Ubiquitin family proteins and their relationship to the proteasome: A structural perspective

Biochimica et Biophysica Acta - Molecular Cell Research

Volumn 1695, Issue 1-3, 2004, Pages 73-87

  Walters, Kylie J ^a   Goh, Amanda M ^b   Wang, Qinghua ^a   Wagner, Gerhard ^b   Howley, Peter M ^b  

^a UNIVERSITY OF MINNESOTA   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

Author keywords

Proteasome; Protein degradation; Ubiquitin; Ubiquitin like domain

Indexed keywords

POLYUBIQUITIN; PROTEASOME; UBIQUITIN;

DEGENERATIVE DISEASE; HUMAN; HUNTINGTON CHOREA; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PARKINSONISM; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DEGRADATION; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEIN TARGETING; REVIEW;

AMINO ACID SEQUENCE; ANIMALS; CONSERVED SEQUENCE; CRYSTALLOGRAPHY, X-RAY; ELECTROSTATICS; HUMANS; MAGNETIC RESONANCE SPECTROSCOPY; MOLECULAR SEQUENCE DATA; PROTEASOME ENDOPEPTIDASE COMPLEX; PROTEIN INTERACTION MAPPING; PROTEIN STRUCTURE, TERTIARY; PROTEINS; UBIQUITIN;

EID: 9644260470     PISSN: 01674889     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbamcr.2004.10.005     Document Type: Review

References (98)

