E2 ubiquitin-conjugating enzymes regulate the deubiquitinating activity of OTUB1 (original) (raw)

References

  1. Komander, D. & Rape, M. The ubiquitin code. Annu. Rev. Biochem. 81, 203–229 (2012).
    CAS PubMed Google Scholar
  2. Komander, D., Clague, M.J. & Urbe, S. Breaking the chains: structure and function of the deubiquitinases. Nat. Rev. Mol. Cell Biol. 10, 550–563 (2009).
    Article CAS Google Scholar
  3. Amerik, A.Y., Swaminathan, S., Krantz, B.A., Wilkinson, K.D. & Hochstrasser, M. In vivo disassembly of free polyubiquitin chains by yeast Ubp14 modulates rates of protein degradation by the proteasome. EMBO J. 16, 4826–4838 (1997).
    Article CAS Google Scholar
  4. Balakirev, M.Y., Tcherniuk, S.O., Jaquinod, M. & Chroboczek, J. Otubains: a new family of cysteine proteases in the ubiquitin pathway. EMBO Rep. 4, 517–522 (2003).
    Article CAS Google Scholar
  5. Wang, T. et al. Evidence for bidentate substrate binding as the basis for the K48 linkage specificity of otubain 1. J. Mol. Biol. 386, 1011–1023 (2009).
    Article CAS Google Scholar
  6. Soares, L. et al. Two isoforms of otubain 1 regulate T cell anergy via GRAIL. Nat. Immunol. 5, 45–54 (2004).
    Article CAS Google Scholar
  7. 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 Google Scholar
  8. Sun, X.X., Challagundla, K.B. & Dai, M.S. Positive regulation of p53 stability and activity by the deubiquitinating enzyme Otubain 1. EMBO J. 31, 576–592 (2012).
    Article CAS Google Scholar
  9. Goncharov, T. et al. OTUB1 modulates c-IAP1 stability to regulate signalling pathways. EMBO J. 32, 1103–1114 (2013).
    Article CAS Google Scholar
  10. Nakada, S. et al. Non-canonical inhibition of DNA damage-dependent ubiquitination by OTUB1. Nature 466, 941–946 (2010).
    Article CAS Google Scholar
  11. Sowa, M.E., Bennett, E.J., Gygi, S.P. & Harper, J.W. Defining the human deubiquitinating enzyme interaction landscape. Cell 138, 389–403 (2009).
    Article CAS Google Scholar
  12. Wiener, R., Zhang, X., Wang, T. & Wolberger, C. The mechanism of OTUB1-mediated inhibition of ubiquitination. Nature 483, 618–622 (2012).
    Article CAS Google Scholar
  13. Juang, Y.C. et al. OTUB1 co-opts Lys48-linked ubiquitin recognition to suppress E2 enzyme function. Mol. Cell 45, 384–397 (2012).
    Article CAS Google Scholar
  14. Edelmann, M.J. et al. Structural basis and specificity of human otubain 1-mediated deubiquitination. Biochem. J. 418, 379–390 (2009).
    Article CAS Google Scholar
  15. Jin, J., Li, X., Gygi, S.P. & Harper, J.W. Dual E1 activation systems for ubiquitin differentially regulate E2 enzyme charging. Nature 447, 1135–1138 (2007).
    Article CAS Google Scholar
  16. Haas, A.L. & Bright, P.M. The dynamics of ubiquitin pools within cultured human lung fibroblasts. J. Biol. Chem. 262, 345–351 (1987).
    CAS PubMed Google Scholar
  17. Plechanovová, A. et al. Mechanism of ubiquitylation by dimeric RING ligase RNF4. Nat. Struct. Mol. Biol. 18, 1052–1059 (2011).
    Article Google Scholar
  18. Pruneda, J.N., Stoll, K.E., Bolton, L.J., Brzovic, P.S. & Klevit, R.E. Ubiquitin in motion: structural studies of the ubiquitin-conjugating enzyme approximately ubiquitin conjugate. Biochemistry 50, 1624–1633 (2011).
    Article CAS Google Scholar
  19. Schwanhäusser, B. et al. Global quantification of mammalian gene expression control. Nature 473, 337–342 (2011).
    Article Google Scholar
  20. Ventii, K.H. & Wilkinson, K.D. Protein partners of deubiquitinating enzymes. Biochem. J. 414, 161–175 (2008).
    Article CAS Google Scholar
  21. Wing, S.S. Deubiquitinating enzymes: the importance of driving in reverse along the ubiquitin-proteasome pathway. Int. J. Biochem. Cell Biol. 35, 590–605 (2003).
    Article CAS Google Scholar
  22. Dantuma, N.P., Groothuis, T.A., Salomons, F.A. & Neefjes, J. A dynamic ubiquitin equilibrium couples proteasomal activity to chromatin remodeling. J. Cell Biol. 173, 19–26 (2006).
    Article CAS Google Scholar
  23. Kimura, Y. et al. An inhibitor of a deubiquitinating enzyme regulates ubiquitin homeostasis. Cell 137, 549–559 (2009).
    Article CAS Google Scholar
  24. Stanisić, V., Malovannaya, A., Qin, J., Lonard, D.M. & O'Malley, B.W. OTU domain-containing ubiquitin aldehyde-binding protein 1 (OTUB1) deubiquitinates estrogen receptor (ER) α and affects ERα transcriptional activity. J. Biol. Chem. 284, 16135–16145 (2009).
    Article Google Scholar
  25. Plechanovová, A., Jaffray, E., Tatham, M.H., Naismith, J.H. & Hay, R.T. Structure of a RING E3 ligase and ubiquitin-loaded E2 primed for catalysis. Nature 489, 115–120 (2012).
    Article Google Scholar
  26. Reverter, D. & Lima, C.D. A basis for SUMO protease specificity provided by analysis of human Senp2 and a Senp2-SUMO complex. Structure 12, 1519–1531 (2004).
    Article CAS Google Scholar
  27. Sakata, E. et al. Crystal structure of UbcH5b~ubiquitin intermediate: insight into the formation of the self-assembled E2~Ub conjugates. Structure 18, 138–147 (2010).
    Article CAS Google Scholar
  28. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997).
    Article CAS Google Scholar
  29. McCoy, A.J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007).
    Article CAS Google Scholar
  30. Ozkan, E., Yu, H. & Deisenhofer, J. Mechanistic insight into the allosteric activation of a ubiquitin-conjugating enzyme by RING-type ubiquitin ligases. Proc. Natl. Acad. Sci. USA 102, 18890–18895 (2005).
    Article CAS Google Scholar
  31. Vijay-Kumar, S., Bugg, C.E. & Cook, W.J. Structure of ubiquitin refined at 1.8 A resolution. J. Mol. Biol. 194, 531–544 (1987).
    Article CAS Google Scholar
  32. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004).
    Article Google Scholar
  33. Winn, M.D. et al. Overview of the CCP4 suite and current developments. Acta Crystallogr. D Biol. Crystallogr. 67, 235–242 (2011).
    Article CAS Google Scholar
  34. Winn, M.D., Murshudov, G.N. & Papiz, M.Z. Macromolecular TLS refinement in REFMAC at moderate resolutions. Methods Enzymol. 374, 300–321 (2003).
    Article CAS Google Scholar
  35. Afonine, P.V. et al. Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr. D Biol. Crystallogr. 68, 352–367 (2012).
    Article CAS Google Scholar
  36. Schneider, C.A., Rasband, W.S. & Eliceiri, K.W. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9, 671–675 (2012).
    Article CAS Google Scholar

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