Bioenerg. Biomembr. 37 (3): 155–64. doi:10.1007/s10863-005-6570-z. PMID 16167172. 
  10. ^ Hippenstiel S, Schmeck B, N'Guessan PD, Seybold J, Krüll M, Preissner K, Eichel-Streiber CV, Suttorp N (October 2002). "Rho protein inactivation induced apoptosis of cultured human endothelial cells". Am. J. Physiol. Lung Cell Mol. Physiol. 283 (4): L830–8. doi:10.1152/ajplung.00467.2001. PMID 12225960. 
  11. ^ Arbel, Nir; Shoshan-Barmatz, Varda (2010-02-26). "Voltage-dependent anion channel 1-based peptides interact with Bcl-2 to prevent antiapoptotic activity". The Journal of Biological Chemistry. 285 (9): 6053–6062. doi:10.1074/jbc.M109.082990. ISSN 1083-351X. PMC 2825399Freely accessible. PMID 20037155. 
  12. ^ Fesik SW, Shi Y (2001). "Controlling the caspases". Science. 294 (5546): 1477–1478. doi:10.1126/science.1062236. PMID 11711663. 
  13. ^ Dejean LM, Martinez-Caballero S, Manon S, Kinnally KW (February 2006). "Regulation of the mitochondrial apoptosis-induced channel, MAC, by BCL-2 family proteins". Biochim. Biophys. Acta. 1762 (2): 191–201. doi:10.1016/j.bbadis.2005.07.002. PMID 16055309. 
  14. ^ Antonsson, B.; Montessuit, S.; Lauper, S.; Eskes, R.; Martinou, J. C. (2000-01-15). "Bax oligomerization is required for channel-forming activity in liposomes and to trigger cytochrome c release from mitochondria". The Biochemical Journal. 345 Pt 2: 271–278. ISSN 0264-6021. PMC 1220756Freely accessible. PMID 10620504. 
  15. ^ Chao DT, Korsmeyer SJ (1998). "BCL-2 family: regulators of cell death". Annu. Rev. Immunol. 16: 395–419. doi:10.1146/annurev.immunol.16.1.395. PMID 9597135. 
  16. ^ Muchmore, S. W.; Sattler, M.; Liang, H.; Meadows, R. P.; Harlan, J. E.; Yoon, H. S.; Nettesheim, D.; Chang, B. S.; Thompson, C. B. (1996-05-23). "X-ray and NMR structure of human Bcl-xL, an inhibitor of programmed cell death". Nature. 381 (6580): 335–341. doi:10.1038/381335a0. ISSN 0028-0836. PMID 8692274. 
  17. ^ Reed JC, Zha H, Aime-Sempe C, Takayama S, Wang HG (1996). "Structure-function analysis of Bcl-2 family proteins. Regulators of programmed cell death". Adv. Exp. Med. Biol. 406: 99–112. doi:10.1007/978-1-4899-0274-0_10. PMID 8910675. 
  18. ^ Michael Kastan; Abeloff, Martin D.; Armitage, James O.; Niederhuber, John E. (2008). Abeloff's clinical oncology (4th ed.). Philadelphia: Churchill Livingstone/Elsevier. ISBN 0-443-06694-9. 

This article incorporates text from the public domain Pfam and InterPro IPR000712 As of this edit, this article uses content from "1.A.21 The Bcl-2 (Bcl-2) Family", which is licensed in a way that permits reuse under the Creative Commons Attribution-ShareAlike 3.0 Unported License, but not under the GFDL. All relevant terms must be followed.

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.

Apoptosis regulator M11, B cell 2 leukaemia/lymphoma like Provide feedback

PF02180. Bcl-2_3 is a small family of eukaryotic proteins associated with autophagy. The family is found in association with PF00452.

Literature references

  1. Cruz-Reyes J, Tata JR;, Gene. 1995;158:171-179.: Cloning, characterization and expression of two Xenopus bcl-2-like cell-survival genes. PUBMED:7607538 EPMC:7607538

  2. Ku B, Woo JS, Liang C, Lee KH, Hong HS, E X, Kim KS, Jung JU, Oh BH;, PLoS Pathog. 2008;4:e25.: Structural and biochemical bases for the inhibition of autophagy and apoptosis by viral BCL-2 of murine gamma-herpesvirus 68. PUBMED:18248095 EPMC:18248095


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR029450

Some herpesviruses encode homologues of the antiapoptotic, cellular Bcl-2 to promote viral replication and pathogenesis. Members of this small group of viral proteins are homologues of Bcl-2 and seem to inhibit autophagy through binding to autophagy effector Beclin1 [PUBMED:18797192].

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
(3)
Full
(0)
Representative proteomes UniProt
(4)
NCBI
(21)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
Jalview View            View  View   
HTML View                 
PP/heatmap 1                

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

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

Format an alignment

  Seed
(3)
Full
(0)
Representative proteomes UniProt
(4)
NCBI
(21)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
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
(3)
Full
(0)
Representative proteomes UniProt
(4)
NCBI
(21)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
Raw Stockholm Download             Download   Download    
Gzipped 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: Jackhmmer:P89884
Previous IDs: none
Type: Family
Author: Coggill P
Number in seed: 3
Number in full: 0
Average length of the domain: 0.00 aa
Average identity of full alignment: 0 %
Average coverage of the sequence by the domain: 0.00 %

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 25.0 25.0
Trusted cut-off 25.3 25.3
Noise cut-off 24.7 24.5
Model length: 126
Family (HMM) version: 4
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 2 interactions for this family. More...

Bcl-2_3 BH3