Structure and Function of IAP and Bcl‐2 Proteins

Abstract

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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References

Adams JM (2003) Ways of dying: multiple pathways to apoptosis. Genes & Development 17: 2481–2495.

Ashkenazi A and Dixit VM (1998) Death receptors: signaling and modulation. Science 281: 1305–1308.

Bertrand MJ, Milutinovic S, Dickson KM et al. (2008) cIAP1 and cIAP2 facilitate cancer cell survival by functioning as E3 ligases that promote RIP1 ubiquitination. Molecular Cell 30: 689–700.

Chen L, Willis SN, Wei A et al. (2005) Differential targeting of prosurvival Bcl‐2 proteins by their BH3‐only ligands allows complementary apoptotic function. Molecular Cell 17: 393–403.

Crook NE, Clem RJ and Miller LK (1993) An apoptosis‐inhibiting baculovirus gene with a zinc finger‐like motif. Journal of Virology 67: 2168–2174.

Gyrd‐Hansen M, Darding M, Miasari M et al. (2008) IAPs contain an evolutionarily conserved ubiquitin‐binding domain that regulates NF‐κB as well as cell survival and oncogenesis. Nature Cell Biology 10: 1309–1317.

Hanahan D and Weinberg RA (2000) The hallmarks of cancer. Cell 100: 57–70.

Hinds MG, Lackmann M, Skea GL et al. (2003) The structure of Bcl‐w reveals a role for the C‐terminal residues in modulating biological activity. EMBO Journal 22: 1497–1507.

Hinds MG, Norton RS, Vaux DL and Day CL (1999) Solution structure of a baculoviral inhibitor of apoptosis (IAP) repeat. Nature Structural Biology 6: 648–651.

Hinds MG, Smits C, Fredericks‐Short R et al. (2007) Bim, Bad and Bmf: intrinsically unstructured BH3‐only proteins that undergo a localized conformational change upon binding to prosurvival Bcl‐2 targets. Cell Death & Differentiation 14: 128–136.

Lee EF, Czabotar PE, Smith BJ et al. (2007) Crystal structure of ABT‐737 complexed with Bcl‐xL: implications for selectivity of antagonists of the Bcl‐2 family. Cell Death & Differentiation 14: 1711–1713.

Mace PD, Linke K, Feltham R et al. (2008) Structures of the cIAP2 RING domain reveal conformational changes associated with ubiquitin‐conjugating enzyme (E2) recruitment. Journal of Biological Chemistry 283: 31633–31640.

Muchmore SW, Sattler M, Liang H et al. (1996) X‐ray and NMR structure of human Bcl‐xL, an inhibitor of programmed cell death. Nature 381: 335–341.

Oltersdorf T, Elmore SW, Shoemaker AR et al. (2005) An inhibitor of Bcl‐2 family proteins induces regression of solid tumours. Nature 435: 677–681.

Riedl SJ, Renatus M, Schwarzenbacher R et al. (2001) Structural basis for the inhibition of caspase‐3 by XIAP. Cell 104: 791–800.

Riedl SJ and Shi Y (2004) Molecular mechanisms of caspase regulation during apoptosis. Nature Reviews. Molecular Cell Biology 5: 897–907.

Salvesen GS and Abrams JM (2004) Caspase activation – stepping on the gas or releasing the brakes? Lessons from humans and flies. Oncogene 23: 2774–2784.

Sattler M, Liang H, Nettesheim D et al. (1997) Structure of Bcl‐xL‐Bak peptide complex: recognition between regulators of apoptosis. Science 275: 983–986.

Shiozaki EN, Chai J, Rigotti DJ et al. (2003) Mechanism of XIAP‐mediated inhibition of caspase‐9. Molecular Cell 11: 519–527.

Srinivasula SM, Hegde R, Saleh A et al. (2001) A conserved XIAP‐interaction motif in caspase‐9 and Smac/DIABLO regulates caspase activity and apoptosis. Nature 410: 112–116.

Sun C, Cai M, Gunasekera AH et al. (1999) NMR structure and mutagenesis of the inhibitor‐of‐apoptosis protein XIAP. Nature 401: 818–822.

Suzuki M, Youle RJ and Tjandra N (2000) Structure of Bax: coregulation of dimer formation and intracellular localization. Cell 103: 645–654.

Varfolomeev E, Blankenship JW, Wayson SM et al. (2007) IAP antagonists induce autoubiquitination of c‐IAPs, NF‐κB activation, and TNFα‐dependent apoptosis. Cell 131: 669–681.

Vaux DL and Silke J (2005) IAPs, RINGs and ubiquitylation. Nature Reviews. Molecular Cell Biology 6: 287–297.

Vince JE, Wong WW, Khan N et al. (2007) IAP antagonists target cIAP1 to induce TNFα‐dependent apoptosis. Cell 131: 682–693.

Vucic D and Fairbrother WJ (2007) The inhibitor of apoptosis proteins as therapeutic targets in cancer. Clinical Cancer Research 13: 5995–6000.

Wei MC, Zong WX, Cheng EH et al. (2001) Proapoptotic BAX and BAK: a requisite gateway to mitochondrial dysfunction and death. Science 292: 727–730.

Wilson‐Annan J, O'Reilly LA, Crawford SA et al. (2003) Proapoptotic BH3‐only proteins trigger membrane integration of prosurvival Bcl‐w and neutralize its activity. Journal of Cell Biology 162: 877–887.

Youle RJ and Strasser A (2008) The BCL‐2 protein family: opposing activities that mediate cell death. Nature Reviews. Molecular Cell Biology 9: 47–59.

Zong WX, Lindsten T, Ross AJ et al. (2001) BH3‐only proteins that bind pro‐survival Bcl‐2 family members fail to induce apoptosis in the absence of Bax and Bak. Genes & Development 15: 1481–1486.

Further Reading

Adams JM and Cory S (2007) The Bcl‐2 apoptotic switch in cancer development and therapy. Oncogene 26: 1324–1337.

Danial NN and Korsmeyer SJ (2004) Cell death: critical control points. Cell 116: 205–219.

Keskin O, Gursoy A, Ma B and Nussinov R (2008) Principles of protein–protein interactions: what are the preferred ways for proteins to interact? Chemical Reviews 108: 1225–1244.

Lacasse E, Mahoney D, Cheung H et al. (2008) IAP‐targeted therapies for cancer. Oncogene 27: 6252–6275.

Lessene G, Czabotar PE and Colman PM (2008) BCL‐2 family antagonists for cancer therapy. Nature Reviews. Drug Discovery 7: 989–1000.

Pickart CM (2001) Mechanisms underlying ubiquitination. Annual Review of Biochemistry 70: 503–533.

Reed JC, Doctor KS and Godzik A (2004) The domains of apoptosis: a genomics perspective. Science's STKE 2004: re9.

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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. http://www.els.net [doi: 10.1002/9780470015902.a0021983]