Structure and Function of IAP and Bcl‐2 Proteins


Interactions between pro‐apoptotic and pro‐survival proteins control the apoptotic programme in cells. Regulation of caspases, the proteolytic enzymes that destroy the cell, is critical and the actions of the inhibitor of apoptosis (IAP) and B‐cell lymphoma‐2 (Bcl‐2) proteins control the life–death switch. IAP proteins can inhibit caspases and signal the destruction of regulatory molecules. In contrast, in mammals, the Bcl‐2 family controls mitochondrial integrity and the release of factors that activate caspases or block the action of IAPs. Structures of many of these proteins, and the complexes they form, are now available and underpin current models of apoptosis. Here we review key features of these structures and highlight how these studies have led to the development of antagonist compounds that allow the pro‐survival effects of IAP and Bcl‐2 proteins to be negated.

Key Concepts

  • Caspases are kept inactive in healthy cells by the actions of molecules that inhibit their oligomerization and processing.

  • Pro‐survival Bcl‐2 proteins have a hydrophobic BH3‐binding groove that is required for binding both pro‐apoptotic BH3‐only and Bax‐like proteins.

  • Bcl‐2 proteins exhibit conformational plasticity and can adopt distinct conformations that are required for their activity.

  • The IBM‐binding site on the BIR domains is required for direct inhibition of caspases by IAPs.

  • The RING domain of IAP proteins mediates their ubiquitin E3‐ligase activity, and is required for the pro‐apoptotic activity of IAP‐antagonist molecules.

  • Structures of molecules that prevent caspase activation, in complex with their inhibitors, have guided the development of antagonist compounds that have therapeutic potential.

Keywords: apoptosis; Bcl‐2; IAP; protein–protein interactions; BH3

Figure 1.

Schematic highlighting of the points at which IAP and Bcl‐2 proteins regulate caspase activity. The structural basis for inhibition of caspase‐9 and effector caspases by IAPs is well understood. In contrast, inhibition of caspase‐8 occurs indirectly and these complexes have not been characterized in detail. Structures are also available for many Bcl‐2 proteins, including complexes between different classes, but it remains uncertain how Bcl‐2 inhibits Bax, and the structure of the pro‐apoptotic Bax (or Bak) complex has eluded analysis.

Figure 2.

Bcl‐2 protein domain organization and function. (a) Domain structure of Bcl‐2 proteins. Pro‐survival Bcl‐2 proteins bear up to four Bcl‐2 homology domains BH1–BH4 and a hydrophobic C‐terminal region (TM), necessary for their membrane localization. The coloured bars represent the helices α1–α9 in the three‐dimensional structure. The pro‐apoptotic Bax‐like proteins have BH1‐3, and 9 α helices that have a similar arrangement as their pro‐survival counterparts. In contrast, the BH3‐only proteins bear only a BH3 domain. The consensus sequence for the BH3 domain is shown (see text). (b) The Bcl‐2 family mediated caspase‐activation pathway. Bax and Bak control the release pro‐apoptotic molecules from mitochondria that lead to caspase activation. Pro‐survival proteins block the action of the Bax‐like proteins, but when activated by apoptotic stimuli BH3‐only proteins block the activity of pro‐survival Bcl‐2 proteins.

Figure 3.

Structures of Bcl‐2 proteins. Structures of C‐terminally truncated Mcl‐1 alone and in complex with the BH3 domain from Noxa are shown. Mcl‐1 forms a small helical bundle with a binding groove formed by the helices α2–α5 and α8. The helices are labelled α1–α8 and the N‐ and C‐termini for Mcl‐1, N and C. In the Mcl‐1:Noxa complex structure the N‐ and C‐termini for Noxa are labelled N′ and C′. The structure of pro‐survival Bcl‐w and pro‐apoptotic Bax are also shown and their termini are indicated. The ribbon diagram shows that the structures of pro‐survival and the multidomain pro‐apoptotic proteins have the same topology, with the C‐terminal helix, α9, lying in the binding groove.

Figure 4.

Structure and organization of IAPs. (a) Domain arrangement of selected mammalian IAPs. (b) The BIR domain has a compact structure centred on a single zinc ion (grey ball). The structure of BIR3 from XIAP is shown (PDB code 1g3f). (c) The C‐terminal RING domain binds two zinc ions and has a conserved fold that is common to all RING domains. In IAPs residues N‐ and C‐terminal to the core RING domain mediate dimer formation. The structure of the cIAP2 RING dimer is shown (PDB code 3eb5). (d) An enzyme cascade mediates ubiquitylation. Isopeptide bond formation between the C‐terminus of ubiquitin and lysine residues in target proteins depends on ATP and E1, E2 and E3 enzymes. Substrate (S) (top) and autoubiquitylation (bottom) by RING E3 ligases is shown.

Figure 5.

Structure‐based development of drugs that antagonize IAPs and pro‐survival Bcl‐2 proteins. (a) Structure of a chimeric BIR3 domain showing the IBM‐binding pocket with either a peptide or a small molecule antagonist present (PDB codes 2I3H and 2I3I). The BIR domain is shown as a surface and the bound ligands as stick representation. (b) Bcl‐xL is shown bound to the BH3 domain of Bim and to ABT‐737, a small molecule anatagonist (PDB codes 1PQ1 and 2YXJ) that occupies the same binding groove. Bcl‐xL is shown as a surface, Bim as a ribbon and ABT‐737 as a stick model. The IBM‐binding site adopts a similar conformation when bound to both peptide and small molecule antagonist, whereas the binding groove of Bcl‐xL adopts a distinct structure when bound to ABT‐737.



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Hinds, Mark G, Mace, Peter D, and Day, Catherine L(Sep 2009) Structure and Function of IAP and Bcl‐2 Proteins. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0021983]