Mechanism, specificity and structure of the deubiquitinases

Subcellular Biochemistry

Volumn 54, Issue , 2010, Pages 69-87

  Komander, David ^a  

^a MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DEUBIQUITINASE; UBIQUITIN;

CATALYSIS; CHEMISTRY; ENZYME SPECIFICITY; HUMAN; PROTEIN PROCESSING; PROTEIN TERTIARY STRUCTURE;

CATALYSIS; HUMANS; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEIN STRUCTURE, TERTIARY; SUBSTRATE SPECIFICITY; UBIQUITIN; UBIQUITIN-SPECIFIC PROTEASES;

EID: 80052265841     PISSN: 03060225     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4419-6676-6_6     Document Type: Article

References (106)

1. Hershko, A., Ciechanover, A. (1998) The ubiquitin system. Annu Rev Biochem 67: pp. 425-79
2. Chen, Z.J., Sun, L.J. (2009) Nonproteolytic functions of ubiquitin in cell signaling. Mol Cell 33: pp. 275-86
3. Ikeda, F., Dikic, I. (2008) Atypical ubiquitin chains: new molecular signals. ‘Protein Modifications: Beyond the Usual Suspects’ review series. EMBO Rep 9: pp. 536-42
4. Komander, D. (2009) The emerging complexity of protein ubiquitination. Biochem Soc Trans 37: pp. 937-53
5. Kirisako, T., Kamei, K., Murata, S. (2006) A ubiquitin ligase complex assembles linear polyubiquitin chains. EMBO J 25: pp. 4877-87
6. Nijman, S.M., Luna-Vargas, M.P., Velds, A. (2005) A genomic and functional inventory of deubiquitinating enzymes. Cell 123: pp. 773-86
7. Komander, D., Clague, M.J., Urbe, S. (2009) Breaking the chains: structure and function of the deubiquitinases. Nat Rev Mol Cell Biol 10: pp. 550-63
8. Burrows, J.F., McGrattan, M.J., Johnston, J.A. (2005) The DUB/USP17 deubiquitinating enzymes, a multigene family within a tandemly repeated sequence. Genomics 85: pp. 524-9
9. Amerik, A., Swaminathan, S., Krantz, B.A. (1997) In vivo disassembly of free polyubiquitin chains by yeast Ubp14 modulates rates of protein degradation by the proteasome. EMBO J 16: pp. 4826-38
10. Finley, D. (2009) Recognition and processing of ubiquitin-protein conjugates by the proteasome. Annu Rev Biochem 78: pp. 477-513
11. Popov, N., Wanzel, M., Madiredjo, M. (2007) The ubiquitin-specific protease USP28 is required for MYC stability. Nat Cell Biol 9: pp. 765-74
12. Zhang, D., Zaugg, K., Mak, T.W. (2006) A role for the deubiquitinating enzyme USP28 in control of the DNA-damage response. Cell 126: pp. 529-42
13. Li, M., Brooks, C.L., Kon, N. (2004) A dynamic role of HAUSP in the p53-Mdm2 pathway. Mol Cell 13: pp. 879-86
14. Li, M., Chen, D., Shiloh, A. (2002) Deubiquitination of p53 by HAUSP is an important pathway for p53 stabilization. Nature 416: pp. 648-53
15. Biggs, P.J., Wooster, R., Ford, D. (1995) Familial cylindromatosis (turban tumour syndrome) gene localised to chromosome 16q12–q13: evidence for its role as a tumour suppressor gene. Nat Genet 11: pp. 441-3
16. Brummelkamp, T.R., Nijman, S.M., Dirac, A.M. (2003) Loss of the cylindromatosis tumour suppressor inhibits apoptosis by activating NF-kappaB. Nature 424: pp. 797-801
17. Kovalenko, A., Chable-Bessia, C., Cantarella, G. (2003) The tumour suppressor CYLD negatively regulates NF-kappaB signalling by deubiquitination. Nature 424: pp. 801-5
18. Trompouki, E., Hatzivassiliou, E., Tsichritzis, T. (2003) CYLD is a deubiquitinating enzyme that negatively regulates NF-kappaB activation by TNFR family members. Nature 424: pp. 793-6
19. Komander, D., Lord, C.J., Scheel, H. (2008) The structure of the CYLD USP domain explains its specificity for Lys63-linked polyubiquitin and reveals a B box module. Mol Cell 29: pp. 451-64
