Ubiquitin and its binding domains

Frontiers in Bioscience

Volumn 17, Issue 6, 2012, Pages 2140-2157

  Randles, Leah ^a   Walters, Kylie J ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

Author keywords

Function; Review; Structure; UBD; Ubiquitin; Ubiquitination

Indexed keywords

EID: 84860427832     PISSN: 27686701     EISSN: 27686698     Source Type: Journal    
DOI: 10.2741/4042     Document Type: Article

References (153)

1. A. Ciechanover and R. Ben-Saadon: N-terminal ubiquitination: more protein substrates join in. Trends Cell Biol, 14(3), 103-6 (2004). (Pubitemid 38293450)
2. K. Cadwell and L. Coscoy: Ubiquitination on nonlysine residues by a viral E3 ubiquitin ligase. Science, 309(5731), 127-30 (2005). (Pubitemid 40934990)
3. T. Ravid and M. Hochstrasser: Autoregulation of an E2 enzyme by ubiquitin-chain assembly on its catalytic residue. Nat Cell Biol, 9(4), 422-7 (2007). (Pubitemid 46511075)
4. R. J. Deshaies and C. A. Joazeiro: RING domain E3 ubiquitin ligases. Annu Rev Biochem, 78, 399-434 (2009).
5. A. L. Haas, J. V. Warms, A. Hershko and I. A. Rose: Ubiquitin-activating enzyme. Mechanism and role in protein-ubiquitin conjugation. J Biol Chem, 257(5), 2543-8 (1982).
6. B. T. Dye and B. A. Schulman: Structural mechanisms underlying posttranslational modification by ubiquitin-like proteins. Annu Rev Biophys Biomol Struct, 36, 131-50 (2007). (Pubitemid 46998113)
7. B. A. Schulman and J. W. Harper: Ubiquitin-like protein activation by E1 enzymes: the apex for downstream signalling pathways. Nat Rev Mol Cell Biol, 10(5), 319-31 (2009).
8. D. Rotin and S. Kumar: Physiological functions of the HECT family of ubiquitin ligases. Nat Rev Mol Cell Biol, 10(6), 398-409 (2009).
9. D. M. Wenzel, A. Lissounov, P. S. Brzovic and R. E. Klevit: UBCH7 reactivity profile reveals parkin and HHARI to be RING/HECT hybrids. Nature, 474(7349), 105-8 (2011).
10. J. Peng, D. Schwartz, J. E. Elias, C. C. Thoreen, D. Cheng, G. Marsischky, J. Roelofs, D. Finley and S. P. Gygi: A proteomics approach to understanding protein ubiquitination. Nat Biotechnol, 21(8), 921-6 (2003). (Pubitemid 36936199)
11. T. Kirisako, K. Kamei, S. Murata, M. Kato, H. Fukumoto, M. Kanie, S. Sano, F. Tokunaga, K. Tanaka and K. Iwai: A ubiquitin ligase complex assembles linear polyubiquitin chains. EMBO J, 25(20), 4877-87 (2006). (Pubitemid 44607032)
12. C. Tagwerker, K. Flick, M. Cui, C. Guerrero, Y. Dou, B. Auer, P. Baldi, L. Huang and P. Kaiser: A tandem affinity tag for two-step purification under fully denaturing conditions: application in ubiquitin profiling and protein complex identification combined with in vivocross-linking. Mol Cell Proteomics, 5(4), 737-48 (2006).
13. P. Xu, D. M. Duong, N. T. Seyfried, D. Cheng, Y. Xie, J. Robert, J. Rush, M. Hochstrasser, D. Finley and J. Peng: Quantitative proteomics reveals the function of unconventional ubiquitin chains in proteasomal degradation. Cell, 137(1), 133-45 (2009).
14. E. B. Dammer, C. H. Na, P. Xu, N. T. Seyfried, D. M. Duong, D. Cheng, M. Gearing, H. Rees, J. J. Lah, A. I. Levey, J. Rush and J. Peng: Polyubiquitin linkage profiles in three models of proteolytic stress suggest the etiology of Alzheimer disease. J Biol Chem, 286(12), 10457-65 (2011).
15. F. Ikeda and I. Dikic: Atypical ubiquitin chains: new molecular signals. 'Protein Modifications: Beyond the Usual Suspects' review series. EMBO Rep, 9(6), 536-42 (2008). (Pubitemid 351772916)
16. H. T. Kim, K. P. Kim, F. Lledias, A. F. Kisselev, K. M. Scaglione, D. Skowyra, S. P. Gygi and A. L. Goldberg: Certain pairs of ubiquitin-conjugating enzymes (E2s) and ubiquitin-protein ligases (E3s) synthesize nondegradable forked ubiquitin chains containing all possible isopeptide linkages. J Biol Chem, 282(24), 17375-86 (2007). (Pubitemid 47100279)
17. D. Finley: Recognition and processing of ubiquitinprotein conjugates by the proteasome. Annu Rev Biochem, 78, 477-513 (2009).
