Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

The central unit within the 19S regulatory particle of the proteasome

Nature Structural & Molecular Biology volume 15, pages 573–580 (2008)Cite this article

Abstract

The 26S proteasome is a multisubunit enzyme composed of a cylindrical catalytic core (20S) and a regulatory particle (19S) that together perform the essential degradation of cellular proteins tagged by ubiquitin. To date, however, substrate trajectory within the complex remains elusive. Here we describe a previously unknown functional unit within the 19S, comprising two subunits, Rpn1 and Rpn2. These toroids physically link the site of substrate recruitment with the site of proteolysis. Rpn2 interfaces with the 20S, whereas Rpn1 sits atop Rpn2, serving as a docking site for a substrate-recruitment factor. The 19S ATPases encircle the Rpn1-Rpn2 stack, covering the remainder of the 20S surface. Both Rpn1-Rpn2 and the ATPases are required for substrate translocation and gating of the proteolytic channel. Similar pairing of units is found in unfoldases and nuclear transporters, exposing common features of these protein nanomachines.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Toroidal shape of Rpn1 and Rpn2 monomers.
Figure 2: Rpn1 and Rpn2 assemble as a unit onto the α-ring of the 20S CP.
Figure 3: Rpn1-Rpn2 stack extends the 20S proteolytic channel.
Figure 4: Raw AFM topograph of a 20S + Rpn2 + Rpn1 mixture in solution.
Figure 5: Rpn1-Rpn2 unit (labeled Rpn1-2) influences traffic through the proteolytic channel.
Figure 6: Two functional units within the base.
Figure 7: Rpn1-Rpn2 recruits ubiquitin-like domains to the epicenter of the base.
Figure 8: A model for how Rpn1-Rpn2 mediates substrate reception and translocation through the proteasome.

Similar content being viewed by others

References

  1. Maupin-Furlow, J.A. et al. Proteasomes from structure to function: perspectives from Archaea. Curr. Top. Dev. Biol. 75, 125–169 (2006).

    Article  CAS  Google Scholar 

  2. Baker, T.A. & Sauer, R.T. ATP-dependent proteases of bacteria: recognition logic and operating principles. Trends Biochem. Sci. 31, 647–653 (2006).

    Article  CAS  Google Scholar 

  3. Voges, D., Zwickl, P. & Baumeister, W. The 26S proteasome: a molecular machine designed for controlled proteolysis. Annu. Rev. Biochem. 68, 1015–1068 (1999).

    Article  CAS  Google Scholar 

  4. Zwickl, P., Baumeister, W. & Steven, A. Dis-assembly lines: the proteasome and related ATPase-assisted proteases. Curr. Opin. Struct. Biol. 10, 242–250 (2000).

    Article  CAS  Google Scholar 

  5. Glickman, M.H. & Ciechanover, A. The ubiquitin-proteasome proteolytic pathway: destruction for the sake of construction. Physiol. Rev. 82, 373–428 (2002).

    Article  CAS  Google Scholar 

  6. Pickart, C.M. & Cohen, R.E. Proteasomes and their kin: proteases in the machine age. Nat. Rev. Mol. Cell Biol. 5, 177–187 (2004).

    Article  CAS  Google Scholar 

  7. Schmidt, M., Hanna, J., Elsasser, S. & Finley, D. Proteasome-associated proteins: regulation of a proteolytic machine. Biol. Chem. 386, 725–737 (2005).

    Article  CAS  Google Scholar 

  8. Groll, M. et al. Structure of 20S proteasome from yeast at a 2.4 resolution. Nature 386, 463–471 (1997).

    Article  CAS  Google Scholar 

  9. Groll, M. et al. A gated channel into the core particle of the proteasome. Nat. Struct. Biol. 7, 1062–1067 (2000).

    Article  CAS  Google Scholar 

  10. Bajorek, M., Finley, D. & Glickman, M.H. Proteasome disassembly and downregulation is correlated with viability during stationary phase. Curr. Biol. 13, 1140–1144 (2003).