20. Komander, D., Reyes-Turcu, F., Licchesi, J.D. (2009) Molecular discrimination of structurally equivalent Lys 63-linked and linear polyubiquitin chains. EMBO Rep 10: pp. 466-73
21. Ikeda, F., Dikic, I. (2006) CYLD in ubiquitin signaling and tumor pathogenesis. Cell 125: pp. 643-5
22. Sun, S.C. (2010) CYLD: a tumor suppressor deubiquitinase regulating NF-kappaB activation and diverse biological processes. Cell Death Differ 17: pp. 25-34
23. Malynn, B.A., Ma, A. (2009) A20 takes on tumors:tumor suppression by an ubiquitin-editing enzyme. J Exp Med 206: pp. 977-80
24. Wertz, I., O’Rourke, K., Zhou, H. (2004) De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-kappaB signalling. Nature 430: pp. 694-9
25. Tran, H., Hamada, F., Schwarz-Romond, T., Bienz, M. (2008) Trabid, a new positive regulator of Wnt-induced transcription with preference for binding and cleaving K63-linked ubiquitin chains. Genes Dev 22: pp. 528-42
26. Kayagaki, N., Phung, Q., Chan, S. (2007) DUBA: A Deubiquitinase That Regulates Type I Interferon Production. Science 318: pp. 1628-32
27. Reyes-Turcu, F.E., Ventii, K.H. (2009) Regulation and cellular roles of ubiquitin-specific deubiquitinating enzymes. Annu Rev Biochem 78: pp. 363-97
28. Reyes-Turcu, F.E., Wilkinson, K.D. (2009) Polyubiquitin binding and disassembly by deubiquitinating enzymes. Chem Rev 109: pp. 1495-508
29. Storer, A.C., Menard, R. (1994) Catalytic mechanism in papain family of cysteine peptidases. Methods Enzymol 244: pp. 486-500
30. Johnston, S.C., Larsen, C.N., Cook, W.J. (1997) Crystal structure of a deubiquitinating enzyme (human UCH-L3) at 1.8 A resolution. EMBO J 16: pp. 3787-96
31. Borodovsky, A., Ovaa, H., Kolli, N. (2002) Chemistry-based functional proteomics reveals novel members of the deubiquitinating enzyme family. Chem Biol 9: pp. 1149-59
32. Love, K.R., Catic, A., Schlieker, C. (2007) Mechanisms, biology and inhibitors of deubiquitinating enzymes. Nat Chem Biol 3: pp. 697-705
33. Hershko, A., Rose, I.A. (1987) Ubiquitin-aldehyde: a general inhibitor of ubiquitin-recycling processes. Proc Natl Acad Sci USA 84: pp. 1829-33
34. Love, K.R., Pandya, R.K., Spooner, E. (2009) Ubiquitin C-terminal electrophiles are activity-based probes for identification and mechanistic study of ubiquitin conjugating machinery. ACS Chem Biol 4: pp. 275-87
35. Hu, M., Li, P., Li, M. (2002) Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde. Cell 111: pp. 1041-54
36. Johnston, S.C., Riddle, S.M., Cohen, R.E. (1999) Structural basis for the specificity of ubiquitin C-terminal hydrolases. EMBO J 18: pp. 3877-87
37. Messick, T.E., Russell, N.S., Iwata, A.J. (2008) Structural basis for ubiquitin recognition by the Otu1 ovarian tumor domain protein. J Biol Chem 283: pp. 11038-49
38. Edelmann, M.J., Iphofer, A., Akutsu, M. (2009) Structural basis and specificity of human otubain 1-mediated deubiquitination. Biochem J 418: pp. 379-90
39. Maytal-Kivity, V., Reis, N., Hofmann, K. (2002) MPN+, a putative catalytic motif found in a subset of MPN domain proteins from eukaryotes and prokaryotes, is critical for Rpn11 function. BMC Biochem 3: pp. 28
40. Tran, H.J., Allen, M.D., Lowe, J. (2003) Structure of the Jab1/MPN domain and its implications for proteasome function. Biochemistry 42: pp. 11460-5
41. Sato, Y., Yoshikawa, A., Yamagata, A. (2008) Structural basis for specific cleavage of Lys 63-linked polyubiquitin chains. Nature 455: pp. 358-62
42. Hochstrasser, M. (2009) Origin and function of ubiquitin-like proteins. Nature 458: pp. 422-9
43. Dye, B.T., Schulman, B.A. (2007) Structural mechanisms underlying posttranslational modification by ubiquitin-like proteins. Annu Rev Biophys Biomol Struct 36: pp. 131-50
44. Iwai, K., Tokunaga, F. (2009) Linear polyubiquitination: a new regulator of NF-kappaB activation. EMBO Rep 10: pp. 706-13
45. Huang, T.T., Nijman, S.M., Mirchandani, K.D. (2006) Regulation of monoubiquitinated PCNA by DUB autocleavage. Nat Cell Biol 8: pp. 339-47
46. Barford, D., Das, A.K., Egloff, M.P. (1998) The structure and mechanism of protein phosphatases: insights into catalysis and regulation. Annu Rev Biophys Biomol Struct 27: pp. 133-64
47. Hu, M., Li, P., Song, L. (2005) Structure and mechanisms of the proteasome-associated deubiquitinating enzyme USP14. EMBO J 24: pp. 3747-56
48. Newton, K., Matsumoto, M.L., Wertz, I.E. (2008) Ubiquitin chain editing revealed by polyubiquitin linkage-specific antibodies. Cell 134: pp. 668-78
49. Sowa, M.E., Bennett, E.J., Gygi, S.P. (2009) Defining the Human Deubiquitinating Enzyme Interaction Landscape. Cell 138: pp. 389-403
50. Hassink, G.C., Zhao, B., Sompallae, R. (2009) The ER-resident ubiquitin-specific protease 19 participates in the UPR and rescues ERAD substrates. EMBO Rep 10: pp. 755-61
51. Nakamura, N., Hirose, S. (2008) Regulation of mitochondrial morphology by USP30, a deubiquitinating enzyme present in the mitochondrial outer membrane. Mol Biol Cell 19: pp. 1903-11
52. Zhu, X., Menard, R., Sulea, T. (2007) High incidence of ubiquitin-like domains in human ubiquitin-specific proteases. Proteins 69: pp. 1-7
53. Avvakumov, G.V., Walker, J.R., Xue, S. (2006) Amino-terminal dimerization, NRDP1-rhodanese interaction and inhibited catalytic domain conformation of the ubiquitin-specific protease 8 (USP8). J Biol Chem 281: pp. 38061-70
54. Komander, D., Barford, D. (2008) Structure of the A20 OTU domain and mechanistic insights into deubiquitination. Biochem J 409: pp. 77-85
55. Catic, A., Fiebiger, E., Korbel, G.A. (2007) Screen for ISG15-crossreactive deubiquitinases. PLoS ONE 2: pp. e679
56. Nicholson, B., Leach, C.A., Goldenberg, S.J. (2008) Characterization of ubiquitin and ubiquitin-like-protein isopeptidase activities. Protein Sci 17: pp. 1035-43
57. Ye, Y., Scheel, H., Hofmann, K. (2009) Dissection of USP catalytic domains reveals five common insertion points. Mol Biosyst 5: pp. 1797-808
58. Reyes-Turcu, F.E., Shanks, J.R. (2008) Recognition of polyubiquitin isoforms by the multiple ubiquitin binding modules of isopeptidase T. J Biol Chem 283: pp. 19581-92
59. Cohn, M.A., Kee, Y., Haas, W. (2009) UAF1 is a subunit of multiple deubiquitinating enzyme complexes. J Biol Chem 284: pp. 5343-51
60. Cohn, M.A., Kowal, P., Yang, K. (2007) A UAF1-containing multisubunit protein complex regulates the Fanconi anemia pathway. Mol Cell 28: pp. 786-97
61. Stegmeier, F., Rape, M., Draviam, V.M. (2007) Anaphase initiation is regulated by antagonistic ubiquitination and deubiquitination activities. Nature 446: pp. 876-81
62. Enesa, K., Zakkar, M., Chaudhury, H. (2008) NF-kappaB suppression by the deubiquitinating enzyme Cezanne: a novel negative feedback loop in pro-inflammatory signaling. J Biol Chem 283: pp. 7036-45
63. Nanao, M., Tcherniuk, S., Chroboczek, J. (2004) Crystal structure of human otubain 2. EMBO Rep 5: pp. 783-8
64. Enesa, K., Ito, K., Luongle, A. (2008) Hydrogen peroxide prolongs nuclear localization of NF-kappaB in activated cells by suppressing negative regulatory mechanisms. J Biol Chem 283: pp. 18582-90
65. Lin, S.C., Chung, J.Y., Lamothe, B. (2008) Molecular basis for the unique deubiquitinating activity of the NF-kappaB inhibitor A20. J Mol Biol 376: pp. 526-40
66. Setsuie, R., Wada, K. (2007) The functions of UCH-L1 and its relation to neurodegenerative diseases. Neurochem Int 51: pp. 105-11
67. Wood, M.A., Kaplan, M.P., Brensinger, C.M. (2005) Ubiquitin C-terminal hydrolase L3 (Uchl3) is involved in working memory. Hippocampus 15: pp. 610-21
68. Semenova, E., Wang, X., Jablonski, M.M. (2003) An engineered 800 kilobase deletion of Uchl3 and Lmo7 on mouse chromosome 14 causes defects in viability, postnatal growth and degeneration of muscle and retina. Hum Mol Genet 12: pp. 1301-12
69. Leroy, E., Boyer, R., Auburger, G. (1998) The ubiquitin pathway in Parkinson’s disease. Nature 395: pp. 451-2
70. Yao, T., Song, L., Xu, W. (2006) Proteasome recruitment and activation of the Uch37 deubiquitinating enzyme by Adrm1. Nat Cell Biol 8: pp. 994-1002
71. Qiu, X.B., Ouyang, S.Y., Li, C.J. (2006) hRpn13/ADRM1/GP110 is a novel proteasome subunit that binds the deubiquitinating enzyme, UCH37. EMBO J 25: pp. 5742-53
72. Hamazaki, J., Iemura, S., Natsume, T. (2006) A novel proteasome interacting protein recruits the deubiquitinating enzyme UCH37 to 26S proteasomes. EMBO J 25: pp. 4524-36
73. Jensen, D.E., Proctor, M., Marquis, S.T. (1998) BAP1: a novel ubiquitin hydrolase which binds to the BRCA1 RING finger and enhances BRCA1-mediated cell growth suppression. Oncogene 16: pp. 1097-112
74. Nishikawa, H., Wu, W., Koike, A. (2009) BRCA1-associated protein 1 interferes with BRCA1/BARD1 RING heterodimer activity. Cancer Res 69: pp. 111-9
75. Mallery, D.L., Vandenberg, C.J., Hiom, K. (2002) Activation of the E3 ligase function of the BRCA1/BARD1 complex by polyubiquitin chains. EMBO J 21: pp. 6755-62
76. Misaghi, S., Ottosen, S., Izrael-Tomasevic, A. (2009) Association of C-terminal ubiquitin hydrolase BRCA1-associated protein 1 with cell cycle regulator host cell factor 1. Mol Cell Biol 29: pp. 2181-92
77. Ventii, K.H., Devi, N.S., Friedrich, K.L. (2008) BRCA1-associated protein-1 is a tumor suppressor that requires deubiquitinating activity and nuclear localization. Cancer Res 68: pp. 6953-62
78. Das, C., Hoang, Q.Q., Kreinbring, C.A. (2006) Structural basis for conformational plasticity of the Parkinson’s disease-associated ubiquitin hydrolase UCH-L1. Proc Natl Acad Sci USA 103: pp. 4675-80
79. Misaghi, S., Galardy, P.J., Meester, W.J. (2005) Structure of the ubiquitin hydrolase UCH-L3 complexed with a suicide substrate. J Biol Chem 280: pp. 1512-20
80. Popp, M.W., Artavanis-Tsakonas, K., Ploegh, H.L. (2009) Substrate Filtering by the Active Site Crossover Loop in UCHL3 Revealed by Sortagging and Gain-of-function Mutations. J Biol Chem 284: pp. 3593-602
81. Lam, Y.A., Xu, W., DeMartino, G.N. (1997) Editing of ubiquitin conjugates by an isopeptidase in the 26S proteasome. Nature 385: pp. 737-40
82. Setsuie, R., Sakurai, M., Sakaguchi, Y. (2009) Ubiquitin dimers control the hydrolase activity of UCH-L3. Neurochem Int 54: pp. 314-21
83. Scheel, H., Tomiuk, S., Hofmann, K. (2003) Elucidation of ataxin-3 and ataxin-7 function by integrative bioinformatics. Hum Mol Genet 12: pp. 2845-52
84. Burnett, B., Li, F., Pittman, R.N. (2003) The polyglutamine neurodegenerative protein ataxin-3 binds polyubiquitylated proteins and has ubiquitin protease activity. Hum Mol Genet 12: pp. 3195-205
85. Riess, O., Rub, U., Pastore, A. (2008) SCA3: neurological features, pathogenesis and animal models. Cerebellum 7: pp. 125-37