1. W. Baumeister, J. Walz, F. Zuhl, and E. Seemuller The proteasome: paradigm of a self-compartmentalizing protease Cell 92 1998 367 380
2. O. Coux, K. Tanaka, and A.L. Goldberg Structure and functions of the 20S and 26S proteasomes Annu. Rev. Biochem. 65 1996 801 847
3. W. Hilt, and D.H. Wolf Proteasomes: destruction as a programme Trends Biochem. Sci. 21 1996 96 102
4. A.L. Goldberg, M. Gaczynska, E. Grant, M. Michalek, and K.L. Rock Functions of the proteasome in antigen presentation Cold Spring Harbor Symp. Quant. Biol. 60 1995 479 490
5. M.T. Heemels, and H. Ploegh Generation, translocation, and presentation of MHC class I-restricted peptides Annu. Rev. Biochem. 64 1995 463 491
6. A. Ciechanover The ubiquitin-proteasome pathway: on protein death and cell life EMBO J. 17 1998 7151 7160
7. G.J. Strous, P. van Kerkhof, R. Govers, A. Ciechanover, and A.L. Schwartz The ubiquitin conjugation system is required for ligand-induced endocytosis and degradation of the growth hormone receptor EMBO J. 15 1996 3806 3812
8. L. Hicke, and H. Riezman Ubiquitination of a yeast plasma membrane receptor signals its ligand-stimulated endocytosis Cell 84 1996 277 287
9. O. Soetens, J.O. De Craene, and B. Andre Ubiquitin is required for sorting to the vacuole of the yeast general amino acid permease, Gap1 J. Biol. Chem. 276 2001 43949 43957
10. D.J. Katzmann, M. Babst, and S.D. Emr Ubiquitin-dependent sorting into the multivesicular body pathway requires the function of a conserved endosomal protein sorting complex, ESCRT-I Cell 106 2001 145 155
11. F. Reggiori, and H.R. Pelham Sorting of proteins into multivesicular bodies: ubiquitin-dependent and -independent targeting EMBO J. 20 2001 5176 5186
12. C. Schauber, L. Chen, P. Tongaonkar, I. Vega, D. Lambertson, W. Potts, and K. Madura Rad23 links DNA repair to the ubiquitin/proteasome pathway Nature 391 1998 715 718
13. V. Rapic-Otrin, M.P. McLenigan, D.C. Bisi, M. Gonzalez, and A.S. Levine Sequential binding of UV DNA damage binding factor and degradation of the p48 subunit as early events after UV irradiation Nucleic Acids Res. 30 2002 2588 2598
14. C. Hoege, B. Pfander, G.L. Moldovan, G. Pyrowolakis, and S. Jentsch RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMO Nature 419 2002 135 141
15. R.S. Khush, W.D. Cornwell, J.N. Uram, and B. Lemaitre A ubiquitin-proteasome pathway represses the Drosophila immune deficiency signaling cascade Curr. Biol. 12 2002 1728 1737
16. P. Kaiser, K. Flick, C. Wittenberg, and S.I. Reed Regulation of transcription by ubiquitination without proteolysis: Cdc34/SCF(Met30)-mediated inactivation of the transcription factor Met4 Cell 102 2000 303 314
17. F. Gonzalez, A. Delahodde, T. Kodadek, and S.A. Johnston Recruitment of a 19S proteasome subcomplex to an activated promoter Science 296 2002 548 550
18. C. Wang, J. Xi, T.P. Begley, and L.K. Nicholson Solution structure of ThiS and implications for the evolutionary roots of ubiquitin Nat. Struct. Biol. 8 2001 47 51
19. A. Ciechanover The ubiquitin-proteasome proteolytic pathway Cell 79 1994 13 21
20. M. Hochstrasser Ubiquitin-dependent protein degradation Annu. Rev. Genet. 30 1996 405 439
21. R.D. Vierstra Proteolysis in plants: mechanisms and functions Plant Mol. Biol. 32 1996 275 302
22. J.S. Thrower, L. Hoffman, M. Rechsteiner, and C.M. Pickart Recognition of the polyubiquitin proteolytic signal EMBO J. 19 2000 94 102
23. E.S. Johnson, and G. Blobel Ubc9p is the conjugating enzyme for the ubiquitin-like protein Smt3p J. Biol. Chem. 272 1997 26799 26802