18. M. J. Clague and S. Urbe: Ubiquitin: same molecule, different degradation pathways. Cell, 143(5), 682-5 (2010).
19. K. Haglund and I. Dikic: Ubiquitylation and cell signaling. EMBO J, 24(19), 3353-9 (2005). (Pubitemid 41486773)
20. M. S. Hayden and S. Ghosh: Shared principles in NFkappaB signaling. Cell, 132(3), 344-62 (2008).
21. K. Iwai and F. Tokunaga: Linear polyubiquitination: a new regulator of NF-kappaB activation. EMBO Rep, 10(7), 706-13 (2009).
22. P. Chastagner, A. Israel and C. Brou: Itch/AIP4 mediates Deltex degradation through the formation of K29- linked polyubiquitin chains. EMBO Rep, 7(11), 1147-53 (2006). (Pubitemid 44660572)
23. J. You and C. M. Pickart: A HECT domain E3 enzyme assembles novel polyubiquitin chains. J Biol Chem, 276(23), 19871-8 (2001).
24. A. K. Al-Hakim, A. Zagorska, L. Chapman, M. Deak, M. Peggie and D. R. Alessi: Control of AMPK-related kinases by USP9X and atypical Lys(29)/Lys(33)-linked polyubiquitin chains. Biochem J, 411(2), 249-60 (2008). (Pubitemid 351580177)
25. A. Bremm and D. Komander: Emerging roles for Lys11-linked polyubiquitin in cellular regulation. Trends Biochem Sci, 36(7), 355-63 (2011).
26. H. Nishikawa, S. Ooka, K. Sato, K. Arima, J. Okamoto, R. E. Klevit, M. Fukuda and T. Ohta: Mass spectrometric and mutational analyses reveal Lys-6-linked polyubiquitin chains catalyzed by BRCA1-BARD1 ubiquitin ligase. J Biol Chem, 279(6), 3916-24 (2004). (Pubitemid 38198974)
27. S. Hatakeyama, M. Yada, M. Matsumoto, N. Ishida and K. I. Nakayama: U box proteins as a new family of ubiquitin-protein ligases. J Biol Chem, 276(35), 33111-20 (2001).
28. C. Grabbe and I. Dikic: Functional roles of ubiquitinlike domain (ULD) and ubiquitin-binding domain (UBD) containing proteins. Chem Rev, 109(4), 1481-94 (2009).
29. M. Hochstrasser: Origin and function of ubiquitin-like proteins. Nature, 458(7237), 422-9 (2009).
30. K. E. Sloper-Mould, J. C. Jemc, C. M. Pickart and L. Hicke: Distinct functional surface regions on ubiquitin. The Journal of biological chemistry, 276(32), 30483-9 (2001).
31. W. I. Sundquist, H. L. Schubert, B. N. Kelly, G. C. Hill, J. M. Holton and C. P. Hill: Ubiquitin recognition by the human TSG101 protein. Mol Cell, 13(6), 783-9 (2004). (Pubitemid 38438474)
32. S. Hirano, M. Kawasaki, H. Ura, R. Kato, C. Raiborg, H. Stenmark and S. Wakatsuki: Double-sided ubiquitin binding of Hrs-UIM in endosomal protein sorting. Nat Struct Mol Biol, 13(3), 272-7 (2006). (Pubitemid 43348514)
33. O. F. Lange, N. A. Lakomek, C. Fares, G. F. Schroder, K. F. Walter, S. Becker, J. Meiler, H. Grubmuller, C. Griesinger and B. L. de Groot: Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science, 320(5882), 1471-5 (2008). (Pubitemid 351929422)
34. P. L. Wintrode, G. I. Makhatadze and P. L. Privalov: Thermodynamics of ubiquitin unfolding. Proteins, 18(3), 246-53 (1994). (Pubitemid 24096735)
35. A. Kumar, S. Srivastava and R. V. Hosur: NMR characterization of the energy landscape of SUMO-1 in the native-state ensemble. J Mol Biol, 367(5), 1480-93 (2007). (Pubitemid 46413265)
36. K. Newton, M. L. Matsumoto, I. E. Wertz, D. S. Kirkpatrick, J. R. Lill, J. Tan, D. Dugger, N. Gordon, S. S. Sidhu, F. A. Fellouse, L. Komuves, D. M. French, R. E. Ferrando, C. Lam, D. Compaan, C. Yu, I. Bosanac, S. G. Hymowitz, R. F. Kelley and V. M. Dixit: Ubiquitin chain editing revealed by polyubiquitin linkage-specific antibodies. Cell, 134(4), 668-78 (2008).
37. 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(7211), 358-62 (2008).
38. Y. Ryabov and D. Fushman: Interdomain mobility in di-ubiquitin revealed by NMR. Proteins, 63(4), 787-96 (2006). (Pubitemid 43765133)
39. W. J. Cook, L. C. Jeffrey, E. Kasperek and C. M. Pickart: Structure of tetraubiquitin shows how multiubiquitin chains can be formed. J Mol Biol, 236(2), 601-9 (1994). (Pubitemid 24146303)
40. M. J. Eddins, R. Varadan, D. Fushman, C. M. Pickart and C. Wolberger: Crystal structure and solution NMR studies of Lys48-linked tetraubiquitin at neutral pH. J Mol Biol, 367(1), 204-11 (2007). (Pubitemid 46274722)
41. J. F. Trempe, N. R. Brown, M. E. Noble and J. A. Endicott: A new crystal form of Lys48-linked diubiquitin. Acta Crystallogr Sect F Struct Biol Cryst Commun, 66(Pt 9), 994-8 (2010).