    Article  CAS  Google Scholar 

  11. Osmulski, P.A. & Gaczynska, M. Nanoenzymology of the 20S proteasome: proteasomal actions are controlled by the allosteric transition. Biochemistry 41, 7047–7053 (2002).

    Article  CAS  Google Scholar 

  12. Forster, A., Masters, E.I., Whitby, F.G., Robinson, H. & Hill, C.P. The 1.9 structure of a proteasome-11S activator complex and implications for proteasome-PAN/PA700 interactions. Mol. Cell 18, 589–599 (2005).

    Article  Google Scholar 

  13. Rechsteiner, M. & Hill, C.P. Mobilizing the proteolytic machine: cell biological roles of proteasome activators and inhibitors. Trends Cell Biol. 15, 27–33 (2005).

    Article  CAS  Google Scholar 

  14. Smith, D.M., Benaroudj, N. & Goldberg, A. Proteasomes and their associated ATPases: a destructive combination. J. Struct. Biol. 156, 72–83 (2006).

    Article  CAS  Google Scholar 

  15. Glickman, M.H. et al. A subcomplex of the proteasome regulatory particle required for ubiquitin-conjugate degradation and related to the COP9/Signalosome and eIF3. Cell 94, 615–623 (1998).

    Article  CAS  Google Scholar 

  16. Liu, C.-W. ATP binding and ATP hydrolysis play distinct roles in the function of 26S proteasome. Mol. Cell 24, 39–50 (2006).

    Article  CAS  Google Scholar 

  17. Köhler, A. et al. The axial channel of the proteasome core particle is gated by the Rpt2 ATPase and controls both substrate entry and product release. Mol. Cell 7, 1143–1152 (2001).

    Article  Google Scholar 

  18. Smith, D.M. et al. Docking of the proteasomal ATPases' carboxyl termini in the 20S proteasome's α ring opens the gate for substrate entry. Mol. Cell 27, 731–744 (2007).

    Article  CAS  Google Scholar 

  19. Kajava, A.V., Gorbea, C., Ortega, J., Rechsteiner, M. & Steven, A.C. New HEAT-like repeat motifs in proteins regulating proteasome structure and function. J. Struct. Biol. 146, 425–430 (2004).

    Article  CAS  Google Scholar 

  20. Kajava, A.V. What curves α-solenoids? Evidence for an α-helical toroid structure of Rpn1 and Rpn2 proteins of the 26S proteasome. J. Biol. Chem. 277, 49791–49798 (2002).

    Article  CAS  Google Scholar 

  21. Ortega, J. et al. The axial channel of the 20 S proteasome opens upon binding of the PA200 activator. J. Mol. Biol. 346, 1221–1227 (2005).

    Article  CAS  Google Scholar 

  22. Chen, X., Barton, L.F., Chi, Y., Clurman, B.E. & Roberts, J.M. Ubiquitin-independent degradation of cell-cycle inhibitors by the REGγ proteasome. Mol. Cell 26, 843–852 (2007).

    Article  CAS  Google Scholar 

  23. Dorn, I.T., Eschrich, R., Seemuller, E., Guckenberger, R. & Tampe, R. High-resolution AFM-imaging and mechanistic analysis of the 20S proteasome. J. Mol. Biol. 288, 1027–1036 (1999).

    Article  CAS  Google Scholar 

  24. Thess, A. et al. Specific orientation and two-dimensional crystallization of the proteasome at metal-chelating lipid interfaces. J. Biol. Chem. 277, 36321–36328 (2002).

    Article  CAS  Google Scholar 

  25. Glickman, M.H., Rubin, D.M., Fried, V.A. & Finley, D. The regulatory particle of the S. cerevisiae proteasome. Mol. Cell. Biol. 18, 3149–3162 (1998).

