An ankyrin-repeat ubiquitin-binding domain determines TRABID's specificity for atypical ubiquitin chains (original) (raw)

• Komander, D. The emerging complexity of protein ubiquitination. Biochem. Soc. Trans. 37, 937–953 (2009).
  Article CAS PubMed Google Scholar
• Ikeda, F. & Dikic, I. Atypical ubiquitin chains: new molecular signals. 'Protein Modifications: Beyond the Usual Suspects' review series. EMBO Rep. 9, 536–542 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Xu, P. et al. Quantitative proteomics reveals the function of unconventional ubiquitin chains in proteasomal degradation. Cell 137, 133–145 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Dammer, E.B. et al. Polyubiquitin linkage profiles in three models of proteolytic stress suggest the etiology of Alzheimer disease. J. Biol. Chem. 286, 10457–10465 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Wang, M., Cheng, D., Peng, J. & Pickart, C.M. Molecular determinants of polyubiquitin linkage selection by an HECT ubiquitin ligase. EMBO J. 25, 1710–1719 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Hay-Koren, A., Caspi, M., Zilberberg, A. & Rosin-Arbesfeld, R. The EDD E3 ubiquitin ligase ubiquitinates and up-regulates β-catenin. Mol. Biol. Cell 22, 399–411 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Chastagner, P., Israël, A. & Brou, C. Itch/AIP4 mediates Deltex degradation through the formation of K29-linked polyubiquitin chains. EMBO Rep. 7, 1147–1153 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Al-Hakim, A.K. et al. Control of AMPK-related kinases by USP9X and atypical lysine(29)/lysine(33)-linked polyubiquitin chains. Biochem. J. 411, 249–260 (2008).
  Article CAS PubMed Google Scholar
• Johnson, E.S., Ma, P.C., Ota, I.M. & Varshavsky, A. A proteolytic pathway that recognizes ubiquitin as a degradation signal. J. Biol. Chem. 270, 17442–17456 (1995).
  Article CAS PubMed Google Scholar
• Koegl, M. et al. A novel ubiquitination factor, E4, is involved in multiubiquitin chain assembly. Cell 96, 635–644 (1999).
  Article CAS PubMed Google Scholar
• Virdee, S., Ye, Y., Nguyen, D.P., Komander, D. & Chin, J.W. Engineered diubiquitin synthesis reveals Lys29-isopeptide specificity of an OTU deubiquitinase. Nat. Chem. Biol. 6, 750–757 (2010).
  Article CAS PubMed Google Scholar
• El Oualid, F. et al. Chemical synthesis of ubiquitin, ubiquitin-based probes, and diubiquitin. Angew. Chem. Int. Edn Engl. 49, 10149–10153 (2010).
  Article CAS Google Scholar
• Kumar, K.S., Spasser, L., Erlich, L.A., Bavikar, S.N. & Brik, A. Total chemical synthesis of di-ubiquitin chains. Angew. Chem. Int. Edn Engl. 49, 9126–9131 (2010).
  Article CAS Google Scholar
• Virdee, S. et al. Traceless and site-specific ubiquitination of recombinant proteins. J. Am. Chem. Soc. 133, 10708–10711 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Komander, D., Clague, M.J. & Urbé, S. Breaking the chains: structure and function of the deubiquitinases. Nat. Rev. Mol. Cell Biol. 10, 550–563 (2009).
  Article CAS PubMed Google Scholar
• Nijman, S.M.B. et al. A genomic and functional inventory of deubiquitinating enzymes. Cell 123, 773–786 (2005).
  Article CAS PubMed Google Scholar
• Komander, D. et al. Molecular discrimination of structurally equivalent lysine 63-linked and linear polyubiquitin chains. EMBO Rep. 10, 466–473 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• McCullough, J., Clague, M.J. & Urbé, S. AMSH is an endosome-associated ubiquitin isopeptidase. J. Cell Biol. 166, 487–492 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Cooper, E.M. et al. K63-specific deubiquitination by two JAMM/MPN+ complexes: BRISC-associated Brcc36 and proteasomal Poh1. EMBO J. 28, 621–631 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Edelmann, M.J. et al. Structural basis and specificity of human otubain 1-mediated deubiquitination. Biochem. J. 418, 379–390 (2009).
  Article CAS PubMed Google Scholar
• Bremm, A., Freund, S.M. & Komander, D. Lys11-linked ubiquitin chains adopt compact conformations and are preferentially hydrolyzed by the deubiquitinase Cezanne. Nat. Struct. Mol. Biol. 17, 939–947 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Nanao, M.H. et al. Crystal structure of human otubain 2. EMBO Rep. 5, 783–788 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Komander, D. & Barford, D. Structure of the A20 OTU domain and mechanistic insights into deubiquitination. Biochem. J. 409, 77–85 (2008).
  Article CAS PubMed Google Scholar
• Lin, S.C. et al. Molecular basis for the unique deubiquitinating activity of the NF-κB inhibitor A20. J. Mol. Biol. 376, 526–540 (2008).
  Article CAS PubMed Google Scholar
• Messick, T.E. et al. Structural basis for ubiquitin recognition by the Otu1 ovarian tumor domain protein. J. Biol. Chem. 283, 11038–11049 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Akutsu, M., Ye, Y., Virdee, S., Chin, J.W. & Komander, D. Molecular basis for ubiquitin and ISG15 cross-reactivity in viral ovarian tumor domains. Proc. Natl. Acad. Sci. USA 108, 2228–2233 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Capodagli, G.C. et al. Structural analysis of a viral ovarian tumor domain protease from the Crimean-Congo hemorrhagic fever virus in complex with covalently bonded ubiquitin. J. Virol. 85, 3621–3630 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• James, T.W. et al. Structural basis for the removal of ubiquitin and interferon-stimulated gene 15 by a viral ovarian tumor domain-containing protease. Proc. Natl. Acad. Sci. USA 108, 2222–2227 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Dikic, I., Wakatsuki, S. & Walters, K.J. Ubiquitin-binding domains—from structures to functions. Nat. Rev. Mol. Cell Biol. 10, 659–671 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Hymowitz, S.G. & Wertz, I.E. A20: from ubiquitin editing to tumour suppression. Nat. Rev. Cancer 10, 332–341 (2010).
  Article CAS PubMed Google Scholar
• Kayagaki, N. et al. DUBA: a deubiquitinase that regulates type I interferon production. Science 318, 1628–1632 (2007).
  Article CAS PubMed Google Scholar
• Li, S. et al. Regulation of virus-triggered signaling by OTUB1- and OTUB2-mediated deubiquitination of TRAF3 and TRAF6. J. Biol. Chem. 285, 4291–4297 (2010).
  Article CAS PubMed Google Scholar
• Uchiyama, K. et al. VCIP135, a novel essential factor for p97/p47-mediated membrane fusion, is required for Golgi and ER assembly in vivo. J. Cell Biol. 159, 855–866 (2002).
  Article CAS PubMed PubMed Central Google Scholar
• Ernst, R., Mueller, B., Ploegh, H.L. & Schlieker, C. The otubain YOD1 is a deubiquitinating enzyme that associates with p97 to facilitate protein dislocation from the ER. Mol. Cell 36, 28–38 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Tran, H., Hamada, F., Schwarz-Romond, T. & Bienz, M. Trabid, a new positive regulator of Wnt-induced transcription with preference for binding and cleaving K63-linked ubiquitin chains. Genes Dev. 22, 528–542 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Evans, P.C. et al. Isolation and characterization of two novel A20-like proteins. Biochem. J. 357, 617–623 (2001).
  Article CAS PubMed PubMed Central Google Scholar
• Holm, L. & Rosenstrom, P. Dali server: conservation mapping in 3D. Nucleic Acids Res. 38, W545–W549 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Li, J., Mahajan, A. & Tsai, M.D. Ankyrin repeat: a unique motif mediating protein-protein interactions. Biochemistry 45, 15168–15178 (2006).
  Article CAS PubMed Google Scholar
• Sato, Y. et al. Structural basis for specific cleavage of lysine 63-linked polyubiquitin chains. Nature 455, 358–362 (2008).
  Article CAS PubMed Google Scholar
• de Vries, S.J., van Dijk, M. & Bonvin, A.M. The HADDOCK web server for data-driven biomolecular docking. Nat. Protoc. 5, 883–897 (2010).
  Article CAS PubMed Google Scholar
• Mosavi, L.K., Cammett, T.J., Desrosiers, D.C. & Peng, Z.Y. The ankyrin repeat as molecular architecture for protein recognition. Protein Sci. 13, 1435–1448 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Sato, Y., Yoshikawa, A., Yamashita, M., Yamagata, A. & Fukai, S. Structural basis for specific recognition of lysine 63-linked polyubiquitin chains by NZF domains of TAB2 and TAB3. EMBO J. 28, 3903–3909 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Kulathu, Y., Akutsu, M., Bremm, A., Hofmann, K. & Komander, D. Two-sided ubiquitin binding explains specificity of the TAB2 NZF domain. Nat. Struct. Mol. Biol. 16, 1328–1330 (2009).
  Article CAS PubMed Google Scholar
• Bosanac, I. et al. Ubiquitin binding to A20 ZnF4 is required for modulation of NF-κB signaling. Mol. Cell 40, 548–557 (2010).
  Article CAS PubMed Google Scholar
• Reyes-Turcu, F.E., Shanks, J.R., Komander, D. & Wilkinson, K.D. Recognition of polyubiquitin isoforms by the multiple ubiquitin binding modules of isopeptidase T. J. Biol. Chem. 283, 19581–19592 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Ohshima, R. et al. Putative tumor suppressor EDD interacts with and up-regulates APC. Genes Cells 12, 1339–1345 (2007).
  Article CAS PubMed Google Scholar
• Tanaka, N. et al. Structural basis for recognition of 2′,5′-linked oligoadenylates by human ribonuclease L. EMBO J. 23, 3929–3938 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Pape, T. & Schneider, T.R. HKL2map: a graphical user interface for macromolecular phasing with SHELX programs. J. Appl. Crystallogr. 37, 843–844 (2004).
  Article CAS Google Scholar
• Bricogne, G., Vonrhein, C., Flensburg, C., Schiltz, M. & Paciorek, W. Generation, representation and flow of phase information in structure determination: recent developments in and around SHARP 2.0. Acta Crystallogr. D Biol. Crystallogr. 59, 2023–2030 (2003).
  Article CAS PubMed Google Scholar
• Perrakis, A., Morris, R. & Lamzin, V.S. Automated protein model building combined with iterative structure refinement. Nat. Struct. Biol. 6, 458–463 (1999).
  Article CAS PubMed Google Scholar
• Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004).
  Article PubMed Google Scholar
• Adams, P.D. et al. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. D Biol. Crystallogr. 58, 1948–1954 (2002).
  Article PubMed Google Scholar
• Neidhardt, F.C., Bloch, P.L. & Smith, D.F. Culture medium for enterobacteria. J. Bacteriol. 119, 736–747 (1974).
  CAS PubMed PubMed Central Google Scholar