42. R. Varadan, M. Assfalg, S. Raasi, C. Pickart and D. Fushman: Structural determinants for selective recognition of a Lys48-linked polyubiquitin chain by a UBA domain. Mol Cell, 18(6), 687-98 (2005). (Pubitemid 40804804)
43. D. Komander, F. Reyes-Turcu, J. D. Licchesi, P. Odenwaelder, K. D. Wilkinson and D. Barford: Molecular discrimination of structurally equivalent Lys 63-linked and linear polyubiquitin chains. EMBO Rep, 10(5), 466-73 (2009).
44. A. Bremm, S. M. Freund and D. Komander: Lys11- linked ubiquitin chains adopt compact conformations and are preferentially hydrolyzed by the deubiquitinase Cezanne. Nat Struct Mol Biol, 17(8), 939-47 (2010).
45. M. L. Matsumoto, K. E. Wickliffe, K. C. Dong, C. Yu, I. Bosanac, D. Bustos, L. Phu, D. S. Kirkpatrick, S. G. Hymowitz, M. Rape, R. F. Kelley and V. M. Dixit: K11- linked polyubiquitination in cell cycle control revealed by a K11 linkage-specific antibody. Mol Cell, 39(3), 477-84 (2010).
46. D. Fushman and O. Walker: Exploring the linkage dependence of polyubiquitin conformations using molecular modeling. J Mol Biol, 395(4), 803-14 (2010).
47. S. Pinato, M. Gatti, C. Scandiuzzi, S. Confalonieri and L. Penengo: UMI, a novel RNF168 ubiquitin binding domain involved in the DNA damage signaling pathway. Mol Cell Biol, 31(1), 118-26 (2011).
48. K. Hofmann and L. Falquet: A ubiquitin-interacting motif conserved in components of the proteasomal and lysosomal protein degradation systems. Trends Biochem Sci, 26(6), 347-50 (2001). (Pubitemid 32530646)
49. S. Polo, S. Confalonieri, A. E. Salcini and P. P. Di Fiore: EH and UIM: endocytosis and more. Sci STKE, 2003(213), re17 (2003).
50. S. Pinato, C. Scandiuzzi, N. Arnaudo, E. Citterio, G. Gaudino and L. Penengo: RNF168, a new RING finger, MIU-containing protein that modifies chromatin by ubiquitination of histones H2A and H2AX. BMC Mol Biol, 10, 55 (2009).
51. C. Raiborg and H. Stenmark: Hrs and endocytic sorting of ubiquitinated membrane proteins. Cell Struct Funct, 27(6), 403-8 (2002). (Pubitemid 36267709)
52. C. Raiborg, T. E. Rusten and H. Stenmark: Protein sorting into multivesicular endosomes. Curr Opin Cell Biol, 15(4), 446-55 (2003). (Pubitemid 36928047)
53. Q. Wang, P. Young and K. J. Walters: Structure of S5a bound to monoubiquitin provides a model for polyubiquitin recognition. J Mol Biol, 348(3), 727-39 (2005). (Pubitemid 40515679)
54. 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(3), 280-90 (2009).
55. K. A. Swanson, R. S. Kang, S. D. Stamenova, L. Hicke and I. Radhakrishnan: Solution structure of Vps27 UIMubiquitin complex important for endosomal sorting and receptor downregulation. EMBO J, 22(18), 4597-606 (2003). (Pubitemid 37162896)
56. A. X. Song, C. J. Zhou, Y. Peng, X. C. Gao, Z. R. Zhou, Q. S. Fu, J. Hong, D. H. Lin and H. Y. Hu: Structural transformation of the tandem ubiquitin-interacting motifs in ataxin-3 and their cooperative interactions with ubiquitin chains. PLoS One, 5(10), e13202 (2010).
57. Y. Sato, A. Yoshikawa, H. Mimura, M. Yamashita, A. Yamagata and S. Fukai: Structural basis for specific recognition of Lys 63-linked polyubiquitin chains by tandem UIMs of RAP80. EMBO J, 28(16), 2461-8 (2009).
58. J. J. Sims and R. E. Cohen: Linkage-specific avidity defines the lysine 63-linked polyubiquitin-binding preference of rap80. Mol Cell, 33(6), 775-83 (2009).
59. S. Raasi, R. Varadan, D. Fushman and C. M. Pickart: Diverse polyubiquitin interaction properties of ubiquitinassociated domains. Nat Struct Mol Biol, 12(8), 708-14 (2005). (Pubitemid 43086277)
60. O. V. Baboshina and A. L. Haas: Novel multiubiquitin chain linkages catalyzed by the conjugating enzymes E2EPF and RAD6 are recognized by 26 S proteasome subunit 5. J Biol Chem, 271(5), 2823-31 (1996).
61. L. Jin, A. Williamson, S. Banerjee, I. Philipp and M. Rape: Mechanism of ubiquitin-chain formation by the human anaphase-promoting complex. Cell, 133(4), 653-65 (2008). (Pubitemid 351636306)
62. K. Hofmann: Ubiquitin-binding domains and their role in the DNA damage response. DNA Repair (Amst), 8(4), 544-56 (2009).
63. S. Rahighi, F. Ikeda, M. Kawasaki, M. Akutsu, N. Suzuki, R. Kato, T. Kensche, T. Uejima, S. Bloor, D. Komander, F. Randow, S. Wakatsuki and I. Dikic: Specific recognition of linear ubiquitin chains by NEMO is important for NF-kappaB activation. Cell, 136(6), 1098- 109 (2009).
64. Y. C. Lo, S. C. Lin, C. C. Rospigliosi, D. B. Conze, C. J. Wu, J. D. Ashwell, D. Eliezer and H. Wu: Structural basis for recognition of diubiquitins by NEMO. Mol Cell, 33(5), 602-15 (2009).
65. A. Yoshikawa, Y. Sato, M. Yamashita, H. Mimura, A. Yamagata and S. Fukai: Crystal structure of the NEMO ubiquitin-binding domain in complex with Lys 63-linked di-ubiquitin. FEBS Lett, 583(20), 3317-22 (2009).
66. C. K. Ea, L. Deng, Z. P. Xia, G. Pineda and Z. J. Chen: Activation of IKK by TNFalpha requires site-specific ubiquitination of RIP1 and polyubiquitin binding by NEMO. Mol Cell, 22(2), 245-57 (2006).
67. C. J. Wu, D. B. Conze, T. Li, S. M. Srinivasula and J. D. Ashwell: Sensing of Lys 63-linked polyubiquitination by NEMO is a key event in NF-kappaB activation [corrected]. Nat Cell Biol, 8(4), 398-406 (2006).
68. M. Bienko, C. M. Green, N. Crosetto, F. Rudolf, G. Zapart, B. Coull, P. Kannouche, G. Wider, M. Peter, A. R. Lehmann, K. Hofmann and I. Dikic: Ubiquitin-binding domains in Y-family polymerases regulate translesion synthesis. Science, 310(5755), 1821-4 (2005). (Pubitemid 41814383)
69. M. G. Bomar, S. D'Souza, M. Bienko, I. Dikic, G. C. Walker and P. Zhou: Unconventional ubiquitin recognition by the ubiquitin-binding motif within the Y family DNA polymerases iota and Rev1. Mol Cell, 37(3), 408-17 (2010).
70. G. Prag, S. Misra, E. A. Jones, R. Ghirlando, B. A. Davies, B. F. Horazdovsky and J. H. Hurley: Mechanism of ubiquitin recognition by the CUE domain of Vps9p. Cell, 113(5), 609-20 (2003). (Pubitemid 36694186)
71. T. D. Mueller and J. Feigon: Solution structures of UBA domains reveal a conserved hydrophobic surface for protein-protein interactions. Journal of molecular biology, 319(5), 1243-55 (2002). (Pubitemid 34729432)
72. D. Zhang, S. Raasi and D. Fushman: Affinity makes the difference: nonselective interaction of the UBA domain of Ubiquilin-1 with monomeric ubiquitin and polyubiquitin chains. J Mol Biol, 377(1), 162-80 (2008).
73. R. Varadan, M. Assfalg, A. Haririnia, S. Raasi, C. Pickart and D. Fushman: Solution conformation of Lys63- linked di-ubiquitin chain provides clues to functional diversity of polyubiquitin signaling. The Journal of biological chemistry, 279(8), 7055-63 (2004). (Pubitemid 38248851)
74. Q. Wang, A. M. Goh, P. M. Howley and K. J. Walters: Ubiquitin recognition by the DNA repair protein hHR23a. Biochemistry, 42(46), 13529-35 (2003). (Pubitemid 37444903)
75. S. Raasi, I. Orlov, K. G. Fleming and C. M. Pickart: Binding of polyubiquitin chains to ubiquitin-associated (UBA) domains of HHR23A. J Mol Biol, 341(5), 1367-79 (2004). (Pubitemid 39092321)
76. 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 damageinducible proteins. J Mol Biol, 313(5), 955-63 (2001). (Pubitemid 33081893)
77. S. C. Shih, G. Prag, S. A. Francis, M. A. Sutanto, J. H. Hurley and L. Hicke: A ubiquitin-binding motif required for intramolecular monoubiquitylation, the CUE domain. EMBO J, 22(6), 1273-81 (2003). (Pubitemid 36362691)
78. K. M. Donaldson, H. Yin, N. Gekakis, F. Supek and C. A. Joazeiro: Ubiquitin signals protein trafficking via interaction with a novel ubiquitin binding domain in the membrane fusion regulator, Vps9p. Curr Biol, 13(3), 258- 62 (2003). (Pubitemid 36178306)
79. M. Akutsu, M. Kawasaki, Y. Katoh, T. Shiba, Y. Yamaguchi, R. Kato, K. Kato, K. Nakayama and S. Wakatsuki: Structural basis for recognition of ubiquitinated cargo by Tom1-GAT domain. FEBS Lett, 579(24), 5385-91 (2005). (Pubitemid 41395160)
80. G. Prag, S. Lee, R. Mattera, C. N. Arighi, B. M. Beach, J. S. Bonifacino and J. H. Hurley: Structural mechanism for ubiquitinated-cargo recognition by the Golgi-localized, gamma-ear-containing, ADP-ribosylation-factor-binding proteins. Proc Natl Acad Sci USA, 102(7), 2334-9 (2005). (Pubitemid 40279376)
81. A. Lange, D. Hoeller, H. Wienk, O. Marcillat, J. M. Lancelin and O. Walker: NMR Reveals a Different Mode of Binding of the Stam2 VHS Domain to Ubiquitin and Diubiquitin. Biochemistry (2010).
82. E. Mizuno, K. Kawahata, M. Kato, N. Kitamura and M. Komada: STAM proteins bind ubiquitinated proteins on the early endosome via the VHS domain and ubiquitininteracting motif. Mol Biol Cell, 14(9), 3675-89 (2003). (Pubitemid 37151618)
83. Y. H. Hong, H. C. Ahn, J. Lim, H. M. Kim, H. Y. Ji, S. Lee, J. H. Kim, E. Y. Park, H. K. Song and B. J. Lee: Identification of a novel ubiquitin binding site of STAM1 VHS domain by NMR spectroscopy. FEBS Lett, 583(2), 287-92 (2009).
84. X. Ren and J. H. Hurley: VHS domains of ESCRT-0 cooperate in high-avidity binding to polyubiquitinated cargo. EMBO J, 29(6), 1045-54 (2010).
85. Y. Sato, A. Yoshikawa, M. Yamashita, A. Yamagata and S. Fukai: Structural basis for specific recognition of Lys 63-linked polyubiquitin chains by NZF domains of TAB2 and TAB3. EMBO J, 28(24), 3903-9 (2009).
86. Y. Kulathu, M. Akutsu, A. Bremm, K. Hofmann and D. Komander: Two-sided ubiquitin binding explains specificity of the TAB2 NZF domain. Nat Struct Mol Biol, 16(12), 1328-30 (2009).
87. S. L. Alam, J. Sun, M. Payne, B. D. Welch, B. K. Blake, D. R. Davis, H. H. Meyer, S. D. Emr and W. I. Sundquist: Ubiquitin interactions of NZF zinc fingers. EMBO J, 23(7), 1411-21 (2004). (Pubitemid 38579502)
88. A. Kanayama, R. B. Seth, L. Sun, C. K. Ea, M. Hong, A. Shaito, Y. H. Chiu, L. Deng and Z. J. Chen: TAB2 and TAB3 activate the NF-kappaB pathway through binding to polyubiquitin chains. Mol Cell, 15(4), 535-48 (2004). (Pubitemid 39141781)
89. B. Wang, S. L. Alam, H. H. Meyer, M. Payne, T. L. Stemmler, D. R. Davis and W. I. Sundquist: Structure and ubiquitin interactions of the conserved zinc finger domain of Npl4. J Biol Chem, 278(22), 20225-34 (2003). (Pubitemid 36799220)
90. L. Penengo, M. Mapelli, A. G. Murachelli, S. Confalonieri, L. Magri, A. Musacchio, P. P. Di Fiore, S. Polo and T. R. Schneider: Crystal structure of the ubiquitin binding domains of rabex-5 reveals two modes of interaction with ubiquitin. Cell, 124(6), 1183-95 (2006).
91. S. Lee, Y. C. Tsai, R. Mattera, W. J. Smith, M. S. Kostelansky, A. M. Weissman, J. S. Bonifacino and J. H. Hurley: Structural basis for ubiquitin recognition and autoubiquitination by Rabex-5. Nat Struct Mol Biol, 13(3), 264-71 (2006). (Pubitemid 43348513)
92. F. E. Reyes-Turcu, J. R. Horton, J. E. Mullally, A. Heroux, X. Cheng and K. D. Wilkinson: The ubiquitin binding domain ZnF UBP recognizes the C-terminal diglycine motif of unanchored ubiquitin. Cell, 124(6), 1197-208 (2006).
93. T. Slagsvold, R. Aasland, S. Hirano, K. G. Bache, C. Raiborg, D. Trambaiolo, S. Wakatsuki and H. Stenmark: Eap45 in mammalian ESCRT-II binds ubiquitin via a phosphoinositide-interacting GLUE domain. J Biol Chem, 280(20), 19600-6 (2005). (Pubitemid 41379482)
94. 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(7194), 481-8 (2008). (Pubitemid 351733317)
95. 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(7194), 548-52 (2008). (Pubitemid 351733316)
96. S. L. Alam, C. Langelier, F. G. Whitby, S. Koirala, H. Robinson, C. P. Hill and W. I. Sundquist: Structural basis for ubiquitin recognition by the human ESCRT-II EAP45 GLUE domain. Nat Struct Mol Biol, 13(11), 1029-30 (2006). (Pubitemid 44684857)
97. S. Hirano, N. Suzuki, T. Slagsvold, M. Kawasaki, D. Trambaiolo, R. Kato, H. Stenmark and S. Wakatsuki: Structural basis of ubiquitin recognition by mammalian Eap45 GLUE domain. Nat Struct Mol Biol, 13(11), 1031-2 (2006). (Pubitemid 44684858)
98. M. A. Lemmon: Pleckstrin homology domains: two halves make a hole? Cell, 120(5), 574-6 (2005). (Pubitemid 40343070)
99. J. Yan, W. Wen, W. Xu, J. F. Long, M. E. Adams, S. C. Froehner and M. Zhang: Structure of the split PH domain and distinct lipid-binding properties of the PH-PDZ supramodule of alpha-syntrophin. EMBO J, 24(23), 3985- 95 (2005). (Pubitemid 41752868)
100. 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(3), 404-15 (2010).
101. Q. Deveraux, V. Ustrell, C. Pickart and M. Rechsteiner: A 26 S protease subunit that binds ubiquitin conjugates. The Journal of biological chemistry, 269(10), 7059-61 (1994). (Pubitemid 24217884)
102. C. M. Pickart: Mechanisms underlying ubiquitination. Annu Rev Biochem, 70, 503-33 (2001). (Pubitemid 32663902)
103. P. S. Brzovic, A. Lissounov, D. E. Christensen, D. W. Hoyt and R. E. Klevit: A UbcH5/ubiquitin noncovalent complex is required for processive BRCA1-directed ubiquitination. Mol Cell, 21(6), 873-80 (2006). (Pubitemid 43376136)
104. E. Sakata, T. Satoh, S. Yamamoto, Y. Yamaguchi, M. Yagi-Utsumi, E. Kurimoto, K. Tanaka, S. Wakatsuki and K. Kato: Crystal structure of UbcH5b∼ubiquitin intermediate: insight into the formation of the selfassembled E2∼Ub conjugates. Structure, 18(1), 138-47 (2010).
105. I. Bosanac, L. Phu, B. Pan, I. Zilberleyb, B. Maurer, V. M. Dixit, S. G. Hymowitz and D. S. Kirkpatrick: Modulation of K11-linkage formation by variable loop residues within UbcH5A. J Mol Biol, 408(3), 420-31 (2011).
106. S. Karkkainen, M. Hiipakka, J. H. Wang, I. Kleino, M. Vaha-Jaakkola, G. H. Renkema, M. Liss, R. Wagner and K. Saksela: Identification of preferred protein interactions by phage-display of the human Src homology-3 proteome. EMBO Rep, 7(2), 186-91 (2006).
107. B. J. Mayer: SH3 domains: complexity in moderation. J Cell Sci, 114(Pt 7), 1253-63 (2001). (Pubitemid 32409462)
108. Y. He, L. Hicke and I. Radhakrishnan: Structural basis for ubiquitin recognition by SH3 domains. J Mol Biol, 373(1), 190-6 (2007). (Pubitemid 47390722)
109. I. Bezsonova, M. C. Bruce, S. Wiesner, H. Lin, D. Rotin and J. D. Forman-Kay: Interactions between the three CIN85 SH3 domains and ubiquitin: implications for CIN85 ubiquitination. Biochemistry, 47(34), 8937-49 (2008).
110. S. D. Stamenova, M. E. French, Y. He, S. A. Francis, Z. B. Kramer and L. Hicke: Ubiquitin binds to and regulates a subset of SH3 domains. Mol Cell, 25(2), 273-84 (2007). (Pubitemid 46109609)
111. A. X. Song, C. J. Zhou, X. Guan, K. H. Sze and H. Y. Hu: Solution structure of the N-terminal domain of DC-UbP/UBTD2 and its interaction with ubiquitin. Protein Sci, 19(5), 1104-9 (2010).
112. N. Pashkova, L. Gakhar, S. C. Winistorfer, L. Yu, S. Ramaswamy and R. C. Piper: WD40 repeat propellers define a ubiquitin-binding domain that regulates turnover of F box proteins. Mol Cell, 40(3), 433-43 (2010).
113. F. Okumura, K. Yoshida, F. Liang and S. Hatakeyama: MDA-9/syntenin interacts with ubiquitin via a novel ubiquitin-binding motif. Mol Cell Biochem, 352(1-2), 163-72 (2011).
114. Y. G. Gao, A. X. Song, Y. H. Shi, Y. G. Chang, S. X. Liu, Y. Z. Yu, X. T. Cao, D. H. Lin and H. Y. Hu: Solution structure of the ubiquitin-like domain of human DC-UbP from dendritic cells. Protein Sci, 14(8), 2044- 50 (2005).
115. J. E. Mullally, T. Chernova and K. D. Wilkinson: Doa1 is a Cdc48 adapter that possesses a novel ubiquitin binding domain. Mol Cell Biol, 26(3), 822-30 (2006). (Pubitemid 43146478)
116. N. S. Russell and K. D. Wilkinson: Identification of a novel 29-linked polyubiquitin binding protein, Ufd3, using polyubiquitin chain analogues. Biochemistry, 43(16), 4844- 54 (2004). (Pubitemid 38509105)
117. K. J. Walters, P. J. Lech, A. M. Goh, Q. Wang and P. M. Howley: DNA-repair protein hHR23a alters its protein structure upon binding proteasomal subunit S5a. Proc Natl Acad Sci USA, 100(22), 12694-9 (2003). (Pubitemid 37339961)
118. T. Woelk, B. Oldrini, E. Maspero, S. Confalonieri, E. Cavallaro, P. P. Di Fiore and S. Polo: Molecular mechanisms of coupled monoubiquitination. Nat Cell Biol, 8(11), 1246-54 (2006). (Pubitemid 44660589)
119. D. Hoeller and I. Dikic: Regulation of ubiquitin receptors by coupled monoubiquitination. Sub-cellular biochemistry, 54, 31-40 (2010).
120. S. Polo, S. Sigismund, M. Faretta, M. Guidi, M. R. Capua, G. Bossi, H. Chen, P. De CamilliCamilli and P. P. Di Fiore: A single motif responsible for ubiquitin recognition and monoubiquitination in endocytic proteins. Nature, 416(6879), 451-5 (2002). (Pubitemid 34272882)
121. D. Hoeller, N. Crosetto, B. Blagoev, C. Raiborg, R. Tikkanen, S. Wagner, K. Kowanetz, R. Breitling, M. Mann, H. Stenmark and I. Dikic: Regulation of ubiquitin-binding proteins by monoubiquitination. Nat Cell Biol, 8(2), 163-9 (2006).
122. H. H. Meyer, Y. Wang and G. Warren: Direct binding of ubiquitin conjugates by the mammalian p97 adaptor complexes, p47 and Ufd1-Npl4. EMBO J, 21(21), 5645-52 (2002). (Pubitemid 35315264)
123. X. Yuan, P. Simpson, C. McKeown, H. Kondo, K. Uchiyama, R. Wallis, I. Dreveny, C. Keetch, X. Zhang, C. Robinson, P. Freemont and S. Matthews: Structure, dynamics and interactions of p47, a major adaptor of the AAA ATPase, p97. EMBO J, 23(7), 1463-73 (2004). (Pubitemid 38579507)
124. T. Hunter: The age of crosstalk: phosphorylation, ubiquitination, and beyond. Molecular cell, 28(5), 730-8 (2007). (Pubitemid 350217067)
125. K. Miura and P. M. Hasegawa: Sumoylation and other ubiquitin-like post-translational modifications in plants. Trends in cell biology, 20(4), 223-32 (2010).
126. F. Desiere, E. W. Deutsch, A. I. Nesvizhskii, P. Mallick, N. L. King, J. K. Eng, A. Aderem, R. Boyle, E. Brunner, S. Donohoe, N. Fausto, E. Hafen, L. Hood, M. G. Katze, K. A. Kennedy, F. Kregenow, H. Lee, B. Lin, D. Martin, J. A. Ranish, D. J. Rawlings, L. E. Samelson, Y. Shiio, J. D. Watts, B. Wollscheid, M. E. Wright, W. Yan, L. Yang, E. C. Yi, H. Zhang and R. Aebersold: Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol, 6(1), R9 (2005).
127. C. N. Pang, E. Gasteiger and M. R. Wilkins: Identification of arginine- and lysine-methylation in the proteome of Saccharomyces cerevisiae and its functional implications. BMC Genomics, 11, 92 (2010).
128. A. Hershko, A. Ciechanover, H. Heller, A. L. Haas and I. A. Rose: Proposed role of ATP in protein breakdown: conjugation of protein with multiple chains of the polypeptide of ATP-dependent proteolysis. Proceedings of the National Academy of Sciences of the United States of America, 77(4), 1783-6 (1980).
129. K. D. Wilkinson, M. K. Urban and A. L. Haas: Ubiquitin is the ATP-dependent proteolysis factor I of rabbit reticulocytes. The Journal of biological chemistry, 255(16), 7529-32 (1980). (Pubitemid 11239455)
130. 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(10), 5461-7 (1998). (Pubitemid 28124009)
131. S. Sugiyama, S. Kishida, K. Chayama, S. Koyama and A. Kikuchi: Ubiquitin-interacting motifs of Epsin are involved in the regulation of insulin-dependent endocytosis. Journal of biochemistry, 137(3), 355-64 (2005). (Pubitemid 40628442)
132. R. Mattera, Y. C. Tsai, A. M. Weissman and J. S. Bonifacino: The Rab5 guanine nucleotide exchange factor Rabex-5 binds ubiquitin (Ub) and functions as a Ub ligase through an atypical Ub-interacting motif and a zinc finger domain. J Biol Chem, 281(10), 6874-83 (2006). (Pubitemid 43847623)
133. M. G. Bomar, S. D'Souza, M. Bienko, I. Dikic, G. C. Walker and P. Zhou: Unconventional ubiquitin recognition by the ubiquitin-binding motif within the Y family DNA polymerases iota and Rev1. Molecular cell, 37(3), 408-17 (2010).
134. D. Burschowsky, F. Rudolf, G. Rabut, T. Herrmann, M. Peter and G. Wider: Structural analysis of the conserved ubiquitin-binding motifs (UBMs) of the translesion polymerase iota in complex with ubiquitin. The Journal of biological chemistry, 286(2), 1364-73 (2011).
135. S. Wagner, I. Carpentier, V. Rogov, M. Kreike, F. Ikeda, F. Lohr, C. J. Wu, J. D. Ashwell, V. Dotsch, I. Dikic and R. Beyaert: Ubiquitin binding mediates the NF-kappaB inhibitory potential of ABIN proteins. Oncogene, 27(26), 3739-45 (2008). (Pubitemid 351912974)
136. A. Ohno, J. Jee, K. Fujiwara, T. Tenno, N. Goda, H. Tochio, H. Kobayashi, H. Hiroaki and M. Shirakawa: Structure of the UBA domain of Dsk2p in complex with ubiquitin molecular determinants for ubiquitin recognition. Structure, 13(4), 521-32 (2005).
137. Y. Kang, R. A. Vossler, L. A. Diaz-Martinez, N. S. Winter, D. J. Clarke and K. J. Walters: UBL/UBA ubiquitin receptor proteins bind a common tetraubiquitin chain. J Mol Biol, 356(4), 1027-35 (2006). (Pubitemid 43145954)
138. R. Varadan, M. Assfalg, S. Raasi, C. Pickart and D. Fushman: Structural determinants for selective recognition of a Lys48-linked polyubiquitin chain by a UBA domain. Molecular cell, 18(6), 687-98 (2005). (Pubitemid 40804804)
139. V. Kirkin, T. Lamark, Y. S. Sou, G. Bjorkoy, J. L. Nunn, J. A. Bruun, E. Shvets, D. G. McEwan, T. H. Clausen, P. Wild, I. Bilusic, J. P. Theurillat, A. Overvatn, T. Ishii, Z. Elazar, M. Komatsu, I. Dikic and T. Johansen: A role for NBR1 in autophagosomal degradation of ubiquitinated substrates. Mol Cell, 33(4), 505-16 (2009).
140. S. Isogai, D. Morimoto, K. Arita, S. Unzai, T. Tenno, J. Hasegawa, Y. S. Sou, M. Komatsu, K. Tanaka, M. Shirakawa and H. Tochio: Crystal structure of the UBA domain of p62 and its interaction with ubiquitin. J Biol Chem, 286(36), 31864-74 (2011).
141. Y. Katoh, Y. Shiba, H. Mitsuhashi, Y. Yanagida, H. Takatsu and K. Nakayama: Tollip and Tom1 form a complex and recruit ubiquitin-conjugated proteins onto early endosomes. J Biol Chem, 279(23), 24435-43 (2004). (Pubitemid 38725307)
142. M. Kawasaki, T. Shiba, Y. Shiba, Y. Yamaguchi, N. Matsugaki, N. Igarashi, M. Suzuki, R. Kato, K. Kato, K. Nakayama and S. Wakatsuki: Molecular mechanism of ubiquitin recognition by GGA3 GAT domain. Genes to cells : devoted to molecular & cellular mechanisms, 10(7), 639-54 (2005). (Pubitemid 40932345)
143. R. Puertollano and J. S. Bonifacino: Interactions of GGA3 with the ubiquitin sorting machinery. Nature cell biology, 6(3), 244-51 (2004). (Pubitemid 38344363)
144. Y. Ai, J. Wang, R. E. Johnson, L. Haracska, L. Prakash and Z. Zhuang: A novel ubiquitin binding mode in the S. cerevisiae translesion synthesis DNA polymerase eta. Mol Biosyst, 7(6), 1874-82 (2011).
145. G. Cui, R. C. Benirschke, H. F. Tuan, N. Juranic, S. Macura, M. V. Botuyan and G. Mer: Structural basis of ubiquitin recognition by translesion synthesis DNA polymerase iota. Biochemistry, 49(47), 10198-207 (2010).
146. H. Iha, J. M. Peloponese, L. Verstrepen, G. Zapart, F. Ikeda, C. D. Smith, M. F. Starost, V. Yedavalli, K. Heyninck, I. Dikic, R. Beyaert and K. T. Jeang: Inflammatory cardiac valvulitis in TAX1BP1-deficient mice through selective NF-kappaB activation. EMBO J, 27(4), 629-41 (2008). (Pubitemid 351273127)
147. D. Komander and D. Barford: Structure of the A20 OTU domain and mechanistic insights into deubiquitination. The Biochemical journal, 409(1), 77-85 (2008).
148. C. Boyault, B. Gilquin, Y. Zhang, V. Rybin, E. Garman, W. Meyer-Klaucke, P. Matthias, C. W. Muller and S. Khochbin: HDAC6-p97/VCP controlled polyubiquitin chain turnover. EMBO J, 25(14), 3357-66 (2006). (Pubitemid 44141793)
149. D. Seigneurin-Berny, A. Verdel, S. Curtet, C. Lemercier, J. Garin, S. Rousseaux and S. Khochbin: Identification of components of the murine histone deacetylase 6 complex: link between acetylation and ubiquitination signaling pathways. Mol Cell Biol, 21(23), 8035-44 (2001). (Pubitemid 33051794)
150. O. Pornillos, S. L. Alam, R. L. Rich, D. G. Myszka, D. R. Davis and W. I. Sundquist: Structure and functional interactions of the Tsg101 UEV domain. EMBO J, 21(10), 2397-406 (2002). (Pubitemid 34546712)
151. C. Tsui, A. Raguraj and C. M. Pickart: Ubiquitin binding site of the ubiquitin E2 variant (UEV) protein Mms2 is required for DNA damage tolerance in
152. Q. S. Fu, C. J. Zhou, H. C. Gao, Y. J. Jiang, Z. R. Zhou, J. Hong, W. M. Yao, A. X. Song, D. H. Lin and H. Y. Hu: Structural basis for ubiquitin recognition by a novel domain from human phospholipase A2-activating protein. J Biol Chem, 284(28), 19043-52 (2009).
153. P. Bellare, A. K. Kutach, A. K. Rines, C. Guthrie and E. J. Sontheimer: Ubiquitin binding by a variant Jab1/MPN domain in the essential pre-mRNA splicing factor Prp8p. RNA, 12(2), 292-302 (2006). (Pubitemid 43121934)