    Article  CAS  Google Scholar 

  26. Rubin, D.M., Glickman, M.H., Larsen, C.N., Dhruvakumar, S. & Finley, D. Active site mutants in the six regulatory particle ATPases reveal multiple roles for ATP in the proteasome. EMBO J. 17, 4909–4919 (1998).

    Article  CAS  Google Scholar 

  27. Marques, A.J., Glanemann, C., Ramos, P.C. & Dohmen, R.J. The C-terminal extension of the β7 subunit and activator complexes stabilize nascent 20S proteasomes and promote their maturation. J. Biol. Chem. 282, 34869–34876 (2007).

    Article  CAS  Google Scholar 

  28. Isono, E. et al. The assembly pathway of the 19S regulatory particle of the yeast 26S proteasome. Mol. Biol. Cell 18, 569–580 (2007).

    Article  CAS  Google Scholar 

  29. Nickell, S. et al. Structural analysis of the 26S proteasome by cryoelectron tomography. Biochem. Biophys. Res. Commun. 353, 115–120 (2007).

    Article  CAS  Google Scholar 

  30. Kurucz, E. et al. Assembly of the Drosophila 26 S proteasome is accompanied by extensive subunit rearrangements. Biochem. J. 365, 527–536 (2002).

    Article  CAS  Google Scholar 

  31. Walz, J. et al. 26S proteasome structure revealed by three-dimensional electron microscopy. J. Struct. Biol. 121, 19–29 (1998).

    Article  CAS  Google Scholar 

  32. Iwanczyk, J. et al. Structure of the Blm10–20S proteasome complex by cryo-electron microscopy. Insights into the mechanism of activation of mature yeast proteasomes. J. Mol. Biol. 363, 648–659 (2006).

    Article  CAS  Google Scholar 

  33. Strickland, E., Hakala, K., Thomas, P.J. & DeMartino, G.N. Recognition of misfolding proteins by PA700, the regulatory subcomplex of the 26S proteasome. J. Biol. Chem. 275, 5565–5572 (2000).

    Article  CAS  Google Scholar 

  34. Braun, B.C. et al. The base of the proteasome regulatory particle exhibits chaperone-like activity. Nat. Cell Biol. 1, 221–226 (1999).

    Article  CAS  Google Scholar 

  35. Navon, A. & Goldberg, A.L. Proteins are unfolded on the surface of the ATPase ring before transport into the proteasome. Mol. Cell 8, 1339–1349 (2001).

    Article  CAS  Google Scholar 

  36. Elsasser, S. et al. Proteasome subunit Rpn1 binds ubiquitin-like protein domains. Nat. Cell Biol. 4, 725–730 (2002).

    Article  CAS  Google Scholar 

  37. Seeger, M. et al. Interaction of the anaphase-promoting complex/cyclosome and proteasome protein complexes with multiubiquitin chain-binding proteins. J. Biol. Chem. 278, 16791–16796 (2003).

    Article  CAS  Google Scholar 

  38. Saeki, Y., Sone, T., Toh-e, A. & Yokosawa, H. Identification of ubiquitin-like protein-binding subunits of the 26S proteasome. Biochem. Biophys. Res. Commun. 296, 813–819 (2002).

    Article  CAS  Google Scholar 

  39. Chen, L. & Madura, K. Rad23 promotes the targeting of proteolytic substrates to the proteasome. Mol. Cell. Biol. 22, 4902–4913 (2002).

    Article  CAS  Google Scholar 

  40. Lee, S., Choi, J.-M. & Tsai, F.T.F. Visualizing the ATPase cycle in a protein disaggregating machine: structural basis for substrate binding by ClpB. Mol. Cell 25, 261–271 (2007).

    Article  CAS  Google Scholar 

  41. Lum, R., Tkach, J.M., Vierling, E. & Glover, J.R. Evidence for an unfolding/threading mechanism for protein disaggregation by Saccharomyces cerevisiae Hsp104. J. Biol. Chem. 279, 29139–29146 (2004).

