Proteasomes: Molecular Machines for Protein Degradation
Part 7. Polyamides and Complex Proteinaceous Materials
Dr. Susanne Witt,
Prof. Dr. Wolfgang Baumeister,
Dr. Susanne Witt
- [email protected]
- +49-89-8578-2648 | Fax: +49-89-8578-2641
Max-Planck-Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18a, Martinsried, Germany, 82152
Search for more papers by this authorProf. Dr. Wolfgang Baumeister
- [email protected]
- +49-89-8578-2652 | Fax: +49-89-8578-2641
Max-Planck-Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18a, Martinsried, Germany, 82152
Search for more papers by this authorDr. Susanne Witt,
Prof. Dr. Wolfgang Baumeister,
Dr. Susanne Witt
- [email protected]
- +49-89-8578-2648 | Fax: +49-89-8578-2641
Max-Planck-Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18a, Martinsried, Germany, 82152
Search for more papers by this authorProf. Dr. Wolfgang Baumeister
- [email protected]
- +49-89-8578-2652 | Fax: +49-89-8578-2641
Max-Planck-Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18a, Martinsried, Germany, 82152
Search for more papers by this authorFirst published: 15 January 2005
Abstract
- Introduction: Controlling Intracellular Proteolysis
- Historical Outline
- Occurrence and Subunit Composition of 20S Proteasomes
- Structural Features of the 20S Proteasome
- Catalytic Mechanism of the 20S Proteasome
- Processing and Assembly of 20S Proteasomes
- Size Distribution of 20S Proteasome Products
- The 19S Regulatory Complex
- Subcomplexes and Subunits of the 19S Regulator
- The PA28 Activator
- Outlook and Perspectives
References
- Aravind, L., Ponting, C. P. (1998) Homologues of 26S proteasome subunits are regulators of transcription and translation, Protein Sci. 7, 1250–1254.
- Arrigo, A. P., Tanaka, K., Goldberg, A. L., Welch, W. J. (1988) Identity of the 19S ‘prosome' particle with the multifunctional protease complex of mammalian cells (the proteasome), Nature 331, 192–194.
- Asano, K., Vornlocher, H. P., Richtercook, N. J., Merrick, W. C., Hinnebusch, A. G., Hershey, J. W. B. (1997) Structure of cDNAs encoding human eukaryotic initiation factor 3 subunits–possible roles in RNA binding and macromolecular assembly, J. Biol. Chem. 272, 27042–27052.
- Baboshina, O. V., Haas, A. L. (1996) Identification of a novel family of ubiquitin-conjugating enzymes with distinct amino-terminal extensions, J. Biol. Chem. 271, 2789–2794.
- Baumeister, W., Walz, J., Zühl, F., Seemüller, E. (1998) The proteasome–paradigm of a self-compartimentalizing protease, Cell 92, 367–380.
- Beal, R., Deveraux, Q., Xia, G., Rechsteiner, M., Pickart, C. (1996) Surface hydrophobic residues of multiubiquitin chains essential for proteolytic targeting, Proc. Natl. Acad. Sci. USA 93, 861–866.
- Beal, R. E., Toscanocantaffa, D., Young, P., Rechsteiner, M., Pickart, C. M. (1998) The hydrophobic effect contributes to polyubiquitin chain recognition, Biochemistry 37, 2925–2934.
- Benaroudj, N., Goldberg, A. L. (2000) PAN, the Proteasome-Activating Nucleotidase from Archaebacteria, is a protein-unfolding molecular chaperone, Nature Cell Biol. 2, 833–839.
- Bogyo, M., Wang, E. W. (2002) Proteasome inhibitors: complex tools for a complex enzyme, in: The Proteasome-Ubiquitin Protein Degradation Pathway ( P. Zwickl, W. Baumeister, Eds.), Berlin, Heidelberg, New York: Springer-Verlag, 185–208.
- Bonifacino, J. S., Weissman, A. M. (1998) Ubiquitin and the control of protein fate in the secretory and endocytic pathways, Annu. Rev. Cell Dev. Biol. 14, 19–57.
- Bouzat, J. L., McNeil, L. K., Robertson, H. M., Solter, L. F., Nixon, J. E., Beever, J. E., Gaskins, H. R., Olsen, G., Subramaniam, S., Sogin, M. L., Lewin, H. A. (2000) Phylogenomic analysis of the a proteasome gene family from early-diverging eukaryotes, J. Mol. Evolution 51, 532–543.
- Brannigan, J. A., Dodson, G., Duggleby, H. J., Moody, P. C. E., Smith, J. L., Tomchick, D. R., Murzin, A. G. (1995) A protein catalytic framework with an N-terminal nucleophile is capable of self-activation, Nature 378, 416–419.
- Braun, B. C., Glickman, M., Kraft, R., Dahlmann, B., Kloetzel, P. M., Finley, D., Schmidt, M. (1999) The base of the proteasome regulatory particle exhibits chaperone-like activity, Nature Cell Biol. 1, 221–226.
- Cascio, P., Call, M., Petre, B. M., Walz, T., Goldberg, A. L. (2002) Properties of the hybrid form of the 26S proteasome containing both 19S and PA28 complexes, EMBO J 21, 2636–2645.
- Chen, P., Hochstrasser, M. (1996) Autocatalytic subunit processing couples active site formation in the 20S proteasome to completion of assembly, Cell 86, 961–972.
- Coux, O., Tanaka, K., Goldberg, A. L. (1996) Structure and function of the 20S and 26S proteasomes, Annu. Rev. Biochem. 65, 801–847.
- Craiu, A., Gaczynska, M., Akopian, T., Gramm, C. F., Fenteany, G., Goldberg, A. L., Rock, K. L. (1997) Lactacystin and clasto-lactacystin beta-lactone modify multiple proteasome beta-subunits and inhibit intracellular protein degradation and major histocompatibility complex Class I antigen presentation, J. Biol. Chem. 272, 13437–13445.
- Dahlmann, B., Kuehn, L., Rutschmann, L., Reinauer, H. (1985) Purification and characterization of a multicatalytic high molecular mass proteinase from rat skeletal muscle, Biochem. J. 228, 161–170.
- Dahlmann, B., Kopp, F., Kuehn, L., Niedel, B., Pfeifer, G., Hegerl, R., Baumeister, W. (1989) The multicatalytic proteinase (proteasome) is ubiquitinous from Eukaryotes to Archaeabacteria, FEBS Lett. 251, 125–131.
- De Mot, R., Nagy, I., Walz, J., Baumeister, W. (1999) Proteasomes and other self-compartmentalizing proteases in procaryotes, Trends Microbiol. 7, 88–92.
- DeMartino, G. N. and Slaughter, C. A. (1999) The proteasome, a novel protease regulated by multiple mechanisms, J. Biol. Chem. 274, 22123–22126.
- DeMartino, G. N., Moomaw, C. R., Zagnitko, O. P., Proske, R. J., Chu-Ping, M., Afendis, S. J., Swaffield, J. C., Slaughter, C. A. (1994) PA700, an ATP-dependent activator of the 20 S proteasome, is an ATPase containing multiple member of a nucleotide-binding protein family, J. Biol. Chem. 269, 20878–20884.
- Deveraux, Q., Ustrell, V., Pickart, C., Rechsteiner, M. (1994) A 26 S protease subunit that binds ubiquitin conjugates, J. Biol. Chem. 269, 7059–7061.
- Dick, T. P., Ruppert, T., Groettrup, M., Kloetzel, P. M., Kuehn, L., Koszinowski, U. H., Stevanovic, S., Schild, H., Rammensee, H. G. (1996) Antigen presentation–recent developments, Int. Arch. Allergy Immunol. 110, 299–307.
- Dick, T. P., Nussbaum, A. K., Deeg, M., Heinemeyer, W., Groll, M., Schirle, M., Keilholz, W., Stevanovic, S., Wolf, D. H., Huber, R., Rammensee, H. G., Schild, H. (1998) Contribution of proteasomal β-subunits to the cleavage of peptide substrates analyzed with yeast mutants, J. Biol. Chem. 273, 25637–25646.
- Ditzel, L., Huber, R., Mann, K., Heinemeyer, W., Wolf, D. H., Groll, M. (1998) Conformational constraints for protein self-cleavage in the proteasome, J. Mol. Biol. 279, 1187–1191.
- Dodson, G., Wlodawer, A. (1998) Catalytic triads and their relatives, Trends Biochem. Sci. 23, 347–352.
- Dolenc, I., Seemueller, E., Baumeister, W. (1998) Decelerated degradation of short peptides by the 20s proteasome, FEBS Lett. 424, 357–361.
- Dubiel, W., Pratt, G., Ferrell, K., Rechsteiner, M. (1992) Purification of an 11 S regulator of the multicatalytic protease, J. Biol. Chem. 267, 22369–22377.
- Dubiel, W., Ferrell, K., Rechsteiner, M. (1995) Subunits of the regulatory complex of the 26S protease, Mol. Biol. Reports 21, 27–34.
- Falkenburg, P. E., Haass, C., Kloetzel, P. M., Niedel, B., Kopp, F., Kuehn, L., Dahlmann, B. (1988) Drosophila small cytoplasmic 19S ribonucleoprotein is homologous to the rat multicatalytic proteinase, Nature 331, 190–192.
- Fenteany, G., Standaert, R. F., Lane, W. S., Choi, S., Corey, E. J., Schreiber, S. L. (1995) Inhibition of proteasome activities and subunit-specific amino-terminal threonine modification by lactacystin, Science 268, 726–731.
- Ferrell, K., Wilkinson, C. R. M., Dubiel, W., Gordon, C. (2000) Regulatory subunit interactions of the 26S proteasome, a complex problem, Trends Biochem. Sci. 25, 83–88.
- Früh, K., Yang, Y. (1999) Antigen presentation by MHC Class I and its regulation by interferon gamma, Curr. Opin. Immunol. 11, 76–81.
- Fu, H. Y., Doelling, J. H., Arendt, C. S., Hochstrasser, M., Vierstra, R. D. (1998a) Molecular organization of the 20s proteasome gene family from Arabidopsis thaliana, Genetics 149, 677–692.
- Fu, H. Y., Sadis, S., Rubin, D. M., Glickman, M., Vannocker, S., Finley, D., Vierstra, R. D. (1998b) Multiubiquitin chain binding and protein degradation are mediated by distinct domains within the 26 S proteasome subunit Mcb1, J. Biol. Chem. 273, 1970–1981.
- Glickman, M. H., Rubin, D. M., Coux, O., Wefes, I., Pfeifer, G., Cjeka, Z., Baumeister, W., Fried, V. A., Finley, D. (1998a) A subcomplex of the proteasome regulatory particle required for ubiquitin-conjugate degradation and related to the Cop9-signalosome and Eif3, Cell 94, 615–623.
- Glickman, M. H., Rubin, D. M., Fried, V. A., Finley, D. (1998b) The regulatory particle of the Saccharomyces cerevisiae proteasome, Mol. Cell. Biol. 18, 3149–3162.
- Goldberg, A., Gaczynska, M., Grant, E., Michalek, H., Rock, K. L. (1995) Functions of the proteasome in antigen presentation, Cold Spring Harbor Symp. Quant. Biol. 60, 479–490.
- Gorbea, C., Rechsteiner, M. (2000) The mammalian regulatory complex of the 26S proteasome, in: Proteasomes: The World of Regulatory Proteolysis ( W. Hilt, D. H. Wolf, Eds.), George Town: Eurekah.com/Landes Biosciences, 91–128.
- Gottesman, S. (1996) Proteases and their targets in Escherichia coli, Annu. Rev. Genet. 30, 465–506.
- Gottesman, S., Maurizi, M.R., Wickner, S. (1997) Regulatory subunits of energy-dependent proteases, Cell 91, 435–438.
- Gray, C. W., Slaughter, C. A., DeMartino, G. N. (1994) PA28 activator protein forms regulatory caps on proteasome stacked rings, J. Mol. Biol. 236, 7–15.
- Groettrup, M., Soza, A., Eggers, M., Kuehn, L., Dick, T. P., Schild, H., Rammensee, H. G., Koszinowski, U. H., Kloetzel, P. M. (1996) A role for the proteasome regulator PA28a in antigen presentation, Nature 381, 166–168.
- Groll, M., Ditzel, L., Löwe, J., Stock, D., Bochtler, M., Bartunik, H. D., Huber, R. (1997) Structure of 20s proteasome from yeast at 2.4-Angstrom resolution, Nature 386, 463–471.
- Grziwa, A., Maack, S., Pühler, G., Wiegand, G., Baumeister, W., Jaenicke, R. (1994) Dissociation and reconstitution of Thermoplasma proteasome, Eur. J. Biochem. 223, 1061–1067.
- Haracska, L., Udvardy, A. (1997) Mapping the ubiquitin-binding domains in the P54 regulatory complex subunit of the Drosophila 26s protease, FEBS Lett. 412, 331–336.
- Harris, A. L. (1988) Erythrocyte cylindrin: possible identity with the ubiquitous 20S high molecular weight protease complex and the prosome particle, Indian J. Biochem. Biophys. 25, 459–466.
- Harris, J. R. (1968) Release of a macromolecular protein component from erythrocyte ghosts, Biochim. Biophys. Acta 150, 534–537.
- Harter, C., Wieland, F. (1996) The secretory pathway: mechanisms of protein sorting and transport, Biochim. Biophys. Acta 1286, 75–93.
- Hase, J., Kobashi, K., Nakai, N., Mitsiui, K., Iwata, K., Takadera, T. (1980) The quaternary structure of carp muscle alkaline protease, Biochim. Biophys. Acta 611, 205–213.
- Heemels, M. T., Ploegh, H. (1995) Generation, translocation, and presentation of MHC Class I-restricted peptides, Annu. Rev. Biochem. 64, 463–491.
- Heinemeyer, W. (2000) Active sites and assembly of the 20S proteasome, in: Proteasomes: The World of Regulatory Proteolysis ( W. Hilt, D. Wolf, Eds.), Georgetown: Eurekah.com/Landes Biosciences, 48–70.
- Heinemeyer, W., Fischer, M., Krimmer, T., Stachon, U., Wolf, D. H. (1997) The active sites of the eukaryotic 20 S proteasome and their involvement in subunit precursor processing, J. Biol. Chem. 272, 25200–25209.
- Hendil, K. B., Khan, S., Tanaka, K. (1998) Simultaneous binding of Pa28 and Pa700 activators to 20 S proteasomes, Biochem. J. 332, 661–665.
- Henke, W., Ferrell, K., Bech-Otschir, D., Seeger, M., Schade, R., Jungblut, P., Naumann, M., Dubiel, W. (1999) Comparison of human COP9 signalosome and 26S proteasome ‘lid', Mol. Biol. Reports 26, 29–34.
- Hershko, A., Ciechanover, A. (1998) The ubiquitin system, Annu. Rev. Biochem. 67, 425–479.
- Heusch, M., Lin, L., Geleziunas, R., Greene, W. C. (1999) The generation of nfkb2 P52: mechanism and efficiency, Oncogene 18, 6201–6208.
- Hicke, L. (1999) Gettin' down with ubiquitin: turning off cell-surface receptors, transporters and channels, Trends Cell Biol. 9, 107–112.
- Hilt, W., Wolf, D. H. (1996) Proteasomes: destruction as a programme, Trends Biochem. Sci. 21, 96–102.
- Hofmann, K., Bucher, P. (1998) The PCI domain: a common theme in three multiprotein complexes, Trends Biochem. Sci. 23, 204–205.
- Hölzl, H., Kapelari, B., Kellermann, J., Seemüller, E., Sumegi, M., Udvardy, A., Medalia, O., Sperling, J., Muller, S. A., Engel, A. and Baumeister, W. (2000) The regulatory complex of Drosophila melanogaster 26S proteasomes: subunit composition and localization of a deubiquitylating enzyme, J. Cell Biol. 150, 119–129.
- Horwich, A. L., Weber-Ban, E. U., Finley, D. (1999) Chaperone rings in protein folding and degradation, Proc. Natl. Acad. Sci. USA 96, 11033–11040.
- Hough, R., Pratt, G., Rechsteiner, M. (1987) Purification of two high molecular weight proteases from rabbit reticulocyte lysate, J. Biol. Chem. 262, 8303–8313.
- Hughes, A. L. (1997) Evolution of the proteasome components, Immunogenetics 46, 82–92.
- Hughes, A. L., Yeager, M. (1997) Molecular evolution of the vertebrate immune system, BioEssays 19, 777–786.
- Jelinsky, S. A., Estep, P., Church, G. M., Samson, L. D. (2000) Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: Rpn4 links base excision repair with proteasomes, Mol. Cell. Biol. 20, 8157–8167.
- Kapelari, B., Bech-Otschir, D., Hegerl, R., Schade, R., Dumdey, R., Dubiel, W. (2000) Electron microscopy and subunit-subunit interaction studies reveal a first architecture of COP9 signalosome, J. Mol. Biol. 300, 1169–1178.
- Khan, A. R., James, M. N. (1998) Molecular mechanisms for the conversion of zymogens to active proteolytic enzymes, Protein Sci. 7, 815–836.
- Kisselev, A. F., Akopian, T. N., Goldberg, A. L. (1998) Range of sizes of peptide products generated during degradation of different proteins by archaeal proteasomes, J. Biol. Chem. 273, 1982–1989.
- Kisselev, A. F., Songyang, Z., Goldberg, A. L. (2000) Why does threonine, and not serine, function as the active site nucleophile in proteasomes? J. Biol. Chem. 275, 14831–14837.
- Knipfer, N., Shrader, T. E. (1997) Inactivation of the 20S proteasome in Mycobacterium smegmatis, Mol. Microbiol. 25, 375–383.
- Knowlton, J. R., Johnston, S. C., Whitby, F. G., Realini, C., Zhang, Z. G., Rechsteiner, M., Hill, C. P. (1997) Structure of the proteasome activator Reg-a (Pa28-a), Nature 390, 639–643.
- Kopp, F., Hendil, K. B., Dahlmann, B., Kristensen, P., Sobek, A., Uerkvitz, W. (1997) Subunit arrangement in the human 20S proteasome, Proc. Natl. Acad. Sci. USA 94, 2939–2944.
- Koster, A. J., Walz, J., Lupas, A., Baumeister, W. (1995) Proteasomes of the yeast S. cerevisiae – genes, structure and functions, Mol. Biol. Reports 21, 3–10.
- Larsen, C. N., Finley, D. (1997) Protein translocation channels in the proteasome and other proteases, Cell 91, 431–434.
- Lee, D. H., Goldberg, A. L. (1998) Proteasome inhibitors–valuable new tools for cell biologists, Trends Cell Biol. 8, 397–403.
- Löwe, J., Stock, D., Jap, B., Zwickl, P., Baumeister, W., Huber, R. (1995) Crystal structure of the 20S proteasome from the archaeon T. acidophilum at 3.4 Angstrom resolution, Science 268, 533–539.
- Lupas, A., Flanagan, J. M., Tamura, T., Baumeister, W. (1997) Self-compartmentalizing proteases, Trends Biochem. Sci. 22, 399–404.
- Lupas, A., Koster, A. J., Baumeister, W. (1993) Structural features of 26S and 20S proteasomes, Enzyme Protein 47, 252–273.
- Lupas, A., Zwickl, P., Baumeister, W. (1994) Proteasome sequences in Eubacteria, Trends Biochem. Sci. 19, 533–534.
- Martins de Sa, C., Grossi de Sa, M. F., Akhayat, O., Broders, F., Scherrer, K., Horsch, A., Schmid, H. P. (1986) Prosomes: ubiquity and inter species structural variations, J. Mol. Biol. 187, 479–493.
- Maupin-Furlow, J. A., Aldrich, H. C., Ferry, J. G. (1998) Biochemical characterization of the 20S proteasome from the Methanoarchaeon Methanosarcina thermophila, J. Bacteriol. 180, 1480–1487.
- Maupin-Furlow, J. A., Wilson, H. L., Kaczowka, S. J., Ou, M. S. (2000) Proteasomes in the Archaea: from structure to function, Front. Biosci. 5, D837–D866A.
- Mayr, J., Seemüller, E., Müller, S. A., Engel, A., Baumeister, W. (1998) Late events in the assembly of 20S proteasomes, J. Struct. Biol. 124, 179–188.
- Murakami, Y., Matsufuji, S., Hayashi, S., Tanahashi, N., Tanaka, K. (2000) Degradation of ornithine decarboxylase by the 26S proteasome, Biochem. Biophys. Res. Commun. 267, 1–6.
- Nandi, D., Woodward, E., Ginsburg, D. B., Monaco, J. J. (1997) Intermediates in the formation of mouse 20S proteasomes–implications for the assembly of precursor beta subunits, EMBO J. 16, 5363–5375.
- Oinonen, C., Rouvinen, J. (2000) Structural comparison of Ntn-hydrolases, Protein Sci. 9, 2329–2337.
- Orlowski, M., Wilk, S. (1981) A multicatalytic protease complex from pituitary that forms enkephalin and enkephalin containing peptides, Biochem. Biophys. Res. Commun. 101, 814–822.
- Ortolan, T. G., Tongaonkar, P., Lambertson, D., Chen, L., Schauber, C., Madura, K. (2000) The DNA repair protein rad23 is a negative regulator of multi-ubiquitin chain assembly, Nature Cell Biol. 2, 601–609.
- Palombella, V. J., Conner, E. M., Fuseler, J. W., Destree, A., Davis, J. M., Laroux, F. S., Wolf, R. E., Huang, J. Q., Brand, S., Elliott, P. J., Lazarus, D., McCormack, T., Parent, L., Stein, R., Adams, J., Grisham, R. B. (1998) Role of the proteasome and NF-kappa B in streptococcal cell wall-induced polyarthritis, Proc. Natl. Acad. Sci. USA 95, 15671–15676.
- Pamnani, V., Haas, A. L., Pühler, G., Sanger, H. L., Baumeister, W. (1994) Proteasome associated RNAs are non specific, Eur. J. Biochem. 225, 511–519.
- Parmentier, Y., Bouchez, D., Fleck, J., Genschik, P. (1997) The 20S proteasome gene family in Arabidopsis thaliana, FEBS Lett. 416, 281–285.
- Peters, J. M., Cejka, Z., Harris, J. R., Kleinschmidt, J. A., Baumeister, W. (1993) Structural features of the 26S proteasome complex, J. Mol. Biol. 234, 932–937.
- Pickart, C. M. (2000) Ubiquitin in chains, Trends Biochem. Sci. 25, 544–548.
- Pickart, C. M., VanDemark, A. P. (2000) Opening doors into the proteasome, Nature Struct. Biol. 7, 999–1001.
- Plemper, R. K., Wolf, D. H. (2000) Function of the proteasome in the protein quality control process of the endoplasmic reticulum, in: Proteasomes: The World of Regulatory Proteolysis ( W. Hilt, D. H. Wolf, Eds.), Georgetown: Eurekah.com/Landes Bioscience, 264–301.
- Ramos, P. C., Hockendorff, J., Johnson, E. S., Varshavsky, A., Dohmen, R. J. (1998) Ump1p is required for proper maturation of the 20s proteasome and becomes its substrate upon completion of the assembly, Cell 92, 489–499.
-
Rechsteiner, M.
(1998)
Ump1 is required for proper maturation of the 20S proteasomes and becomes its substrate upon completion of the assembly, in: Ubiquitin and the Biology of the Cell ( J. M. Peters, J. R. Harris, D. Finley, Eds.), New York: Plenum Press,
147–189.
10.1007/978-1-4899-1922-9_6 Google Scholar
- Rechsteiner, M., Hoffmann, L., Dubiel, W. (1993) The multi-catalytic and 26S proteases, J. Biol. Chem. 268, 6065–6068.
- Rechsteiner, M., Realini, C., Ustrell, V. (2000) The proteasome activator 11S REG (PA28) and Class I antigen presentation, Biochem. J. 345, 1–15.
- Rivett, A. J. (1989) The multicatalytic proteinase of mammalian cells, Arch. Biochem. Biophys. 268, 1–8.
- Rock, K. L., Goldberg, A. L. (1999) Degradation of cell proteins and the generation of MHC Class I-presented peptides, Annu. Rev. Immunol. 17, 739–779.
- Rock, K. L., Gramm, C., Rothstein, L., Clark, K., Stein, R., Dick, L., Hwang, D., Goldberg, A. L. (1994) Inhibitors of the proteasome block the degradation of most cell proteins and the generation of peptides presented on MHC Class I molecules, Cell 78, 761–771.
- Rohrwild, M., Pfeifer, G., Santarius, U., Muller, S. A., Huang, H. C., Engel, A., Baumeister, W., Goldberg, A. L. (1997) The ATP-dependent HslVU protease from Escherichia coli is a four-ring structure resembling the proteasome, Nature Struct. Biol. 4, 133–139.
- Rubin, D. M., Vannocker, S., Glickman, M., Coux, O., Wefes, I., Sadis, S., Fu, H. Y., Goldberg, A., Vierstra, R., Finley, D. (1997) ATPase and ubiquitin-binding proteins of the yeast proteasome, Mol. Biol. Reports 24, 17–26.
- Rubin, D. M., Glickman, M. H., Larsen, C. N., Dhruvakumar, S., Finley, D. (1998) Active site mutants in the six regulatory particle ATPases reveal multiple roles for ATP in the proteasome, EMBO J. 17, 4909–4919.
- Ruepp, A., Eckerskorn, C., Bogyo, M., Baumeister, W. (1998) Proteasome function is dispensable under normal but not under heat shock conditions in Thermoplasma acidophilum, FEBS Lett. 425, 87–90.
- Ruepp, A., Graml, W., Santoz-Martinez, M. L., Koretke, K. K., Volker, C., Mewes, H. W., Frishman, D., Stocker, S., Lupas, A. N., Baumeister, W. (2000) The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum, Nature 407, 508–513.
- Russell, S. J., Sathyanarayana, U. G., Johnston, S. A. (1996) Isolation and characterization of Sug2–a novel ATPase family component of the yeast 26 S proteasome, J. Biol. Chem. 271, 32810–32817.
- Russell, S. J., Reed, S. H., Huang, W. Y., Friedberg, E. C., Johnston, S. A. (1999) The 19S regulatory complex of the proteasome functions independently of proteolysis in nucleotide excision repair, Mol. Cell 3, 687–695.
- Schauer, T. M., Nesper, M., Kehl, M., Lottspeich, F., Muller, T. A., Gerisch, G., Baumeister, W. (1993) Proteasomes from Dictiostelium discoideum: characterization of structure and function, J. Struct. Biol. 111, 135–147.
- Schmidt, H. P., Akhayat, O., Martins de Sa, C., Koehler, K., Scherrer, K. (1984) The prosome: a ubiquitous morphologically distinct RNP particle associated with repressed mRNPs and containing ScRNA and a characteristic set of proteins, EMBO J. 3, 29–34.
- Schmidt, M., Zantopf, D., Kraft, R., Kostka, S., Preissner, R., Kloetzel, P. M. (1999) Sequence information within proteasomal prosequences mediates efficient integration of β-subunits into the 20S proteasome complex, J. Mol. Biol. 288, 117–128.
- Schmidtke, G., Schmidt, M., Kloetzel, P. M. (1997) Maturation of mammalian 20S proteasome–purification and characterization of 13S and 16S proteasome precursor complexes, J. Mol. Biol. 268, 95–106.
- Seeger, M., Kraft, R., Ferrell, K., Bechotschir, D., Dumdey, R., Schade, R., Gordon, C., Naumann, M., Dubiel, W. (1998) A novel protein complex involved in signal transduction possessing similarities to 26S proteasome subunits, FASEB J. 12, 469–478.
- Seemüller, E., Lupas, A., Stock, D., Loewe, J., Huber, R., Baumeister, W. (1995) Proteasome of Thermoplasma acidophilum: a threonine protease, Science 268, 579–582.
- Seemüller, E., Lupas, A., Baumeister, W. (1996) Autocatalytic processing of the 20S proteasome, Nature 382, 468–470.
- Seemüller, E., Zwickl, P., Baumeister, W. (2001) Self-processing of subunits of the proteasome, in: The Enzymes, Co- and Posttranslational Proteolysis of Proteins, 3rd edition ( R. E. Dalbey, D. S. Sigman, Eds.), San Diego: Academic Press, 335–371, Vol. XXII.
- Strickland, E., Hakala, K., Thomas, P. J., DeMartino, G. N. (2000) Recognition of misfolding proteins by PA700, the regulatory subcomplex of the 26S proteasome, J. Biol. Chem. 275, 5565–5572.
- Tamura, N., Lottspeich, F., Baumeister, W., Tamura, T. (1998) The role of tricorn protease and its aminopeptidase-interacting factors in cellular protein degradation, Cell, 95, 1–20.
- Tamura, T., Nagy, I., Lupas, A., Lottspeich, F., Cejka, Z., Schoofs, G., Tanaka, K., De Mot, R., Baumeister, W. (1995) The first characterization of a eubacterial proteasome: the 20S complex of Rhodococcus, Curr. Biol. 5, 766–774.
- Tanahashi, N., Murakami, Y., Minami, Y., Shimbara, N., Hendil, K. B., Tanaka, K. (2000) Hybrid proteasomes - induction by interferon-γ and contribution to ATP-dependent proteolysis, J. Biol. Chem. 275, 14336–14345.
- Tanaka, E., Ji, K., Ichichara, A., Waxman, L., Goldberg, A. (1986) A high molecular weight protease in the cytosol of rat liver, J. Biol. Chem. 261, 15197–15203.
- Tanaka, K. (1998) Molecular biology of the proteasome, Biochem. Biophys. Res. Commun. 247, 537–541.
- Tanaka, K., Kasahara, M. (1998) The MHC Class I ligand-generating system–roles of immunoproteasomes and the interferon-γ-inducible proteasome activator PA28, Immunol. Rev. 163, 161–176.
- Thrower, J. S., Hoffman, L., Rechsteiner, M., Pickart, C. M. (2000) Recognition of the polyubiquitin proteolytic signal, EMBO J. 19, 94–104.
- Tomkinson, B. (1999) Tripeptidyl peptidases: enzymes that count, Trends Biochem. Sci. 24, 355–359.
- Udvardy, A. (1993) Purification and characterization of a multiprotein protein of the Drosophila 26S (1500 kDa) proteolytic complex, J. Biol. Chem. 268, 9055–9062.
- Uversky, V. N. (2002) Natively unfolded proteins: a point where biology waits for physics, Protein Sci. 11, 739–756.
- van Nocker, S., Sadis, S., Rubin, D. M., Glickman, M., Fu, H., Coux, O., Wefes, I., Finley, D., Vierstra, R. D. (1996) The multiubiquitin-chain-binding protein Mcb1 is a component of the 26S proteasome in Saccharomyces cerevisiae and plays a nonessential, substrate-specific role in protein turnover, Mol. Cell. Biol. 16, 6020–6028.
- Varshavsky, A. (1997) The ubiquitin system, Trends Biochem. Sci. 22, 383–387.
- Verma, R., Chen, S., Feldman, R., Schieltz, D., Yates, J., Dohmen, T., Deshaies, R. J. (2000) Proteasomal proteomics: identification of nucleotide-sensitive proteasome-interacting proteins by mass spectrometric analysis of affinity-purified proteasomes, Mol. Biol. Cell 11, 3425–3439.
- Voges, D., Zwickl, P., Baumeister, W. (1999) The 26S proteasome: a molecular machine designed for controlled proteolysis, Annu. Rev. Biochem. 68, 1015–1068.
- Wang, W., Chevray, P. M., Nathans, D. (1996) Mammalian SUC1 and c-FOS in the nuclear 26S proteasome, Proc. Natl. Acad. Sci. USA 93, 8236–8240.
- Wei, N., Tsuge, T., Serino, G., Dohmae, N., Takio, K., Matsui, M., Deng, X. W. (1998) The Cop9 complex is conserved between plants and mammals and is related to the 26S proteasome regulatory complex, Curr. Biol. 8, 919–922.
- Wenzel, T., Baumeister, W. (1995) Conformational constraints in protein degradation by the 20S proteasome, Nature Struct. Biol. 2, 199–204.
- Wenzel, T., Eckerskorn, C., Lottspeich, F., Baumeister, W. (1994) Existence of a molecular ruler in proteasomes suggested by analysis of degradation products, FEBS Lett. 349, 205–209.
- Whitby, F. G., Masters, E. I., Kramer, L., Knowlton, J. R., Yao, Y., Wang, C. C., Hill, C. P. (2000) Structural basis for the activation of 20S proteasomes by 11S regulators, Nature 408, 115–120.
- Wickner, S., Maurizi, M. R., Gottesman, S. (1999) Posttranslational quality control: folding, refolding, and degrading proteins, Science 286, 1888–1893.
- Wilk, S., Orlowski, M. (1980) Cation-sensitive neutral endopeptidase: isolation and specificity of the bovine pituitary enzyme, J. Neurochem. 35, 1172–1182.
- Wilk, S., Orlowski, M. (1983) Evidence that pituitary cation-sensitive neutral endopeptidase is a multicatalytic protease complex, J. Neurochem. 40, 842–849.
- Wilkinson, K. D. (2000) Ubiquitination and deubiquitination: targeting of proteins for degradation by the proteasome, Semin. Cell Dev. Biol. 11, 141–148.
- Wolf, S., Nagy, I., Lupas, A., Pfeifer, G., Cejka, Z., Muller, S. A., Engel, A., Demot, R., Baumeister, W. (1998) Characterization of Arc, a divergent member of the Aaa ATPase family from Rhodococcus erythropolis, J. Mol. Biol. 277, 13–25.
- Young, P., Deveraux, Q., Beal, R. E., Pickart, C. M., Rechsteiner, M. (1998) Characterization of two polyubiquitin binding sites in the 26 S protease subunit 5a, J. Biol. Chem. 273, 5461–5467.
- Zhang, Z. G., Krutchinsky, A., Endicott, S., Realini, C., Rechsteiner, M., Standing, K. G. (1999) Proteasome activator 11S REG or PA28: recombinant REG a/REG b hetero-oligomers are heptamers, Biochemistry 38, 5651–5658.
- Zühl, F., Seemüller, E., Golbik, R., Baumeister, W. (1997a) Dissecting the assembly pathway of the 20S proteasome, FEBS Lett. 418, 189–194.
- Zühl, F., Tamura, T., Dolenc, I., Cejka, Z., Nagy, I., De Mot, R., Baumeister, W. (1997b) Subunit topology of the Rhodococcus proteasome, FEBS Lett. 400, 83–90.
- Zwickl, P., Pfeifer, G., Lottspeich, F., Kopp, F., Dahlmann, B., Baumeister, W. (1990) Electron microscopy and image analysis reveals common principles of organization in two large protein complexes: GroEL-type and proteasomes, J. Struct. Biol. 103, 197–203.
- Zwickl, P., Lottspeich, F., Dahlmann, B., Baumeister, W. (1991) Cloning and Sequencing of the gene encoding the large α-subunit of the proteasome from Thermoplasma acidophilum, FEBS Lett. 278, 217–221.
- Zwickl, P., Grziwa, A., Pühler, G., Dahlmann, B., Lottspeich, F., Baumeister, W. (1992a) Primary structure of the Thermoplasma proteasome and its implication for the structure, function, and evolution of the multicatalytic proteinase, Biochemistry 31, 964–972.
- Zwickl, P., Lottspeich, F., Baumeister, W. (1992b) Expression of functional Thermoplasma acidophilum proteasomes in Escherichia coli, FEBS Lett. 312, 157–160.
- Zwickl, P., Kleinz, J., Baumeister, W. (1994) Critical elements in proteasome assembly, Nature Struct. Biol. 1, 765–770.
- Zwickl, P., Baumeister, W., Steven, A. (2000a) Dis-assembly lines: the proteasome and related ATPase-assisted proteases, Curr. Opin. Struct. Biol. 10, 242–250.
- Zwickl, P., Goldberg, A. L., Baumeister, W. (2000b) Proteasomes in prokaryotes, in: Proteasomes: The World of Regulatory Proteolysis ( D. H. Wolf, W. Hilt, Eds.), Georgetown: Eurekah.com/Landes Bioscience, 8–20.
Biopolymers Online: Biology • Chemistry • Biotechnology • Applications
Browse other articles of this reference work:
