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Ubiquitin docking at the proteasome through a novel pleckstrin-homology domain interaction


Targeted protein degradation is largely performed by the ubiquitin–proteasome pathway, in which substrate proteins are marked by covalently attached ubiquitin chains that mediate recognition by the proteasome. It is currently unclear how the proteasome recognizes its substrates, as the only established ubiquitin receptor intrinsic to the proteasome is Rpn10/S5a (ref. 1), which is not essential for ubiquitin-mediated protein degradation in budding yeast2. In the accompanying manuscript we report that Rpn13 (refs 3–7), a component of the nine-subunit proteasome base, functions as a ubiquitin receptor8, complementing its known role in docking de-ubiquitinating enzyme Uch37/UCHL5 (refs 4–6) to the proteasome. Here we merge crystallography and NMR data to describe the ubiquitin-binding mechanism of Rpn13. We determine the structure of Rpn13 alone and complexed with ubiquitin. The co-complex reveals a novel ubiquitin-binding mode in which loops rather than secondary structural elements are used to capture ubiquitin. Further support for the role of Rpn13 as a proteasomal ubiquitin receptor is demonstrated by its ability to bind ubiquitin and proteasome subunit Rpn2/S1 simultaneously. Finally, we provide a model structure of Rpn13 complexed to diubiquitin, which provides insights into how Rpn13 as a ubiquitin receptor is coupled to substrate deubiquitination by Uch37.

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Figure 1: Crystal structure of mRpn13 Pru reveals typical pleckstrin-homology fold.
Figure 2: Structure of Rpn13 Pru–ubiquitin complex defines a novel ubiquitin-binding motif.
Figure 3: Preferential binding to the proximal subunit of K48-linked diubiquitin by Rpn13 Pru allows Uch37 access to the distal subunit.
Figure 4: Structural comparison of ubiquitin receptors complexed with ubiquitin.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Coordinates and structure factors of mRpn13 Pru and mRpn13 Pru–ubiquitin have been deposited in Protein Data Bank under accession numbers 2R2Y and 2Z59, respectively.


  1. Deveraux, Q., Ustrell, V., Pickart, C. & Rechsteiner, M. A 26 S protease subunit that binds ubiquitin conjugates. J. Biol. Chem. 269, 7059–7061 (1994)

    CAS  PubMed  Google Scholar 

  2. Fu, H. et al. Multiubiquitin chain binding and protein degradation are mediated by distinct domains within the 26 S proteasome subunit Mcb1. J. Biol. Chem. 273, 1970–1981 (1998)

    Article  CAS  PubMed  Google Scholar 

  3. Jorgensen, J. P. et al. Adrm1, a putative cell adhesion regulating protein, is a novel proteasome-associated factor. J. Mol. Biol. 360, 1043–1052 (2006)

    Article  CAS  PubMed  Google Scholar 

  4. Yao, T. et al. Proteasome recruitment and activation of the Uch37 deubiquitinating enzyme by Adrm1. Nature Cell Biol. 8, 994–1002 (2006)

    Article  CAS  PubMed  Google Scholar 

  5. Hamazaki, J. et al. A novel proteasome interacting protein recruits the deubiquitinating enzyme UCH37 to 26S proteasomes. EMBO J. 25, 4524–4536 (2006)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Qiu, X. B. et al. hRpn13/ADRM1/GP110 is a novel proteasome subunit that binds the deubiquitinating enzyme, UCH37. EMBO J. 25, 5742–5753 (2006)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Verma, R. et al. Proteasomal proteomics: identification of nucleotide-sensitive proteasome-interacting proteins by mass spectrometric analysis of affinity-purified proteasomes. Mol. Biol. Cell 11, 3425–3439 (2000)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Husnjak, K. et al. Proteasome subunit Rpn13 is a novel ubiquitin receptor. Nature 10.1038/nature06926 (this issue) (2008)

  9. Hirano, S. et al. Structural basis of ubiquitin recognition by mammalian Eap45 GLUE domain. Nature Struct. Mol. Biol. 13, 1031–1032 (2006)

    Article  CAS  Google Scholar 

  10. Kang, R. S. et al. Solution structure of a CUE-ubiquitin complex reveals a conserved mode of ubiquitin binding. Cell 113, 621–630 (2003)

    Article  CAS  PubMed  Google Scholar 

  11. Ohno, A. et al. Structure of the UBA domain of Dsk2p in complex with ubiquitin molecular determinants for ubiquitin recognition. Structure 13, 521–532 (2005)

    Article  CAS  PubMed  Google Scholar 

  12. Ito, T. et al. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci. USA 98, 4569–4574 (2001)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  13. Gandhi, T. K. et al. Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nature Genet. 38, 285–293 (2006)

    Article  CAS  PubMed  Google Scholar 

  14. Chau, V. et al. A multiubiquitin chain is confined to specific lysine in a targeted short-lived protein. Science 243, 1576–1583 (1989)

    Article  ADS  CAS  PubMed  Google Scholar 

  15. Finley, D. et al. Inhibition of proteolysis and cell cycle progression in a multiubiquitination-deficient yeast mutant. Mol. Cell. Biol. 14, 5501–5509 (1994)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Lemmon, M. A. Pleckstrin homology domains: not just for phosphoinositides. Biochem. Soc. Trans. 32, 707–711 (2004)

    Article  CAS  PubMed  Google Scholar 

  17. Fisher, R. D. et al. Structure and ubiquitin binding of the ubiquitin-interacting motif. J. Biol. Chem. 278, 28976–28984 (2003)

    Article  CAS  PubMed  Google Scholar 

  18. Swanson, K. A., Kang, R. S., Stamenova, S. D., Hicke, L. & Radhakrishnan, I. Solution structure of Vps27 UIM-ubiquitin complex important for endosomal sorting and receptor downregulation. EMBO J. 22, 4597–4606 (2003)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Wang, Q., Young, P. & Walters, K. J. Structure of S5a bound to monoubiquitin provides a model for polyubiquitin recognition. J. Mol. Biol. 348, 727–739 (2005)

    Article  CAS  PubMed  Google Scholar 

  20. Lee, S. et al. Structural basis for ubiquitin recognition and autoubiquitination by Rabex-5. Nature Struct. Mol. Biol. 13, 264–271 (2006)

    Article  CAS  Google Scholar 

  21. Penengo, L. et al. Crystal structure of the ubiquitin binding domains of rabex-5 reveals two modes of interaction with ubiquitin. Cell 124, 1183–1195 (2006)

    Article  CAS  PubMed  Google Scholar 

  22. Bomar, M. G., Pai, M. T., Tzeng, S. R., Li, S. S. & Zhou, P. Structure of the ubiquitin-binding zinc finger domain of human DNA Y-polymerase η. EMBO Rep. 8, 247–251 (2007)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Alam, S. L. et al. Structural basis for ubiquitin recognition by the human ESCRT-II EAP45 GLUE domain. Nature Struct. Mol. Biol. 13, 1029–1030 (2006)

    Article  CAS  Google Scholar 

  24. Lam, Y. A., DeMartino, G. N., Pickart, C. M. & Cohen, R. E. Specificity of the ubiquitin isopeptidase in the PA700 regulatory complex of 26 S proteasomes. J. Biol. Chem. 272, 28438–28446 (1997)

    Article  CAS  PubMed  Google Scholar 

  25. Lam, Y. A., Xu, W., DeMartino, G. N. & Cohen, R. E. Editing of ubiquitin conjugates by an isopeptidase in the 26S proteasome. Nature 385, 737–740 (1997)

    Article  ADS  CAS  PubMed  Google Scholar 

  26. Hanna, J. et al. Deubiquitinating enzyme Ubp6 functions noncatalytically to delay proteasomal degradation. Cell 127, 99–111 (2006)

    Article  CAS  PubMed  Google Scholar 

  27. Verma, R. et al. Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome. Science 298, 611–615 (2002)

    Article  ADS  CAS  PubMed  Google Scholar 

  28. Yao, T. & Cohen, R. E. A cryptic protease couples deubiquitination and degradation by the proteasome. Nature 419, 403–407 (2002)

    Article  ADS  CAS  PubMed  Google Scholar 

  29. Crosas, B. et al. Ubiquitin chains are remodeled at the proteasome by opposing ubiquitin ligase and deubiquitinating activities. Cell 127, 1401–1413 (2006)

    Article  CAS  PubMed  Google Scholar 

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The help of G. Bourenkov (DESY, BW6, Hamburg, Germany) during synchrotron data collection is gratefully acknowledged. We also thank J. Lary, J. Cole and the National Analytical Ultracentrifugation Facility of the University of Connecticut for performing the sedimentation experiments. NMR data were acquired at the University of Minnesota and the data processed in the Minnesota Supercomputing Institute’s Basic Sciences Computing Laboratory. This work was supported by National Institutes of Health CA097004 (K.W.), GM43601 (D.F.) and GM008700-Chemistry Biology Interface Training Grant (L.R.), Deutsche Forschungsgemeinschaft (DI 931/3-1) and the Cluster of Excellence ‘Macromolecular Complexes’ of the Goethe University Frankfurt (EXC115) to I.D., and Deutsche Forschungsgemeinschaft SFB740/TP B4 (M.G.).

Author Contributions The crystal structure of mRpn13 was solved by P.S. and M.G. (Fig. 1); the complexed structure of mRpn13–ubiquitin (Figs 2a, b and 4), the model structure of mRpn13–diubiquitin (Fig. 3), and NMR studies (Fig. 2d) were conducted by X.C., L.R., N.Z. and K.J.W.; and identification of the interactions, minimal binding domains, protein purification and western blot analysis (Fig. 2c) were performed by K.H. Plasmids were created by K.H. and S.E. I.D., M.G., D.F. and K.J.W. all contributed to design of the experiments and writing the manuscript.

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Correspondence to Ivan Dikic, Kylie J. Walters or Michael Groll.

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The file contains Supplementary Notes with additional references, Supplementary Tables S1-S2 and Supplementary Figures 1-9 with Legends. (PDF 876 kb)

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Schreiner, P., Chen, X., Husnjak, K. et al. Ubiquitin docking at the proteasome through a novel pleckstrin-homology domain interaction. Nature 453, 548–552 (2008).

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