    Article  CAS  Google Scholar 

  42. Thibault, G., Tsitrin, Y., Davidson, T., Gribun, A. & Houry, W.A. Large nucleotide-dependent movement of the N-terminal domain of the ClpX chaperone. EMBO J. 25, 3367–3376 (2006).

    Article  CAS  Google Scholar 

  43. Martin, A., Baker, T.A. & Sauer, R.T. Distinct static and dynamic interactions control ATPase-peptidase communication in a AAA+ protease. Mol. Cell 27, 41–52 (2007).

    Article  CAS  Google Scholar 

  44. Zolkiewski, M. A camel passes through the eye of a needle: protein unfolding activity of Clp ATPases. Mol. Microbiol. 61, 1094–1100 (2006).

    Article  CAS  Google Scholar 

  45. Wang, J. et al. Nucleotide-dependent conformational changes in a protease-associated ATPase HslU. Structure 9, 1107–1116 (2001).

    Article  CAS  Google Scholar 

  46. Thirumalai, D. & Lorimer, G.H. Chaperonin-mediated protein folding. Annu. Rev. Biophys. Biomol. Struct. 30, 245–269 (2001).

    Article  CAS  Google Scholar 

  47. Horwich, A.L., Weber-Ban, E.U. & Finley, D. Chaperone rings in protein folding and degradation. Proc. Natl. Acad. Sci. USA 96, 11033–11040 (1999).

    Article  CAS  Google Scholar 

  48. Conti, E., Muller, C.W. & Stewart, M. Karyopherin flexibility in nucleocytoplasmic transport. Curr. Opin. Struct. Biol. 16, 237–244 (2006).

    Article  CAS  Google Scholar 

  49. Petosa, C. et al. Architecture of CRM1/Exportin1 suggests how cooperativity is achieved during formation of a nuclear export complex. Mol. Cell 16, 761–775 (2004).

    Article  CAS  Google Scholar 

  50. Osmulski, P.A. & Gaczynska, M. Atomic force microscopy of the proteasome. Methods Enzymol. 398, 414–425 (2005).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank D. Cassel, O. Kleifeld and T. Rosenzweig for comments and critically reading the manuscript. A. Kajava is acknowledged for advice. N. Reis provided technical assistance. We thank D. Fass for assisting with AUC runs and analysis. We thank Y. Matiuhin (Technion) for Rad23 constructs. This work was funded by grants from the Israel Academy of Science/Israel Science Foundation (ISF), The USA-Israel Binational Science Foundation (BSF) and the Malat Family Foundation (via the Technion VP for research) to M.H.G., the NIH R01 grant (M.G.), and the Enhancement Research Grant and San Antonio Cancer Institute (SACI) support for P.A.O. R.R. was partially supported by an anonymous scholarship award (via the Technion Graduate School).

Author information

Authors and Affiliations

  1. Department of Biology, Technion–Israel Institute of Technology, Haifa, 32000, Israel

    Rina Rosenzweig & Michael H Glickman

  2. Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 15355 Lambda Drive, San Antonio, 78245, Texas, USA

    Pawel A Osmulski & Maria Gaczynska

Authors
  1. Rina Rosenzweig
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Pawel A Osmulski
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Maria Gaczynska
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Michael H Glickman
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

R.R. performed biochemical experiments. M.G. and P.A.O. carried out AFM imaging. M.G. and M.H.G. designed and supervised experiments. All authors discussed the results and participated in writing the manuscript.

Corresponding authors

Correspondence to Maria Gaczynska or Michael H Glickman.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–7 and Supplementary Methods (PDF 2832 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Rosenzweig, R., Osmulski, P., Gaczynska, M. et al. The central unit within the 19S regulatory particle of the proteasome. Nat Struct Mol Biol 15, 573–580 (2008). https://doi.org/10.1038/nsmb.1427

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsmb.1427

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing