Unveiling the long-held secrets of the 26S proteasome

Structure

Volumn 21, Issue 9, 2013, Pages 1551-1562

  Förster, Friedrich ^a   Unverdorben, Pia ^a   Śledź, Paweł ^a   Baumeister, Wolfgang ^a  

^a MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

26S PROTEASOME; ADENOSINE TRIPHOSPHATASE; PROTEASOME; UBIQUITIN; UNCLASSIFIED DRUG;

CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; CRYSTALLIZATION; DEGRADATION; ELECTRON MICROSCOPY; ENZYME STRUCTURE; HYDROLYSIS; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN HOMEOSTASIS; REVIEW; X RAY CRYSTALLOGRAPHY;

ANIMALS; HUMANS; MODELS, MOLECULAR; PROTEASOME ENDOPEPTIDASE COMPLEX; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEOLYSIS; UBIQUITINATION;

EID: 84883472009     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2013.08.010     Document Type: Review

References (129)

1. S. Arai, S. Saijo, K. Suzuki, K. Mizutani, Y. Kakinuma, Y. Ishizuka-Katsura, N. Ohsawa, T. Terada, M. Shirouzu, and S. Yokoyama Rotation mechanism of Enterococcus hirae V1-ATPase based on asymmetric crystal structures Nature 493 2013 703 707
2. M.B. Barrault, N. Richet, C. Godard, B. Murciano, B. Le Tallec, E. Rousseau, P. Legrand, J.B. Charbonnier, M.H. Le Du, and R. Guérois Dual functions of the Hsm3 protein in chaperoning and scaffolding regulatory particle subunits during the proteasome assembly Proc. Natl. Acad. Sci. USA 109 2012 E1001 E1010
3. D. Barthelme, and R.T. Sauer Identification of the Cdc48×20S proteasome as an ancient AAA+ proteolytic machine Science 337 2012 843 846
4. F. Beck, P. Unverdorben, S. Bohn, A. Schweitzer, G. Pfeifer, E. Sakata, S. Nickell, J.M. Plitzko, E. Villa, W. Baumeister, and F. Förster Near-atomic resolution structural model of the yeast 26S proteasome Proc. Natl. Acad. Sci. USA 109 2012 14870 14875
5. H.C. Besche, W. Haas, S.P. Gygi, and A.L. Goldberg Isolation of mammalian 26S proteasomes and p97/VCP complexes using the ubiquitin-like domain from HHR23B reveals novel proteasome-associated proteins Biochemistry 48 2009 2538 2549
6. S. Bohn, F. Beck, E. Sakata, T. Walzthoeni, M. Beck, R. Aebersold, F. Förster, W. Baumeister, and S. Nickell Structure of the 26S proteasome from Schizosaccharomyces pombe at subnanometer resolution Proc. Natl. Acad. Sci. USA 107 2010 20992 20997
7. S. Bohn, E. Sakata, F. Beck, G.R. Pathare, J. Schnitger, I. Nágy, W. Baumeister, and F. Förster Localization of the regulatory particle subunit Sem1 in the 26S proteasome Biochem. Biophys. Res. Commun. 435 2013 250 254
8. X. Chen, B.H. Lee, D. Finley, and K.J. Walters Structure of proteasome ubiquitin receptor hRpn13 and its activation by the scaffolding protein hRpn2 Mol. Cell 38 2010 404 415
9. G.A. Cope, G.S. Suh, L. Aravind, S.E. Schwarz, S.L. Zipursky, E.V. Koonin, and R.J. Deshaies Role of predicted metalloprotease motif of Jab1/Csn5 in cleavage of Nedd8 from Cul1 Science 298 2002 608 611
10. P.C. da Fonseca, J. He, and E.P. Morris Molecular model of the human 26S proteasome Mol. Cell 46 2012 54 66
11. B. Dahlmann, F. Kopp, L. Kuehn, B. Niedel, G. Pfeifer, R. Hegerl, and W. Baumeister The multicatalytic proteinase (prosome) is ubiquitous from eukaryotes to archaebacteria FEBS Lett. 251 1989 125 131
12. S. Djuranovic, M.D. Hartmann, M. Habeck, A. Ursinus, P. Zwickl, J. Martin, A.N. Lupas, and K. Zeth Structure and activity of the N-terminal substrate recognition domains in proteasomal ATPases Mol. Cell 34 2009 580 590
13. A. Echalier, Y. Pan, M. Birol, N. Tavernier, L. Pintard, F. Hoh, C. Ebel, N. Galophe, F.X. Claret, and C. Dumas Insights into the regulation of the human COP9 signalosome catalytic subunit, CSN5/Jab1 Proc. Natl. Acad. Sci. USA 110 2013 1273 1278
14. A.M. Ellisdon, L. Dimitrova, E. Hurt, and M. Stewart Structural basis for the assembly and nucleic acid binding of the TREX-2 transcription-export complex Nat. Struct. Mol. Biol. 19 2012 328 336
15. S. Elsasser, R.R. Gali, M. Schwickart, C.N. Larsen, D.S. Leggett, B. Müller, M.T. Feng, F. Tübing, G.A. Dittmar, and D. Finley Proteasome subunit Rpn1 binds ubiquitin-like protein domains Nat. Cell Biol. 4 2002 725 730
16. R.I. Enchev, D.C. Scott, P.C. da Fonseca, A. Schreiber, J.K. Monda, B.A. Schulman, M. Peter, and E.P. Morris Structural basis for a reciprocal regulation between SCF and CSN. Cell Rep 2 2012 616 627
17. E. Estrin, J.R. Lopez-Blanco, P. Chacon, and A. Martin Formation of an intricate helical bundle dictates the assembly of the 26S proteasome lid Structure 21 2013 1624 1635 this issue
18. J.D. Etlinger, and A.L. Goldberg A soluble ATP-dependent proteolytic system responsible for the degradation of abnormal proteins in reticulocytes Proc. Natl. Acad. Sci. USA 74 1977 54 58
19. D. Forouzan, M. Ammelburg, C.F. Hobel, L.J. Ströh, N. Sessler, J. Martin, and A.N. Lupas The archaeal proteasome is regulated by a network of AAA ATPases J. Biol. Chem. 287 2012 39254 39262
20. F. Förster, K. Lasker, F. Beck, S. Nickell, A. Sali, and W. Baumeister An atomic model AAA-ATPase/20S core particle sub-complex of the 26S proteasome Biochem. Biophys. Res. Commun. 388 2009 228 233
21. F. Förster, K. Lasker, S. Nickell, A. Sali, and W. Baumeister Toward an integrated structural model of the 26S proteasome Mol. Cell. Proteomics 9 2010 1666 1677
22. F. Förster, and E. Villa Integration of cryo-EM with atomic and protein-protein interaction data Methods Enzymol. 483 2010 47 72
23. J. Frank Three-Dimensional Electron Microscopy of Macromolecular Assemblies 2006 Oxford University Press Oxford
24. J. Frank, and R.K. Agrawal A ratchet-like inter-subunit reorganization of the ribosome during translocation Nature 406 2000 318 322
25. K. Fukunaga, T. Kudo, A. Toh-e, K. Tanaka, and Y. Saeki Dissection of the assembly pathway of the proteasome lid in Saccharomyces cerevisiae Biochem. Biophys. Res. Commun. 396 2010 1048 1053
26. M. Funakoshi, R.J. Tomko Jr.; H. Kobayashi, and M. Hochstrasser Multiple assembly chaperones govern biogenesis of the proteasome regulatory particle base Cell 137 2009 887 899
27. K.S. Gajiwala, and S.K. Burley Winged helix proteins Curr. Opin. Struct. Biol. 10 2000 110 116
28. M.H. Glickman, D.M. Rubin, O. Coux, I. Wefes, G. Pfeifer, Z. Cjeka, W. Baumeister, V.A. Fried, and D. Finley A subcomplex of the proteasome regulatory particle required for ubiquitin-conjugate degradation and related to the COP9-signalosome and eIF3 Cell 94 1998 615 623
29. S.E. Glynn, A. Martin, A.R. Nager, T.A. Baker, and R.T. Sauer Structures of asymmetric ClpX hexamers reveal nucleotide-dependent motions in a AAA+ protein-unfolding machine Cell 139 2009 744 756
30. S.E. Glynn, A.R. Nager, T.A. Baker, and R.T. Sauer Dynamic and static components power unfolding in topologically closed rings of a AAA+ proteolytic machine Nat. Struct. Mol. Biol. 19 2012 616 622
31. S. Gottesman, M.R. Maurizi, and S. Wickner Regulatory subunits of energy-dependent proteases Cell 91 1997 435 438
32. M. Groll, L. Ditzel, J. Löwe, D. Stock, M. Bochtler, H.D. Bartunik, and R. Huber Structure of 20S proteasome from yeast at 2.4 A resolution Nature 386 1997 463 471
33. J. Hamazaki, S. Iemura, T. Natsume, H. Yashiroda, K. Tanaka, and S. Murata A novel proteasome interacting protein recruits the deubiquitinating enzyme UCH37 to 26S proteasomes EMBO J. 25 2006 4524 4536
34. J. Hanna, N.A. Hathaway, Y. Tone, B. Crosas, S. Elsasser, D.S. Kirkpatrick, D.S. Leggett, S.P. Gygi, R.W. King, and D. Finley Deubiquitinating enzyme Ubp6 functions noncatalytically to delay proteasomal degradation Cell 127 2006 99 111
35. P.C. Havugimana, G.T. Hart, T. Nepusz, H. Yang, A.L. Turinsky, Z. Li, P.I. Wang, D.R. Boutz, V. Fong, and S. Phanse A census of human soluble protein complexes Cell 150 2012 1068 1081
36. J. He, K. Kulkarni, P.C. da Fonseca, D. Krutauz, M.H. Glickman, D. Barford, and E.P. Morris The structure of the 26S proteasome subunit Rpn2 reveals its PC repeat domain as a closed toroid of two concentric α-helical rings Structure 20 2012 513 521
37. A. Hershko, A. Ciechanover, and A. Varshavsky Basic Medical Research Award. The ubiquitin system Nat. Med. 6 2000 1073 1081
38. K. Hofmann, and P. Bucher The PCI domain: a common theme in three multiprotein complexes Trends Biochem. Sci. 23 1998 204 205
39. R. Hough, G. Pratt, and M. Rechsteiner Purification of two high molecular weight proteases from rabbit reticulocyte lysate J. Biol. Chem. 262 1987 8303 8313
40. K. Husnjak, S. Elsasser, N. Zhang, X. Chen, L. Randles, Y. Shi, K. Hofmann, K.J. Walters, D. Finley, and I. Dikic Proteasome subunit Rpn13 is a novel ubiquitin receptor Nature 453 2008 481 488
41. M. Isasa, E.J. Katz, W. Kim, V. Yugo, S. González, D.S. Kirkpatrick, T.M. Thomson, D. Finley, S.P. Gygi, and B. Crosas Monoubiquitination of RPN10 regulates substrate recruitment to the proteasome Mol. Cell 38 2010 733 745
42. T. Ishikawa, F. Beuron, M. Kessel, S. Wickner, M.R. Maurizi, and A.C. Steven Translocation pathway of protein substrates in ClpAP protease Proc. Natl. Acad. Sci. USA 98 2001 4328 4333
43. O. Itsathitphaisarn, R.A. Wing, W.K. Eliason, J. Wang, and T.A. Steitz The hexameric helicase DnaB adopts a nonplanar conformation during translocation Cell 151 2012 267 277
44. A.V. Kajava What curves alpha-solenoids? Evidence for an alpha-helical toroid structure of Rpn1 and Rpn2 proteins of the 26 S proteasome J. Biol. Chem. 277 2002 49791 49798
45. T. Kaneko, J. Hamazaki, S. Iemura, K. Sasaki, K. Furuyama, T. Natsume, K. Tanaka, and S. Murata Assembly pathway of the Mammalian proteasome base subcomplex is mediated by multiple specific chaperones Cell 137 2009 914 925
46. E. Kish-Trier, and C.P. Hill Structural biology of the proteasome Annu. Rev. Biophys. 42 2013 29 49
47. M.F. Kleijnen, J. Roelofs, S. Park, N.A. Hathaway, M. Glickman, R.W. King, and D. Finley Stability of the proteasome can be regulated allosterically through engagement of its proteolytic active sites Nat. Struct. Mol. Biol. 14 2007 1180 1188
48. Y.A. Lam, T.G. Lawson, M. Velayutham, J.L. Zweier, and C.M. Pickart A proteasomal ATPase subunit recognizes the polyubiquitin degradation signal Nature 416 2002 763 767
49. G.C. Lander, E. Estrin, M.E. Matyskiela, C. Bashore, E. Nogales, and A. Martin Complete subunit architecture of the proteasome regulatory particle Nature 482 2012 186 191
50. K. Lasker, F. Förster, S. Bohn, T. Walzthoeni, E. Villa, P. Unverdorben, F. Beck, R. Aebersold, A. Sali, and W. Baumeister Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach Proc. Natl. Acad. Sci. USA 109 2012 1380 1387
51. K. Lasker, J.L. Phillips, D. Russel, J. Velázquez-Muriel, D. Schneidman-Duhovny, E. Tjioe, B. Webb, A. Schlessinger, and A. Sali Integrative structure modeling of macromolecular assemblies from proteomics data Mol. Cell. Proteomics 9 2010 1689 1702
52. D.S. Leggett, J. Hanna, A. Borodovsky, B. Crosas, M. Schmidt, R.T. Baker, T. Walz, H. Ploegh, and D. Finley Multiple associated proteins regulate proteasome structure and function Mol. Cell 10 2002 495 507
53. J. Löwe, D. Stock, B. Jap, P. Zwickl, W. Baumeister, and R. Huber Crystal structure of the 20S proteasome from the archaeon T. acidophilum at 3.4 A resolution Science 268 1995 533 539
54. A. Lupas, W. Baumeister, and K. Hofmann A repetitive sequence in subunits of the 26S proteasome and 20S cyclosome (anaphase-promoting complex) Trends Biochem. Sci. 22 1997 195 196
55. A. Lupas, J.M. Flanagan, T. Tamura, and W. Baumeister Self-compartmentalizing proteases Trends Biochem. Sci. 22 1997 399 404
56. A. Lupas, A.J. Koster, and W. Baumeister Structural features of 26S and 20S proteasomes Enzyme Protein 47 1993 252 273
57. S. Lyapina, G. Cope, A. Shevchenko, G. Serino, T. Tsuge, C. Zhou, D.A. Wolf, N. Wei, A. Shevchenko, and R.J. Deshaies Promotion of NEDD-CUL1 conjugate cleavage by COP9 signalosome Science 292 2001 1382 1385
58. A. Martin, T.A. Baker, and R.T. Sauer Rebuilt AAA + motors reveal operating principles for ATP-fuelled machines Nature 437 2005 1115 1120
59. M.E. Matyskiela, G.C. Lander, and A. Martin Conformational switching of the 26S proteasome enables substrate degradation Nat. Struct. Mol. Biol. 20 2013 781 788
60. J. Moretti, P. Chastagner, S. Gastaldello, S.F. Heuss, A.M. Dirac, R. Bernards, M.G. Masucci, A. Israël, and C. Brou The translation initiation factor 3f (eIF3f) exhibits a deubiquitinase activity regulating Notch activation PLoS Biol. 8 2010 e1000545
61. S. Murata, H. Udono, N. Tanahashi, N. Hamada, K. Watanabe, K. Adachi, T. Yamano, K. Yui, N. Kobayashi, and M. Kasahara Immunoproteasome assembly and antigen presentation in mice lacking both PA28alpha and PA28beta EMBO J. 20 2001 5898 5907
62. S. Nickell, F. Beck, S.H. Scheres, A. Korinek, F. Förster, K. Lasker, O. Mihalache, N. Sun, I. Nagy, and A. Sali Insights into the molecular architecture of the 26S proteasome Proc. Natl. Acad. Sci. USA 106 2009 11943 11947
63. T. Ogura, S.W. Whiteheart, and A.J. Wilkinson Conserved arginine residues implicated in ATP hydrolysis, nucleotide-sensing, and inter-subunit interactions in AAA and AAA+ ATPases J. Struct. Biol. 146 2004 106 112
64. V. Pamnani, T. Tamura, A. Lupas, J. Peters, Z. Cejka, W. Ashraf, and W. Baumeister Cloning, sequencing and expression of VAT, a CDC48/p97 ATPase homologue from the archaeon Thermoplasma acidophilum FEBS Lett. 404 1997 263 268
65. S. Park, X. Li, H.M. Kim, C.R. Singh, G. Tian, M.A. Hoyt, S. Lovell, K.P. Battaile, M. Zolkiewski, and P. Coffino Reconfiguration of the proteasome during chaperone-mediated assembly Nature 497 2013 512 516
66. S. Park, J. Roelofs, W. Kim, J. Robert, M. Schmidt, S.P. Gygi, and D. Finley Hexameric assembly of the proteasomal ATPases is templated through their C termini Nature 459 2009 866 870
67. G.R. Pathare, I. Nagy, S. Bohn, P. Unverdorben, A. Hubert, R. Körner, S. Nickell, K. Lasker, A. Sali, and T. Tamura The proteasomal subunit Rpn6 is a molecular clamp holding the core and regulatory subcomplexes together Proc. Natl. Acad. Sci. USA 109 2012 149 154
68. M.J. Pearce, J. Mintseris, J. Ferreyra, S.P. Gygi, and K.H. Darwin Ubiquitin-like protein involved in the proteasome pathway of Mycobacterium tuberculosis Science 322 2008 1104 1107
69. J.M. Peters, Z. Cejka, J.R. Harris, J.A. Kleinschmidt, and W. Baumeister Structural features of the 26 S proteasome complex J. Mol. Biol. 234 1993 932 937
70. A. Peth, H.C. Besche, and A.L. Goldberg Ubiquitinated proteins activate the proteasome by binding to Usp14/Ubp6, which causes 20S gate opening Mol. Cell 36 2009 794 804
71. A. Peth, N. Kukushkin, M. Bosse, and A.L. Goldberg Ubiquitinated proteins activate the proteasomal ATPases by binding to Usp14 or Uch37 J. Biol. Chem. 288 2013 7781 7790
72. A. Peth, T. Uchiki, and A.L. Goldberg ATP-dependent steps in the binding of ubiquitin conjugates to the 26S proteasome that commit to degradation Mol. Cell 40 2010 671 681
73. S. Prakash, T. Inobe, A.J. Hatch, and A. Matouschek Substrate selection by the proteasome during degradation of protein complexes Nat. Chem. Biol. 5 2009 29 36
74. G. Pühler, S. Weinkauf, L. Bachmann, S. Müller, A. Engel, R. Hegerl, and W. Baumeister Subunit stoichiometry and three-dimensional arrangement in proteasomes from Thermoplasma acidophilum EMBO J. 11 1992 1607 1616
75. M.X. Qian, Y. Pang, C.H. Liu, K. Haratake, B.Y. Du, D.Y. Ji, G.F. Wang, Q.Q. Zhu, W. Song, and Y. Yu Acetylation-mediated proteasomal degradation of core histones during DNA repair and spermatogenesis Cell 153 2013 1012 1024
76. X.B. Qiu, S.Y. Ouyang, C.J. Li, S. Miao, L. Wang, and A.L. Goldberg hRpn13/ADRM1/GP110 is a novel proteasome subunit that binds the deubiquitinating enzyme, UCH37 EMBO J. 25 2006 5742 5753
77. J. Querol-Audi, C. Sun, J.M. Vogan, M.D. Smith, Y. Gu, J.H. Cate, and E. Nogales Architecture of human translation initiation factor 3 Structure 21 2013 920 928
78. J. Rabl, D.M. Smith, Y. Yu, S.C. Chang, A.L. Goldberg, and Y. Cheng Mechanism of gate opening in the 20S proteasome by the proteasomal ATPases Mol. Cell 30 2008 360 368
79. V. Ramakrishnan Ribosome structure and the mechanism of translation Cell 108 2002 557 572
80. M. Rechsteiner, L. Hoffman, and W. Dubiel The multicatalytic and 26 S proteases J. Biol. Chem. 268 1993 6065 6068
81. J. Roelofs, S. Park, W. Haas, G. Tian, F.E. McAllister, Y. Huo, B.H. Lee, F. Zhang, Y. Shi, S.P. Gygi, and D. Finley Chaperone-mediated pathway of proteasome regulatory particle assembly Nature 459 2009 861 865
82. M. Rohrwild, G. Pfeifer, U. Santarius, S.A. Müller, H.C. Huang, A. Engel, W. Baumeister, and A.L. Goldberg The ATP-dependent HslVU protease from Escherichia coli is a four-ring structure resembling the proteasome Nat. Struct. Biol. 4 1997 133 139
83. A.M. Ruschak, T.L. Religa, S. Breuer, S. Witt, and L.E. Kay The proteasome antechamber maintains substrates in an unfolded state Nature 467 2010 868 871
84. D. Russel, K. Lasker, B. Webb, J. Velázquez-Muriel, E. Tjioe, D. Schneidman-Duhovny, B. Peterson, and A. Sali Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies PLoS Biol. 10 2012 e1001244
85. Y. Saeki, and K. Tanaka Assembly and function of the proteasome Methods Mol. Biol. 832 2012 315 337
86. Y. Saeki, A. Toh-E, T. Kudo, H. Kawamura, and K. Tanaka Multiple proteasome-interacting proteins assist the assembly of the yeast 19S regulatory particle Cell 137 2009 900 913
87. E. Sakata, S. Bohn, O. Mihalache, P. Kiss, F. Beck, I. Nagy, S. Nickell, K. Tanaka, Y. Saeki, F. Förster, and W. Baumeister Localization of the proteasomal ubiquitin receptors Rpn10 and Rpn13 by electron cryomicroscopy Proc. Natl. Acad. Sci. USA 109 2012 1479 1484
88. E. Sakata, F. Stengel, K. Fukunaga, M. Zhou, Y. Saeki, F. Förster, W. Baumeister, K. Tanaka, and C.V. Robinson The catalytic activity of Ubp6 enhances maturation of the proteasomal regulatory particle Mol. Cell 42 2011 637 649
89. M. Sanches, B.S. Alves, N.I. Zanchin, and B.G. Guimarães The crystal structure of the human Mov34 MPN domain reveals a metal-free dimer J. Mol. Biol. 370 2007 846 855
90. Y. Sato, A. Yoshikawa, A. Yamagata, H. Mimura, M. Yamashita, K. Ookata, O. Nureki, K. Iwai, M. Komada, and S. Fukai Structural basis for specific cleavage of Lys 63-linked polyubiquitin chains Nature 455 2008 358 362
91. R.T. Sauer, and T.A. Baker AAA+ proteases: ATP-fueled machines of protein destruction Annu. Rev. Biochem. 80 2011 587 612
92. H. Scheel, and K. Hofmann Prediction of a common structural scaffold for proteasome lid, COP9-signalosome and eIF3 complexes BMC Bioinformatics 6 2005 71 80
93. T.M. Schmeing, and V. Ramakrishnan What recent ribosome structures have revealed about the mechanism of translation Nature 461 2009 1234 1242
94. P. Schreiner, X. Chen, K. Husnjak, L. Randles, N. Zhang, S. Elsasser, D. Finley, I. Dikic, K.J. Walters, and M. Groll Ubiquitin docking at the proteasome through a novel pleckstrin-homology domain interaction Nature 453 2008 548 552
95. A. Seelig, P.M. Kloetzel, L. Kuehn, and B. Dahlmann Molecular interaction of the proteasome (multicatalytic proteinase). Evidence that the proteasome is not a constituent of the '26 S' multienzyme complex Biochem. J. 280 1991 225 232
96. E. Seemüller, A. Lupas, D. Stock, J. Löwe, R. Huber, and W. Baumeister Proteasome from Thermoplasma acidophilum: a threonine protease Science 268 1995 579 582
97. M. Sharon, S. Witt, K. Felderer, B. Rockel, W. Baumeister, and C.V. Robinson 20S proteasomes have the potential to keep substrates in store for continual degradation J. Biol. Chem. 281 2006 9569 9575
98. P. Sledź, F. Förster, and W. Baumeister Allosteric effects in the regulation of 26S proteasome activities J. Mol. Biol. 425 2013 1415 1423
99. P. Śledź, P. Unverdorben, F. Beck, G. Pfeifer, A. Schweitzer, F. Förster, and W. Baumeister Structure of the 26S proteasome with ATP-γS bound provides insights into the mechanism of nucleotide-dependent substrate translocation Proc. Natl. Acad. Sci. USA 110 2013 7264 7269
100. D.M. Smith, S.C. Chang, S. Park, D. Finley, Y. Cheng, and A.L. Goldberg Docking of the proteasomal ATPases' carboxyl termini in the 20S proteasome's alpha ring opens the gate for substrate entry Mol. Cell 27 2007 731 744
101. D.M. Smith, H. Fraga, C. Reis, G. Kafri, and A.L. Goldberg ATP binds to proteasomal ATPases in pairs with distinct functional effects, implying an ordered reaction cycle Cell 144 2011 526 538
102. D.M. Smith, G. Kafri, Y. Cheng, D. Ng, T. Walz, and A.L. Goldberg ATP binding to PAN or the 26S ATPases causes association with the 20S proteasome, gate opening, and translocation of unfolded proteins Mol. Cell 20 2005 687 698
103. M.C. Sousa, C.B. Trame, H. Tsuruta, S.M. Wilbanks, V.S. Reddy, and D.B. McKay Crystal and solution structures of an HslUV protease-chaperone complex Cell 103 2000 633 643
104. B.M. Stadtmueller, K. Ferrell, F.G. Whitby, A. Heroux, H. Robinson, D.G. Myszka, and C.P. Hill Structural models for interactions between the 20S proteasome and its PAN/19S activators J. Biol. Chem. 285 2010 13 17
105. C. Sun, A. Todorovic, J. Querol-Audí, Y. Bai, N. Villa, M. Snyder, J. Ashchyan, C.S. Lewis, A. Hartland, and S. Gradia Functional reconstitution of human eukaryotic translation initiation factor 3 (eIF3) Proc. Natl. Acad. Sci. USA 108 2011 20473 20478
106. T. Tamura, I. Nagy, A. Lupas, F. Lottspeich, Z. Cejka, G. Schoofs, K. Tanaka, R. De Mot, and W. Baumeister The first characterization of a eubacterial proteasome: the 20S complex of Rhodococcus Curr. Biol. 5 1995 766 774
107. K. Tanaka The proteasome: overview of structure and functions Proc. Jpn. Acad.; Ser. B, Phys. Biol. Sci. 85 2009 12 36
108. N.D. Thomsen, and J.M. Berger Running in reverse: the structural basis for translocation polarity in hexameric helicases Cell 139 2009 523 534
109. G. Tian, S. Park, M.J. Lee, B. Huck, F. McAllister, C.P. Hill, S.P. Gygi, and D. Finley An asymmetric interface between the regulatory and core particles of the proteasome Nat. Struct. Mol. Biol. 18 2011 1259 1267
110. R.J. Tomko Jr.; M. Funakoshi, K. Schneider, J. Wang, and M. Hochstrasser Heterohexameric ring arrangement of the eukaryotic proteasomal ATPases: implications for proteasome structure and assembly Mol. Cell 38 2010 393 403
111. R.J. Tomko Jr.; and M. Hochstrasser Incorporation of the Rpn12 subunit couples completion of proteasome regulatory particle lid assembly to lid-base joining Mol. Cell 44 2011 907 917
112. L.G. Trabuco, E. Villa, K. Mitra, J. Frank, and K. Schulten Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics Structure 16 2008 673 683
113. S. van Nocker, S. Sadis, D.M. Rubin, M. Glickman, H. Fu, O. Coux, I. Wefes, D. Finley, and R.D. Vierstra 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 1996 6020 6028
114. R. Verma, L. Aravind, R. Oania, W.H. McDonald, J.R. Yates 3rd, E.V. Koonin, and R.J. Deshaies Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome Science 298 2002 611 615
115. R. Verma, S. Chen, R. Feldman, D. Schieltz, J. Yates, J. Dohmen, and R.J. Deshaies Proteasomal proteomics: identification of nucleotide-sensitive proteasome-interacting proteins by mass spectrometric analysis of affinity-purified proteasomes Mol. Biol. Cell 11 2000 3425 3439
116. D. Vilchez, L. Boyer, I. Morantte, M. Lutz, C. Merkwirth, D. Joyce, B. Spencer, L. Page, E. Masliah, and W.T. Berggren Increased proteasome activity in human embryonic stem cells is regulated by PSMD11 Nature 489 2012 304 308
117. D. Vilchez, I. Morantte, Z. Liu, P.M. Douglas, C. Merkwirth, A.P. Rodrigues, G. Manning, and A. Dillin RPN-6 determines C. elegans longevity under proteotoxic stress conditions Nature 489 2012 263 268
118. D. Voges, P. Zwickl, and W. Baumeister The 26S proteasome: a molecular machine designed for controlled proteolysis Annu. Rev. Biochem. 68 1999 1015 1068
119. T. Wang, K.H. Darwin, and H. Li Binding-induced folding of prokaryotic ubiquitin-like protein on the Mycobacterium proteasomal ATPase targets substrates for degradation Nat. Struct. Mol. Biol. 17 2010 1352 1357
120. T. Wenzel, and W. Baumeister Conformational constraints in protein degradation by the 20S proteasome Nat. Struct. Biol. 2 1995 199 204
121. S. Wolf, I. Nagy, A. Lupas, G. Pfeifer, Z. Cejka, S.A. Müller, A. Engel, R. De Mot, and W. Baumeister Characterization of ARC, a divergent member of the AAA ATPase family from Rhodococcus erythropolis J. Mol. Biol. 277 1998 13 25
122. K. Wollenberg, and J.C. Swaffield Evolution of proteasomal ATPases Mol. Biol. Evol. 18 2001 962 974
123. T. Yao, and R.E. Cohen A cryptic protease couples deubiquitination and degradation by the proteasome Nature 419 2002 403 407
124. T. Yao, L. Song, W. Xu, G.N. DeMartino, L. Florens, S.K. Swanson, M.P. Washburn, R.C. Conaway, J.W. Conaway, and R.E. Cohen Proteasome recruitment and activation of the Uch37 deubiquitinating enzyme by Adrm1 Nat. Cell Biol. 8 2006 994 1002
125. Y. Yu, D.M. Smith, H.M. Kim, V. Rodriguez, A.L. Goldberg, and Y. Cheng Interactions of PAN's C-termini with archaeal 20S proteasome and implications for the eukaryotic proteasome-ATPase interactions EMBO J. 29 2009 692 702
126. F. Zhang, M. Hu, G. Tian, P. Zhang, D. Finley, P.D. Jeffrey, and Y. Shi Structural insights into the regulatory particle of the proteasome from Methanocaldococcus jannaschii Mol. Cell 34 2009 473 484
127. N. Zhang, Q. Wang, A. Ehlinger, L. Randles, J.W. Lary, Y. Kang, A. Haririnia, A.J. Storaska, J.L. Cole, D. Fushman, and K.J. Walters Structure of the s5a:k48-linked diubiquitin complex and its interactions with rpn13 Mol. Cell 35 2009 280 290
128. P. Zwickl, F. Lottspeich, and W. Baumeister Expression of functional Thermoplasma acidophilum proteasomes in Escherichia coli FEBS Lett. 312 1992 157 160
129. P. Zwickl, D. Ng, K.M. Woo, H.P. Klenk, and A.L. Goldberg An archaebacterial ATPase, homologous to ATPases in the eukaryotic 26 S proteasome, activates protein breakdown by 20 S proteasomes J. Biol. Chem. 274 1999 26008 26014