24. E.S. Johnson, I. Schwienhorst, R.J. Dohmen, and G. Blobel The ubiquitin-like protein Smt3p is activated for conjugation to other proteins by an Aos1p/Uba2p heterodimer EMBO J. 16 1997 5509 5519
25. S. Sachdev, L. Bruhn, H. Sieber, A. Pichler, F. Melchior, and R. Grosschedl PIASy, a nuclear matrix-associated SUMO E3 ligase, represses LEF1 activity by sequestration into nuclear bodies Genes Dev. 15 2001 3088 3103
26. T. Kahyo, T. Nishida, and H. Yasuda Involvement of PIAS1 in the sumoylation of tumor suppressor p53 Mol. Cell 8 2001 713 718
27. M.J. Matunis, J. Wu, and G. Blobel SUMO-1 modification and its role in targeting the Ran GTPase-activating protein, RanGAP1, to the nuclear pore complex J. Cell Biol. 140 1998 499 509
28. S. Muller, M.J. Matunis, and A. Dejean Conjugation with the ubiquitin-related modifier SUMO-1 regulates the partitioning of PML within the nucleus EMBO J. 17 1998 61 70
29. J. Bies, J. Markus, and L. Wolff Covalent attachment of the SUMO-1 protein to the negative regulatory domain of the c-Myb transcription factor modifies its stability and transactivation capacity J. Biol. Chem. 277 2002 8999 9009
30. S. Muller, M. Berger, F. Lehembre, J.S. Seeler, Y. Haupt, and A. Dejean c-Jun and p53 activity is modulated by SUMO-1 modification J. Biol. Chem. 275 2000 13321 13329
31. M.S. Rodriguez, J.M. Desterro, S. Lain, C.A. Midgley, D.P. Lane, and R.T. Hay SUMO-1 modification activates the transcriptional response of p53 EMBO J. 18 1999 6455 6461
32. J.M. Desterro, M.S. Rodriguez, and R.T. Hay SUMO-1 modification of IkappaBalpha inhibits NF-kappaB activation Mol. Cell 2 1998 233 239
33. H. Ueda, J. Goto, H. Hashida, X. Lin, K. Oyanagi, H. Kawano, H.Y. Zoghbi, I. Kanazawa, and H. Okazawa Enhanced SUMOylation in polyglutamine diseases Biochem. Biophys. Res. Commun. 293 2002 307 313
34. F. Osaka, M. Saeki, S. Katayama, N. Aida, E.A. Toh, K. Kominami, T. Toda, T. Suzuki, T. Chiba, K. Tanaka, and S. Kato Covalent modifier NEDD8 is essential for SCF ubiquitin-ligase in fission yeast EMBO J. 19 2000 3475 3484
35. V.N. Podust, J.E. Brownell, T.B. Gladysheva, R.S. Luo, C. Wang, M.B. Coggins, J.W. Pierce, E.S. Lightcap, and V. Chau A Nedd8 conjugation pathway is essential for proteolytic targeting of p27Kip1 by ubiquitination Proc. Natl. Acad. Sci. U. S. A. 97 2000 4579 4584
36. M. Morimoto, T. Nishida, R. Honda, and H. Yasuda Modification of cullin-1 by ubiquitin-like protein Nedd8 enhances the activity of SCF(skp2) toward p27(kip1) Biochem. Biophys. Res. Commun. 270 2000 1093 1096
37. K. Wu, A. Chen, and Z.Q. Pan Conjugation of Nedd8 to CUL1 enhances the ability of the ROC1-CUL1 complex to promote ubiquitin polymerization J. Biol. Chem. 275 2000 32317 32324
38. M.A. Read, J.E. Brownell, T.B. Gladysheva, M. Hottelet, L.A. Parent, M.B. Coggins, J.W. Pierce, V.N. Podust, R.S. Luo, V. Chau, and V.J. Palombella Nedd8 modification of cul-1 activates SCF(beta(TrCP))-dependent ubiquitination of IkappaBalpha Mol. Cell. Biol. 20 2000 2326 2333
39. M. Ohh, W.Y. Kim, J.J. Moslehi, Y. Chen, V. Chau, M.A. Read, and W.G. Kaelin Jr. An intact NEDD8 pathway is required for Cullin-dependent ubiquitylation in mammalian cells EMBO Rep. 3 2002 177 182
40. W.M. Gray, H. Hellmann, S. Dharmasiri, and M. Estelle Role of the Arabidopsis RING-H2 protein RBX1 in RUB modification and SCF function Plant Cell 14 2002 2137 2144
41. H. Hellmann, and M. Estelle Plant development: regulation by protein degradation Science 297 2002 793 797
42. C. Masutani, K. Sugasawa, J. Yanagisawa, T. Sonoyama, M. Ui, T. Enomoto, K. Takio, K. Tanaka, P.J. van der Spek, and D. Bootsma Purification and cloning of a nucleotide excision repair complex involving the xeroderma pigmentosum group C protein and a human homologue of yeast RAD23 EMBO J. 13 1994 1831 1843
43. F. Miao, M. Bouziane, R. Dammann, C. Masutani, F. Hanaoka, G. Pfeifer, and T.R. O'Connor 3-Methyladenine-DNA glycosylase (MPG protein) interacts with human RAD23 proteins J. Biol. Chem. 275 2000 28433 28438
44. S. Biggins, I. Ivanovska, and M.D. Rose Yeast ubiquitin-like genes are involved in duplication of the microtubule organizing center J. Cell Biol. 133 1996 1331 1346
45. R.D. Miller, L. Prakash, and S. Prakash Defective excision of pyrimidine dimers and interstrand DNA crosslinks in rad7 and rad23 mutants of Saccharomyces cerevisiae Mol. Gen. Genet. 188 1982 235 239
46. Z. Wang, S. Wei, S.H. Reed, X. Wu, J.Q. Svejstrup, W.J. Feaver, R.D. Kornberg, and E.C. Friedberg The RAD7, RAD16, and RAD23 genes of Saccharomyces cerevisiae: requirement for transcription-independent nucleotide excision repair in vitro and interactions between the gene products Mol. Cell. Biol. 17 1997 635 643
47. K. Madura, and A. Varshavsky Degradation of G alpha by the N-end rule pathway Science 265 1994 1454 1458
48. B.L. Bertolaet, D.J. Clarke, M. Wolff, M.H. Watson, M. Henze, G. Divita, and S.I. Reed UBA domains mediate protein-protein interactions between two DNA damage-inducible proteins J. Mol. Biol. 313 2001 955 963
49. L. Chen, U. Shinde, T.G. Ortolan, and K. Madura Ubiquitin-associated (UBA) domains in Rad23 bind ubiquitin and promote inhibition of multi-ubiquitin chain assembly EMBO Rep. 2 2001 933 938
50. S. Elsasser, R.R. Gali, M. Schwickart, C.N. Larsen, D.S. Leggett, B. Muller, M.T. Feng, F. Tubing, G.A. Dittmar, and D. Finley Proteasome subunit Rpn1 binds ubiquitin-like protein domains Nat. Cell Biol. 4 2002 725 730
51. C.R. Wilkinson, M. Seeger, R. Hartmann-Petersen, M. Stone, M. Wallace, C. Semple, and C. Gordon Proteins containing the UBA domain are able to bind to multi-ubiquitin chains Nat. Cell Biol. 3 2001 939 943
52. M.F. Kleijnen, A.H. Shih, P. Zhou, S. Kumar, R.E. Soccio, N.L. Kedersha, G. Gill, and P.M. Howley The hPLIC proteins may provide a link between the ubiquitination machinery and the proteasome Mol. Cell 6 2000 409 419
53. M. Funakoshi, T. Sasaki, T. Nishimoto, and H. Kobayashi Budding yeast Dsk2p is a polyubiquitin-binding protein that can interact with the proteasome Proc. Natl. Acad. Sci. U. S. A. 99 2002 745 750
54. S. Kumar, A.L. Talis, and P.M. Howley Identification of HHR23A as a substrate for E6-associated protein-mediated ubiquitination J. Biol. Chem. 274 1999 18785 18792
55. A.L. Mah, G. Perry, M.A. Smith, and M.J. Monteiro Identification of ubiquilin, a novel presenilin interactor that increases presenilin protein accumulation J. Cell Biol. 151 2000 847 862
56. F.K. Bedford, J.T. Kittler, E. Muller, P. Thomas, J.M. Uren, D. Merlo, W. Wisden, A. Triller, T.G. Smart, and S.J. Moss GABA(A) receptor cell surface number and subunit stability are regulated by the ubiquitin-like protein Plic-1 Nat. Neurosci. 4 2001 908 916
57. E. Junn, S.S. Lee, U.T. Suhr, and M.M. Mouradian Parkin accumulation in aggresomes due to proteasome impairment J. Biol. Chem. 277 2002 47870 47877
58. K.S. McNaught, C. Mytilineou, R. Jnobaptiste, J. Yabut, P. Shashidharan, P. Jennert, and C.W. Olanow Impairment of the ubiquitin-proteasome system causes dopaminergic cell death and inclusion body formation in ventral mesencephalic cultures J. Neurochem. 81 2002 301 306
59. P.S. Fishman, and G.A. Oyler Significance of the parkin gene and protein in understanding Parkinson's disease Curr. Neurol. Neurosci. Rep. 2 2002 296 302
60. S. Takayama, T. Sato, S. Krajewski, K. Kochel, S. Irie, J.A. Millan, and J.C. Reed Cloning and functional analysis of BAG-1: a novel Bcl-2-binding protein with anti-cell death activity Cell 80 1995 279 284
61. P. Zhou, A.A. Lugovskoy, J.S. McCarty, P. Li, and G. Wagner Solution structure of DFF40 and DFF45 N-terminal domain complex and mutual chaperone activity of DFF40 and DFF45 Proc. Natl. Acad. Sci. U. S. A. 98 2001 6051 6055
62. A.A. Lugovskoy, P. Zhou, J.J. Chou, J.S. McCarty, P. Li, and G. Wagner Solution structure of the CIDE-N domain of CIDE-B and a model for CIDE-N/CIDE-N interactions in the DNA fragmentation pathway of apoptosis Cell 99 1999 747 755
63. J. Hohfeld, and S. Jentsch GrpE-like regulation of the hsc70 chaperone by the anti-apoptotic protein BAG-1 EMBO J. 16 1997 6209 6216
64. M. Zeiner, M. Gebauer, and U. Gehring Mammalian protein RAP46: an interaction partner and modulator of 70 kDa heat shock proteins EMBO J. 16 1997 5483 5490
65. S. Takayama, D.N. Bimston, S. Matsuzawa, B.C. Freeman, C. Aime-Sempe, Z. Xie, R.I. Morimoto, and J.C. Reed BAG-1 modulates the chaperone activity of Hsp70/Hsc70 EMBO J. 16 1997 4887 4896
66. D. Bimston, J. Song, D. Winchester, S. Takayama, J.C. Reed, and R.I. Morimoto BAG-1, a negative regulator of Hsp70 chaperone activity, uncouples nucleotide hydrolysis from substrate release EMBO J. 17 1998 6871 6878
67. S.D. Emerson, D.S. Waugh, J.E. Scheffler, K.L. Tsao, K.M. Prinzo, and D.C. Fry Chemical shift assignments and folding topology of the Ras-binding domain of human Raf-1 as determined by heteronuclear three-dimensional NMR spectroscopy Biochemistry 33 1994 7745 7752
68. H. Hiyama, M. Yokoi, C. Masutani, K. Sugasawa, T. Maekawa, K. Tanaka, J.H. Hoeijmakers, and F. Hanaoka Interaction of hHR23 with S5a. The ubiquitin-like domain of hHR23 mediates interaction with S5a subunit of 26 S proteasome J. Biol. Chem. 274 1999 28019 28025
69. 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
70. Y. Saeki, T. Sone, A. Toh-e, and H. Yokosawa Identification of ubiquitin-like protein-binding subunits of the 26S proteasome Biochem. Biophys. Res. Commun. 296 2002 813 819
71. S. Vijay-Kumar, C.E. Bugg, K.D. Wilkinson, and W.J. Cook Three-dimensional structure of ubiquitin at 2.8 A resolution Proc. Natl. Acad. Sci. U. S. A. 82 1985 3582 3585
72. S. Vijay-Kumar, C.E. Bugg, and W.J. Cook Structure of ubiquitin refined at 1.8 A resolution J. Mol. Biol. 194 1987 531 544
73. M.S. Briggs, and H. Roder Early hydrogen-bonding events in the folding reaction of ubiquitin Proc. Natl. Acad. Sci. U. S. A. 89 1992 2017 2021
74. P. Bayer, A. Arndt, S. Metzger, R. Mahajan, F. Melchior, R. Jaenicke, and J. Becker Structure determination of the small ubiquitin-related modifier SUMO-1 J. Mol. Biol. 280 1998 275 286
75. K.J. Walters, M.F. Kleijnen, A.M. Goh, G. Wagner, and P.M. Howley Structural studies of the interaction between ubiquitin family proteins and proteasome subunit S5a Biochemistry 41 2002 1767 1777
76. H. Matsuo, K.J. Walters, K. Teruya, T. Tanaka, G.T. Gassner, S.J. Lippard, Y. Kyogoku, and G. Wagner J. Am. Chem. Soc. 121 1999 9903 9904
77. G. Wagner An account of NMR in structural biology Nat. Struct. Biol. 4 1997 841 844 (Suppl)
78. R. Beal, Q. Deveraux, G. Xia, M. Rechsteiner, and C. Pickart Surface hydrophobic residues of multiubiquitin chains essential for proteolytic targeting Proc. Natl. Acad. Sci. U. S. A. 93 1996 861 866
79. R.E. Beal, D. Toscano-Cantaffa, P. Young, M. Rechsteiner, and C.M. Pickart The hydrophobic effect contributes to polyubiquitin chain recognition Biochemistry 37 1998 2925 2934
80. P. Young, Q. Deveraux, R.E. Beal, C.M. Pickart, and M. Rechsteiner Characterization of two polyubiquitin binding sites in the 26 S protease subunit 5a J. Biol. Chem. 273 1998 5461 5467
81. L. Haracska, and A. Udvardy Mapping the ubiquitin-binding domains in the p54 regulatory complex subunit of the Drosophila 26S protease FEBS Lett. 412 1997 331 336
82. H. Fu, S. Sadis, D.M. Rubin, M. Glickman, S. van Nocker, D. Finley, and R.D. Vierstra Multiubiquitin chain binding and protein degradation are mediated by distinct domains within the 26 S proteasome subunit Mcb1 J. Biol. Chem. 273 1998 1970 1981
83. J. Luders, J. Dem, and J. Hohfeld The ubiquitin-related BAG-1 provides a link between the molecular chaperones Hsc70/Hsp70 and the proteasome J. Biol. Chem. 275 2000 4613 4617
84. J. Demand, S. Alberti, C. Patterson, and J. Hohfeld Cooperation of a ubiquitin domain protein and an E3 ubiquitin ligase during chaperone/proteasome coupling Curr. Biol. 11 2001 1569 1577
85. Q. Deveraux, V. Ustrell, C. Pickart, and M. Rechsteiner A 26 S protease subunit that binds ubiquitin conjugates J. Biol. Chem. 269 1994 7059 7061
86. Q. Deveraux, S. van Nocker, D. Mahaffey, R. Vierstra, and M. Rechsteiner Inhibition of ubiquitin-mediated proteolysis by the Arabidopsis 26 S protease subunit S5a J. Biol. Chem. 270 1995 29660 29663
87. B.L. Bertolaet, D.J. Clarke, M. Wolff, M.H. Watson, M. Henze, G. Divita, and S.I. Reed UBA domains of DNA damage-inducible proteins interact with ubiquitin Nat. Struct. Biol. 8 2001 417 422
88. 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
89. D. Lambertson, L. Chen, and K. Madura Pleiotropic defects caused by loss of the proteasome-interacting factors Rad23 and Rpn10 of Saccharomyces cerevisiae Genetics 153 1999 69 79
90. Y. Saeki, A. Saitoh, A. Toh-e, and H. Yokosawa Ubiquitin-like proteins and Rpn10 play cooperative roles in ubiquitin-dependent proteolysis Biochem. Biophys. Res. Commun. 293 2002 986 992
91. S.J. Russell, S.H. Reed, W. Huang, E.C. Friedberg, and S.A. Johnston The 19S regulatory complex of the proteasome functions independently of proteolysis in nucleotide excision repair Mol. Cell 3 1999 687 695
92. T.G. Ortolan, P. Tongaonkar, D. Lambertson, L. Chen, C. Schauber, and K. Madura The DNA repair protein rad23 is a negative regulator of multi-ubiquitin chain assembly Nat. Cell Biol. 2 2000 601 608
93. L. Chen, and K. Madura Rad23 promotes the targeting of proteolytic substrates to the proteasome Mol. Cell. Biol. 22 2002 4902 4913
94. Q. Zhu, G. Wani, M.A. Wani, and A.A. Wani Human homologue of yeast Rad23 protein A interacts with p300/cyclic AMP-responsive element binding (CREB)-binding protein to down-regulate transcriptional activity of p53 Cancer Res. 61 2001 64 70
95. L. Lommel, T. Ortolan, L. Chen, K. Madura, and K.S. Sweder Proteolysis of a nucleotide excision repair protein by the 26 S proteasome Curr. Genet. 42 2002 9 20
96. R. Koradi, M. Billeter, and K. Wuthrich MOLMOL: a program for display and analysis of macromolecular structures J. Mol. Graph. 14 1996 51 55
97. A.J. Nicholls GRASP Manual, Graphical Representation and Analysis of Structural Properties 1993 Columbia University New York
98. Q. Wang, A.M. Goh, P.M. Howley, and K.J. Walters Ubiquitin recognition by the DNA repair protein hHR23a Biochemistry 42 2003 13529 13535