Three-dimensional structures of proteins involved in programmed cell death

Journal of Molecular Biology

Volumn 274, Issue 3, 1997, Pages 291-302

  Liang, Heng ^a   Fesik, Stephen W ^a  

^a ABBOTT LABORATORIES   (United States)

Author keywords

Apoptosis; Bcl 2; Caspase; Tumor necrosis factor receptor

Indexed keywords

PROTEIN BCL 2; TUMOR NECROSIS FACTOR RECEPTOR;

APOPTOSIS; CELL DEATH; ETIOLOGY; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN STRUCTURE; REVIEW; THREE DIMENSIONAL IMAGING;

EID: 0031555482     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1415     Document Type: Article

References (87)

1. Alnemri, E. S., Livingston, D. J., Nicholson, D. W., Salvesen, G., Thornberry, N. A., Wong, W. W. & Yuan, J. (1996). Human ICE/CED-3 protease nomenclature. Cell, 87, 171.
2. Antonsson, B., Conti, F., Ciavatta, A., Montessuit, S., Lewis, S., Martinou, I., Bernasconi, L., Bernard, A., Mermod, J.-J., Mazzei, G., Maundrell, K., Gambale, F., Sadoul, R. & Martinou, J. -C. (1997). Inhibition of Bax channel-forming activity by Bcl-2. Science, 277, 370-372.
3. Baker, S. J. & Reddy, E. P. (1996). Transducers of life and death: TNF receptor superfamily and associated proteins. Oncogene, 12, 1-9.
4. Bakhshi, A., Jensen, J. P., Goldman, P., Wright, J. J., McBride, O. W., Epstein, A. L. & Korsmyer, S. J. (1985). Cloning the chromosomal break-point of the t(14:18) human lymphomas: cloustering around JH on chromosome 14 and near a transcriptional unit on 18. Cell, 41, 889-906.
5. Banner, D. W., D'Arcy, A., Janes, W., Gentz, R., Schoenfeld, H.-J., Broger, C., Loetscher, H. & Lesslauer, W. (1993). Crystal structure of the soluble human 55 kd TNF receptor-human TNFb complex: implications for TNF receptor: implication for TNF receptor activation. Cell, 73, 431-455.
6. Bennett, M. J., Choe, S. & Eisenberg, D. (1994). Refined structure of dimeric diphtheria toxin at 2.0 Å resolution. Protein Sci. 3, 1444-1463.
7. Boldin, M. P., Mett, I. L., Varfolomeev, E. E., Chumakov, I., Shemer-Avni, Y., Camonis, J. H. & Wallach, D. (1995a). Self-association of the "death domains" of p55 tumor necrosis factor (TNF) receptor and Fas/APO1 prompts signaling for TNF and Fas/APO1 effects. J. Biol. Chem. 270, 387-391.
8. Boldin, M. P., Varfolomeev, E. E., Pancer, Z., Mett, I. L., Camonis, J. H. & Wallach, D. (1995b). A novel protein that interacts with the death domain of Fas/ APO1 contains a sequence motif related to the death domain. J. Biol. Chem. 270, 7795-7798.
9. Boldin, M. P., Goncharov, T. M., Goltsev, Y. V. & Wallach, D. (1996). Involvement of MACH, a novel MORT1/FADD-interacting protease, in Fas/APO-1-and TNF receptor-induced cell death. Cell, 86, 803-815.
10. Boyd, J. M., Malstrom, S., Subramanian, T., Venkatesh, L. K., Schaeper, U., Elangovan, B., D'Sa-Eipper, C. & Chinnadurai, G. (1994). Adenovirus E1B 19 kDa and Bcl-2 proteins interact with a common set of cellular proteins. Cell, 79, 341-351.
11. Branden, C. & Tooze, J. (1991). Introduction to Protein Structure, Garland Publishing, New York.
12. L. EMBO J. 16, 968-977.
13. Ras in Ras-induced apoptosis. J. Biol. Chem. 271, 2376-2379.
14. Chen, P., Lee, P., Otto, L. & Abrams, J. (1996). Apoptotic activity of REAPER is distinct from signaling by the Tumor Necrosis Factor Receptor 1 Death Domain. J. Biol. Chem. 271, 25735-25737.
15. Chinnaiyan, A. M. & Dixit, V. M. (1996). The cell-death machine. Curr. Biol. 6, 555-562.
16. Chinnaiyan, A. M., O'Rourke, K., Tewari, M. & Dixit, V. M. (1995). FADD, a novel death domain-containing protein interacts with the death domain of Fas and initiates apoptosis. Cell, 81, 505-512.
17. Chinnaiyan, A. M., O'Rourke, K., Lane, B. R. & Dixit, V. M. (1997). Interaction of CED-4 with CED-3 and CED-9: a molecular framework for cell death. Science, 275, 1122-1126.
18. Chittenden, T., Flemington, C., Houghton, A. B., Ebb, R. G., Gallo, G. J., Elangovan, B., Chinnadurai, G. & Lutz, R. (1995). A conserved domain in Bak, distinct from BH1 and BH2, mediates cell death and protein binding functions. EMBO J. 14, 5589-5596.
19. Cleary, M. L., Smith, S. D. & Sklar, J. (1986). Cloning and structural analysis of cDNAs for bcl-2 and a hybrid bcl-2/immunoglobin transcript resulting from the t(14:18) translocation. Cell, 47, 19-28.
20. Cramer, W. A., Heymann, J. B., Schendel, S. L., Deriy, B. N., Cohen, F. S., Elkins, P. A. & Stauffacher, C. V. (1995). Structure-function of the channel-forming colicins. Annu. Rev. Biophys. Biomol. Struct. 24, 611-641.
21. 2+ pool depletion. Oncogene, 12, 2051-2056.
22. Eck, M. J. & Sprang, S. R. (1989). The structure of tumor necrosis factor alpha at 2.6 Å resolution: implications for receptor binding. J. Biol. Chem. 264, 17595-17605.
23. Eck, M. J., Ultsch, M., Rinderknecht, E., de Vos, A. M. & Sprang, S. R. (1992). The structure of human lymphotoxin (tumor necrosis factor beta) at 1.9 Å resolution. J. Biol. Chem. 267, 2119-2122.
24. Enari, M., Talanian, R. V., Wong, W. W. & Nagata, S. (1996). Sequential activation of ICE-like and CPP32-like proteases during Fas-mediated apoptosis. Nature, 380, 723-726.
25. Fernandez-Sarabia, M. J. & Bischoff, J. R. (1993). Bcl-2 associates with the ras-related protein R-ras p23. Nature, 366, 274-275.
26. Fraser, A. & Evan, G. (1996). A license to kill. Cell, 85, 781-784.
27. Golstein, P., Marguet, D. & Depraetere, V. (1995). Homology between reaper and the cell death domains of Fas and TNFR1. Cell, 81, 185-186.
28. Gu, Y., Wu, J., Faucheu, C., Lalanne, J.-L., Diu, A., Livingston, D. J. & Su, M. S.-S. (1995). Interleukin-1β converting enzyme requires oligomerization for activity of processed forms in vivo. EMBO J. 14, 1923-1931.
29. Haldar, S., Jena, N. & Croce, C. M. (1995). Inactivation of Bcl-2 by phosphorylation. Proc. Natl Acad. Sci. USA, 92, 4507-4511.
30. Han, J., Sabbatinit, P., Perez, D., Rao, L., Modha, D. & White, E. (1996). The E1B 19 K protein functions as an apoptosis inhibitor by interacting with and inhibiting the p53-inducible and death-promoting Bax protein. Genes Dev. 10, 461-477.
31. Hirsch, T., Marzo, I. & Kroemer, G. (1997). Role of the mitochondrial permeability transition pore in apoptosis. Biosci. Reports, 17, 67-76.
32. Hockenbery, D., Nunez, G., Milliman, C., Schreiber, R. D. & Korsmeyer, S. J. (1990). Bcl-2 is an inner mitochodrial membrane protein that blocks programmed cell death. Nature, 348, 334-336.
33. Hofman, K., Bucher, P. & Tschopp, J. (1997). The CARD domain: a new apoptotic signalling motif. Trends Biochem. Sci. 22, 155-156.
34. Horvitz, H. R., Shaham, S. & Hengartner, M. O. (1994). The genetics of programmed cell death in the nematode Caenorhabditis elegans. Cold Spring Harbor Symp. Quant. Biol. 59, 377-385.
35. Hsu, H., Xiong, J. & Goeddel, D. V. (1995). The TNF receptor 1-associated protein TRADD signals cell death and NF-kappa B activation. Cell, 81, 495-504.
36. Huang, B., Eberstadt, M., Olejniczak, E. T., Meadows, R. P. & Fesik, S. W. (1996). NMR structure and mutagenesis of the Fas (APO-1/CD95) death domain. Nature, 384, 638-641.
37. Irmler, M., Hofman, K., Vaux, D. & Tschopp, J. (1997). Direct physical interaction between the Caenorhabditis elegans 'death proteins' CED-3 and CED-4. FEBS Letters, 406, 189-190.
38. Ito, T., Deng, X., Carr, B. & May, W. S. (1997). Bcl-2 phosphorylation required for anti-apoptosis function. J. Biol. Chem. 272, 11671-11673.
39. Itoh, N. & Nagata, S. (1993). A novel protein domain required for apoptosis. J. Biol. Chem. 268, 10932-10937.
40. James, C., Gschmeissner, S., Fraser, A. & Evan, G. I. (1997). CED-4 induces chromatin condensation in Schizosaccharomyces pombe and is inhibited by directed physical association with CED-9. Curr. Biol. 7, 246-252.
41. Jones, E. Y., Stuart, D. I. & Walker, N. P. (1989). Structure of tumour necrosis factor. Nature, 338, 225-228.
42. Kluck, R. M., Bossy-Wetzel, E., Green, D. R. & Newmeyer, D. D. (1997). The release of cytochrome c from mitochondria: a primary site for bcl-2 regulation of apoptosis. Science, 275, 1132-1136.
43. Liepinsh, E., IIag, L. L., Otting, G. & Ibáez, C. F. (1997). NMR structure of the death domain of the p75 neurotrophin receptor. EMBO J. 16, 4999-5005.
44. 2+. Oncogene, 12, 2259-2266.
45. Martin, S. J. & Green, D. R. (1995). Protease activation during apoptosis: death by a thousand cuts? Cell, 82, 349-352.
46. Martin, S. J., Newmeyer, D. D., Mathias, S., Farschon, D. M., Wang, H. G., Reed, J. C., Kolesnick, R. N. & Green, D. R. (1995). Cell-free reconstitution of Fas-, UV radiation-and ceramide-induced apoptosis. EMBO J. 14, 5191-5200.
47. McCall, K. & Steller, H. (1997). Facing death in the fly: genetic analysis of apoptosis in Drosophila. Trends Genet. 13, 222-226.
48. L forms an ion channel in synthetic lipid membranes. Nature, 385, 353-357.
49. Mittl, P. R. E., Di, Marco S., Krebs, J. F., Bai, X., Karanewsky, D. S., Priestle, J. P., Tomaselli, K. J. & Grütter, M. G. (1997). Structure of recombinant human CPP32 in complex with the tetrapeptide acetyl-Asp-Val-Ala-Asp fluoromethyl ketone. J. Biol. Chem. 272, 6539-6547.
50. Miyashita, T. & Reed, J. C. (1992). bcl-2 gene transfer increases relative resistance of S49.1 and WEHI7.2 lymphoid cells to cell death and DNA fragmentation induced by glucorcorticoids and multiple chemotherapeutic drugs. Cancer Res. 52, 5407-5411.
51. L, an inhibitor of programmed cell death. Nature, 381, 335-341.
52. Muzio, M., Chinnaiya, A. M., Kischkel, F. C., O'Rouke, K., Shevcheko, A., Ni, J., Scaffidi, C., Bretz, J. D., Zhang, M., Gentz, R., Mann, M., Krammer, P. H., Pter, M. E. & Dixit, V. M. (1996). FLICE, a novel FADD-homologous ICE/CED-3-like protease, is recruited to the CD95 (Fas/AP)-1) death-inducing signaling complex. Cell, 85, 817-827.
53. Nagata, S. (1997). Apoptosis by death factor. Cell, 88, 355-365.
54. Naismith, J. H., Devine, T. Q., Brandhuber, B. J. & Sprang, S. R. (1995). Crystallographic evidence for dimerization of unliganded tumor necrosis factor receptor. J. Biol. Chem. 1995, 13303-13307.
55. Naismith, J. H., Devine, T. Q., Kohno, T. & Sprang, S. R. (1996). Structures of the extracellular domain of the type I tumor necrosis factor receptor. Structure, 4, 1251-1262.
56. Nicholson, D. W. (1996). ICE/CED-3-like proteases as therapeutic targets for the control of inappropriate apoptosis. Nature Biotech. 14, 297-301.
57. Park, M. W., Postma, J. P., Pattus, F., Tucker, A. D. & Tsernoglou, D. (1992). Refined structure of the pore-forming domain of colicin A at 2.4 Å resolution. J. Mol. Biol. 224, 639-657.
58. Parker, M. W. & Pattus, F. (1993). Rendering a membrane protein soluble in water: a common packing motif in bacterial protein toxins. Trends Biochem. Sci. 18, 391-394.
59. Petit, P. X., Susin, S.-A., Zamzami, N., Mignotte, B. & Kroemer, G. (1996). Mitochondria and Programmed cell death: back to the future. FEBS Letters, 396, 7-13.
60. Reed, J. C. (1997). Double identity for proteins of the Bcl-2 family. Nature, 387, 773-776.
61. Rothe, M., Wong, S. C., Henzel, W. J. & Goeddel, D. V. (1994). A novel family of putative signal transducers associated with the cytoplasmic domain of the 75 kDa tumor necrosis factor receptor. Cell, 78, 681-692.
62. Rothe, M. M. G., Henzel, W. J., Ayres, T. M. & Goeddel, D. V. (1995). The TNFR2-TRAF signaling complex contains two novel proteins related to baculoviral inhibitor of apoptosis proteins. Cell, 83, 1243-1252.
63. Rotonda, J., Nicholson, D. W., Fazil, K. M., Gallant, M., Gareau, Y., Labelle, M., Peterson, E. P., Rasper, D. M., Ruel, R., Vaillancourt, J. P., Thornberry, N. A. & Decker, J. W. (1996). The three-dimensional structure of apopain/CPP32, a key mediator of apoptosis. Nature Struct. Biol. 3, 619-625.
64. L-Bak peptide complex: recognition between regulators of apoptosis. Science, 275, 983-986.
65. Schendel, S. L., Xie, Z., Montal, M. O., Matsuyama, S., Montal, M. & Reed, J. C. (1997). Channel formation by antiapoptotic protein Bcl-2. Proc. Natl Acad. Sci USA, 94, 5113-5118.
66. Sentman, C. L., Shutter, J. R., Hockenbery, D., Kanagawa, O. & Korsmeyer, S. J. (1991). bcl-2 inhibits multiple forms of apoptosis but not negative selection in thymocytes. Cell, 67, 879-888.
67. Shibasaki, F., Kondo, E., Akagi, T. & McKeon, F. (1997). Suppression of signalling through transcription factor NF-AT by interactions between calcineurin and Bcl-2. Nature, 386, 728-731.
68. Tartaglia, L. A., Ayers, T. M., Wong, G. H. W. & Goeddel, D. V. (1993). A novel domain within the 55 kd TNF receptor signals cell death. Cell, 74, 845-853.
69. Thompson, C. B. (1995). Apoptosis in the pathogenesis and treatment of disease. Science, 267, 1456-1462.
70. Thornberry, N. A., Bull, H. G., Calaycay, J. R., Chapman, K. T., Howard, A. D., Kostura, M. J., Miller, D. K., Molineaux, S. M., Weidner, J. R., Aunins, J., Elliston, K. O., Ayala, J. M., Casno, F. J., Chin, J., Ding, G. J.-F., Egger, L. A., Gaffney, E. P., Kimjuco, G., Palyha, O. C., Raju, S. M., Rolando, A. M., Salley, J. P., Yamin, T.-T., Lee, T. D., Shively, J. E., MacCross, M., Mumford, R. A., Schmidt, J. A. & Tocci, M. J. (1992). A novel heterodimeric cysteine protease is required for interleukin-1 beta processing in monocytes. Nature, 356, 768-774.
71. Tsujimoto, Y., Gorham, J., Cossman, J., Jaffe, E. & Corce, C. M. (1985). The t(14:18) chromosome translocations involved in B cell neoplasms results from mistakes in VDJ joining. Science, 229, 1390-1393.
72. Vaux, D. L., Cory, S. & Adams, T. M. (1988). Bcl-2 promotes the survival of haemopoietic cells and cooperates with c-myc to immortalize pre-B cells. Nature, 355, 440-442.
73. 2 homodimer. Cell, 78, 343-352.
74. Wang, H.-G., Miyashita, T., Takayama, S., Sato, T., Torigoe, T., Krajewski, S., Tanaka, S., Hovey, L. I., Troppmair, J., Rapp, U. R. & Reed, J. C. (1994). Apoptosis regulation by interaction of Bcl-2 protein and Raf-1 kinase. Oncogene, 9, 2751-2756.
75. Wang, H.-G., Takayama, S., Rapp, U. & Reed, J. (1996a). Bcl-2 interacting protein, BAG-1, binds to and activates the kinase Raf-1. Proc. Natl Acad. Sci. 93, 7063-7068.
76. Wang, H. G., Rapp, U. R. & Reed, J. C. (1996b). Bcl-2 targets the protein kinase Raf-1 to mitochondria. Cell, 87, 629-638.
77. White, E. (1996). Life, death, and the pursuit of apoptosis. Genes Dev. 10, 1-15.
78. Wilson, K. P., Black, J.-A. F., Thomson, J. A., Kim, E. E., Griffith, J. P., Navia, M. A., Murcko, M. A., Chambers, S. P., Aldape, R. A., Raybuck, S. A. & Livingston, D. J. (1994). Structure and mechanism of interleukin-1β converting enzyme. Nature, 370, 270-274.
79. Wright, H. T. (1996). The structural puzzle of how serpin serine proteinase inhibitors work. BioEssays, 18, 453-464.
80. Wu, D., Wallen, H. D. & Nuñez, G. (1997). Interaction and regulation of subcellular localization of CED-4 by CED-9. Science, 275, 1126-1129.
81. Wyllie, A. H., Kerr, J. F. R. & Currie, A. R. (1980). Cell death: the significance of apoptosis. Int. Rev. Cytol. 68, 251-306.
82. Yang, E. & Korsmeyer, S. J. (1996). Molecular thanatopsis: a discourse on the BCL2 family and cell death. Blood, 88, 386-401.
83. Yang, J., Liu, X., Bhalla, K., Kim, C. N., Ibrado, A. M., Cai, J., Peng, T.-I., Jones, D. P. & Wang, X. (197). Prevention of apoptosis by Bcl-2: release of cytochrome c from mitochondria blocked. Science, 275, 1129-1132.
84. Yin, X. -M., Oltval, Z. N. & Korsmeyer, S. J. (1994). BH1 and BH2 domains of Bcl-2 are required for inhibition of apoptosis and herterodimerization with Bax. Nature, 369, 321-323.
85. Zha, H., Aimé-Sempé, C., Sato, T. & Reed, J. C. (1996a). Proapoptotic protein Bax heterodimerizes with Bcl-2 and homodimerizes with Bax via a novel domain (BH3) distinct from BH1 and BH2. J. Biol. Chem. 271, 7440-7444.
86. L. Cell, 87, 619-628.
87. Zou, H., Henzel, W. J., Liu, X., Lutschg, A. & Wang, X. (1997). Apaf-1, a human protein homologous to C. elegans CED-4, participates in cytochrome c-dependent activation of caspase-3. Cell, 90, 405-413.