The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Functional site class:
The helical BH3 motif binds BH domains
Functional site description:
The intrinsic apoptosis pathway is mainly regulated by interactions between Bcl-2 family proteins. Interactions between the pro- and anti-apoptotic proteins antagonize their different functions and their ratio determines whether a cell will live or die. This process is evolutionarily conserved and homologues of Bcl-2 proteins are found in metazoa and animal viruses. The pro-apoptotic BH3-only proteins initiate apoptosis either by directly activating BAX-like proteins or by neutralizing anti-apoptotic Bcl-2-like proteins. This interaction is mediated through the BH3 motif of pro-apoptotic proteins and the hydrophobic groove of anti-apoptotic family proteins.Some BH3-only proteins are promiscuous binders, while others show a selective and hierarchical model of binding to Bcl-2 family proteins. Apoptosis relies on these selective modes of interaction between particular subsets of proteins. BH3-mimetic drugs that inactivate specific pro-survival proteins can be designed based on these interaction modes.
ELM Description:
The Bcl-2 homology 3 domain (BH3 motif) is conserved between most core Bcl-2 family members (Aouacheria,2013). The BH3 domain in anti-apoptotic proteins is part of the hydrophobic binding pocket that interacts with BH3 motifs of pro-apoptotic BH3-only and Bax/Bak proteins .The BH3 motif of the BH3-only proteins forms an amphipathic alpha-helix that binds in a hydrophobic groove on the surface of pro-survival Bcl-2proteins composed of BH1-4 domains.
BH3-only proteins exhibit a range of binding selectivities, with some binding all pro-survival proteins and others only binding a subset. Bim and Puma target all anti-apoptotic proteins comparably, Bad and Bmf prefer Bcl-2, Bcl-XL and Bcl-W, Bik and Hrk bind best to Bcl-XL, Bcl-w and A1, while Noxa binds only Mcl-1 and A1.This differential binding is mainly due to differences in a few key residues in the BH3 motif and also in the binding groove (Chen,2005).Although the sequences of BH3 motifs are variable, a short motif is conserved in most of the Bcl-2 family proteins from virus to human (Aouacheria,2015). Variability is mostly seen in the extended 13 residue motif, which contains four hydrophobic groups that are spaced to form the hydrophobic face of the BH3 helix. Subtle differences in the amino acid sequences in these regions contribute to the different binding affinity of BH3 motifs.The key interactions occur between the BH3 motif and the BH1 domain of pro-survival proteins. The first hydrophobic position does not show any strict conservation. Two small residues provide the tight packing of the helix into the groove. The leucine is buried in the interaction interface and packs against conserved residues provided by the pro-survival proteins. The solvent-exposed aspartate forms an ionic interaction with the conserved arginine in the helix capping motif ‘NWGR’ (Day,2008). From various structural and sequence analyses, the more accurate and generalised form of the motif is retrieved as ….[LIFVYME][ASGC][^P]{2}L[^P]{2}[IVMTL][GACS][D][^P][FVLMI].
Pattern: ....[LIFVYMTE][ASGC][^P]{2}L[^P]{2}[IVMTL][GACS][D][^P][FVLMI].
Pattern Probability: 0.0000022
Present in taxon: Metazoa
Interaction Domain:
Bcl-2 (PF00452) Apoptosis regulator proteins, Bcl-2 family (Stochiometry: 1 : 1)
o See 19 Instances for LIG_BH_BH3_1
o Abstract
Apoptosis or Programmed Cell Death is an evolutionarily conserved process that plays an important role in the removal of infected, damaged, or unwanted cells. Dysregulation of this process can lead to a variety of disorders, including neurodegenerative diseases and cancer. The Bcl-2 family proteins function upstream of caspases as regulators of ‘life-or-death’ decisions in response to various intrinsic and extrinsic stimuli.They are characterized by the presence of conserved sequence motifs known as Bcl-2 homology domains (BH1-BH4). In addition to BH domains, they frequently have a hydrophobic C-terminal part that is important for localization to the mitochondrial outer membrane (MOM), endoplasmic reticulum (ER) and the nuclear envelope (Petros,2004). Members of the Bcl-2 family are grouped into pro- and anti-apoptotic proteins. The anti-apoptotic proteins contain all four BH domains. The pro-apoptotic group contains two subgroups: (i) the multi-domain (BH1-3) containing proteins, and (ii) the single BH3 motif containing proteins. This BH3 motif is required for the killing activity of these pro-apoptotic proteins (Lomonosova,2009).
Different BH3-only proteins sense different stress condition and in response promote apoptosis by binding to and regulating anti-apoptotic Bcl-2 family proteins. The anti-apoptotic Bcl-2 proteins prevent apoptosis either by sequestering activator BH3-only proteins tBID-BIM-PUMA-NOXA thereby preventing them from activating BAX-BAK, or by sequestering partially activated, BH3-exposed monomeric BAX-BAK to prevent their homo-oligomerization (Chen,2015). Many theories have been postulated to explain how BH3 domains regulate apoptosis. In general, to initiate apoptosis, all pro-survival proteins must be neutralized by the BH3-only proteins, then the activator BH3 proteins promote BAX/BAK to undergo oligomerization and insert into the mitochondrial outer membrane, resulting in mitochondrial outer membrane permeabilization (MOMP). As a consequence of MOMP, apoptogenic particles are released from the mitochondria and the regulated disintegration of the cell is initiated (17306210).
The BH3-only proteins are generally promiscuous binders. While some bind all anti-apoptotic proteins with nearly equal affinity, others have differential binding specificity and affinity (Chen,2005). The interaction between the pro- and anti-apoptotic members is mediated through a hydrophobic cleft formed by the BH1-3 domains of anti-apoptotic members and the BH3 motifs of pro-apoptotic proteins. The BH3 motif folds into an amphipathic helix in the hydrophobic groove of the anti-apoptotic proteins upon binding (Petros,2004). The generalized BH3 motif has a consensus pattern of ….[LIFVYME][ASGC][^P]{2}L[^P]{2}[IVMTL][GACS][D][^P][FVLMI]. Viral BH3-containing proteins were also found to regulate apoptosis in infected host cells and manipulate it to their own advantage (Mohd-Ismail,2009).
BH-BH3 interactions are considered to be highly promising targets for protein-protein interaction inhibition. Small molecules inhibitors of BCL-2, such as ABT-199, are expected to play a role in cancer therapy, provided that unwanted side effects can be controlled (Davids,2013).
o 15 selected references:

o 17 GO-Terms:

o 19 Instances for LIG_BH_BH3_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
O88498-4 Bcl2l11
39 55 RPEIRIAQELRRIGDEFNET TP 2 Rattus norvegicus (Norway rat)
O88498-3 Bcl2l11
56 72 RPEIRIAQELRRIGDEFNET TP 1 Rattus norvegicus (Norway rat)
O88498-1 Bcl2l11
142 158 RPEIRIAQELRRIGDEFNET TP 1 Rattus norvegicus (Norway rat)
O61667 egl-1
65 81 SIGYEIGSKLAAMCDDFDAQ TP 6 Caenorhabditis elegans
Q99ML1 Bbc3
133 149 EWAREIGAQLRRMADDLNAQ TP 4 Mus musculus (House mouse)
Q9JM54 Pmaip1
70 86 ADLKDECAQLRRIGDKVNLR TP 6 Mus musculus (House mouse)
Q9JM54 Pmaip1
19 35 ELPPEFAAQLRKIGDKVYCT TP 5 Mus musculus (House mouse)
Q07813 Bax
55 71 ASTKKLSECLRRIGDELDSN TP 3 Mus musculus (House mouse)
Q16611 BAK1
70 86 STMGQVGRQLAIIGDDINRR TP 3 Homo sapiens (Human)
Q92934 BAD
106 122 WAAQRYGRELRRMSDEFVDS TP 3 Homo sapiens (Human)
O70337 Bik
47 63 EGRNQVALRLACIGDEMDLC TP 1 Mus musculus (House mouse)
Q13323 BIK
53 69 EGSDALALRLACIGDEMDVS TP 3 Homo sapiens (Human)
O00198 HRK
29 45 SAAQLTAARLKALGDELHQR TP 3 Homo sapiens (Human)
1972 1988 VMTQEVGQLLQDMGDDVYQQ TP 3 Homo sapiens (Human)
P70444 Bid
82 98 EIIHNIARHLAQIGDEMDHN TP 2 Mus musculus (House mouse)
Q91ZE9 Bmf
130 146 RAEVQIARKLQCIADQFHRL TP 2 Mus musculus (House mouse)
O43521-3 BCL2L11
54 70 RPEIWIAQELRRIGDEFNAY TP 2 Homo sapiens (Human)
O54918-2 Bcl2l11
86 102 RPEIRIAQELRRIGDEFNET TP 5 Mus musculus (House mouse)
Q14457 BECN1
108 124 GTMENLSRRLKVTGDLFDIM TP 5 Homo sapiens (Human)
Please cite: ELM 2016-data update and new functionality of the eukaryotic linear motif resource. (PMID:26615199)

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