86. Williams, A.J., Paulson, H.L. (2008) Polyglutamine neurodegeneration: protein misfolding revisited. Trends Neurosci 31: pp. 521-8
87. Mao, Y., Senic-Matuglia, F., Fiore, P.P. (2005) Deubiquitinating function of ataxin-3: insights from the solution structure of the Josephin domain. Proc Natl Acad Sci USA 102: pp. 12700-5
88. Nicastro, G., Menon, R.P., Masino, L. (2005) The solution structure of the Josephin domain of ataxin-3: structural determinants for molecular recognition. Proc Natl Acad Sci USA 102: pp. 10493-8
89. Nicastro, G., Habeck, M., Masino, L. (2006) Structure validation of the Josephin domain of ataxin-3: conclusive evidence for an open conformation. J Biomol NMR 36: pp. 267-77
90. Nicastro, G., Masino, L., Esposito, V. (2009) The josephin domain of ataxin-3 contains two distinct ubiquitin binding sites. Biopolymers 91: pp. 1203-14
91. Todi, S.V., Winborn, B.J., Scaglione, K.M. (2009) Ubiquitination directly enhances activity of the deubiquitinating enzyme ataxin-3. EMBO J 28: pp. 372-82
92. Berke, S.J., Chai, Y., Marrs, G.L. (2005) Defining the role of ubiquitin-interacting motifs in the polyglutamine disease protein, ataxin-3. J Biol Chem 280: pp. 32026-34
93. Sims, J.J., Cohen, R.E. (2009) Linkage-specific avidity defines the lysine 63-linked polyubiquitin-binding preference of rap80. Mol Cell 33: pp. 775-83
94. Winborn, B.J., Travis, S.M., Todi, S.V. (2008) The deubiquitinating enzyme ataxin-3, a polyglutamine disease protein, edits Lys63 linkages in mixed linkage ubiquitin chains. J Biol Chem 283: pp. 26436-43
95. Williams, R.L., Urbe, S. (2007) The emerging shape of the ESCRT machinery. Nat Rev Mol Cell Biol 8: pp. 355-68
96. Cooper, E.M., Cutcliffe, C., Kristiansen, T.Z. (2009) K63-specific deubiquitination by two JAMM/MPN+ complexes: BRISC-associated Brcc36 and proteasomal Poh1. EMBO J 28: pp. 621-31
97. Shao, G., Lilli, D.R., Patterson-Fortin, J. (2009) The Rap80-BRCC36 de-ubiquitinating enzyme complex antagonizes RNF8-Ubc13-dependent ubiquitination events at DNA double strand breaks. Proc Natl Acad Sci USA 106: pp. 3166-71
98. Wang, B., Elledge, S.J. (2007) Ubc13/Rnf8 ubiquitin ligases control foci formation of the Rap80/Abraxas/Brca1/ Brcc36 complex in response to DNA damage. Proc Natl Acad Sci USA 104: pp. 20759-63
99. Dong, Y., Hakimi, M.A., Chen, X. (2003) Regulation of BRCC, a holoenzyme complex containing BRCA1 and BRCA2, by a signalosome-like subunit and its role in DNA repair. Mol Cell 12: pp. 1087-99
100. Cope, G.A., Suh, G.S., Aravind, L. (2002) Role of predicted metalloprotease motif of Jab1/Csn5 in cleavage of Nedd8 from Cul1. Science 298: pp. 608-11
101. Zhu, P., Zhou, W., Wang, J. (2007) A histone H2A deubiquitinase complex coordinating histone acetylation and H1 dissociation in transcriptional regulation. Mol Cell 27: pp. 609-21
102. Pena, V., Liu, S., Bujnicki, J.M. (2007) Structure of a multipartite protein-protein interaction domain in splicing factor prp8 and its link to retinitis pigmentosa. Mol Cell 25: pp. 615-24
103. McCullough, J., Clague, M.J., Urbe, S. (2004) AMSH is an endosome-associated ubiquitin isopeptidase. J Cell Biol 166: pp. 487-92
104. Xu, P., Duong, D.M., Seyfried, N.T. (2009) Quantitative proteomics reveals the function of unconventional ubiquitin chains in proteasomal degradation. Cell 137: pp. 133-45
105. Peng, J., Schwartz, D., Elias, J.E. (2003) A proteomics approach to understanding protein ubiquitination. Nat Biotechnol 21: pp. 921-6
106. Shanmugham, A., Ovaa, H. (2008) DUBs and disease: activity assays for inhibitor development. Curr Opin Drug Discov Devel 11: pp. 688-96