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.

  • Letter
  • Published:

Structural basis for the activation of 20S proteasomes by 11S regulators

Nature volume 408, pages 115–120 (2000)Cite this article

Abstract

Most of the non-lysosomal proteolysis that occurs in eukaryotic cells is performed by a nonspecific and abundant barrel-shaped complex called the 20S proteasome1. Substrates access the active sites, which are sequestered in an internal chamber, by traversing a narrow opening2 (α-annulus) that is blocked in the unliganded 20S proteasome by amino-terminal sequences of α-subunits3. Peptide products probably exit the 20S proteasome through the same opening. 11S regulators (also called PA26 (ref. 4), PA28 (ref. 5) and REG6,7) are heptamers4,8,9 that stimulate 20S proteasome peptidase activity in vitro and may facilitate product release in vivo. Here we report the co-crystal structure of yeast 20S proteasome with the 11S regulator from Trypanosoma brucei4 (PA26). PA26 carboxy-terminal tails provide binding affinity by inserting into pockets on the 20S proteasome, and PA26 activation loops induce conformational changes in α-subunits that open the gate separating the proteasome interior from the intracellular environment. The reduction in processivity expected for an open conformation of the exit gate may explain the role of 11S regulators in the production of ligands for major histocompatibility complex class I molecules10,11.

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: Structure of the PA26–proteasome complex.
Figure 2: Structure of PA26.
Figure 3: Conformational change in 20S proteasome α-subunits.
Figure 4: Mechanism of binding.
Figure 5: Mechanism of activation.

Similar content being viewed by others

References

  1. Baumeister, W., Walz, JK., Zuhl, F. & Seemuller, E. The proteasome: paradigm of a self-compartmentalizing protease. Cell 92, 367–380 (1998).

    Article  CAS  Google Scholar 

  2. Wenzel, T. & Baumeister, W. Conformational constraints in protein degradation by the 20S proteasome. Nature Struct. Biol. 2, 199–204 ( 1995).

    Article  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  4. Yao, Y. et al. Structural and functional characterizations of the proteasome-activating protein PA26 from Trypanosoma brucei. J. Biol. Chem. 274, 33921–333930 (1999 ).

    Article  CAS  Google Scholar 

  5. Ma, C.-P., Slaughter, C. A. & DeMartino, G. N. Identification, purification, and characterization of a protein activator (PA28) of the 20S proteasome (macropain). J. Biol. Chem. 267, 10515–10523 (1992).

    CAS  PubMed  Google Scholar 

  6. Dubiel, W., Pratt, G., Ferrell, K. & Rechsteiner, M. Purification of an 11S regulator of the multicatalytic protease. J. Biol. Chem. 267, 22369–22377 ( 1992).

    CAS  PubMed  Google Scholar 

  7. Realini, C. et al. Characterization of recombinant REGα, REGβ and REGγ proteasome activators. J. Biol. Chem. 272 , 25483–25492 (1997).

    Article  CAS  Google Scholar 

  8. Knowlton, J. R. et al. Structure of the proteasome activator REGα (PA28α). Nature 390, 639–643 (1997).

    Article  ADS  CAS  Google Scholar 

  9. Zhang, Z. et al. Proteasome activator 11S REG or PA28: Recombinant REGα/REGβ hetero-oligomers are heptamers. Biochemistry 38, 5651–5658 (1999).

    Article  CAS  Google Scholar 

  10. Groettrup, M. et al. A role for the proteasome regulator PA28α in antigen presentation. Nature 381, 166– 168 (1996).

    Article  ADS  CAS  Google Scholar 

  11. Preckel, T. et al. Impaired immunoproteasome assembly and immune responses in PA28-/- mice. Science 286, 2162–2165 (1999).

    Article  CAS  Google Scholar 

  12. Gray, C. W., Slaughter, C. A. & DeMartino, G. N. PA28 activator protein forms regulatory caps on proteasome stacked rings. J. Mol. Biol. 236, 7– 15 (1994).

    Article  CAS  Google Scholar 

  13. Zhang, Z. et al. Identification of an activation region in the proteasome activator REGα. Proc. Natl Acad. Sci. USA 95, 2807–2811 (1998).

    Article  ADS  CAS  Google Scholar 

  14. Song, X., von Kampen, J., Slaughter, C. A. & DeMartino, G. N. Relative functions of the α and β subunits of the proteasome activator, PA28. J. Biol. Chem. 272, 27994– 28000 (1997).

    Article  CAS  Google Scholar 

  15. Li, J., Gao, X., Joss, L. & Rechsteiner, M. The proteasome activator 11 S REG or PA28: chimeras implicate carboxyl-terminal sequences in oligomerization and proteasome binding but not in the activation of specific proteasome catalytic subunits. J. Mol. Biol. 299, 641–654 (2000).

    Article  CAS  Google Scholar 

  16. Dick, T. P. et al. Coordinated dual cleavages induced by the proteasome regulator PA28 lead to dominant MHC ligands. Cell 86, 253–262 (1996).

    Article  CAS  Google Scholar 

  17. Rechsteiner, M. in Ubiquitin and the Biology of the Cell (eds Peters, J.-M., Harris, J. R. & Finley, D.) 147–189 (Plenum, New York, 1998).

    Book  Google Scholar 

  18. Hendil, K. B., Khan, S. & Tanaka, K. Simultaneous binding of PA28 and PA700 activators to 20S proteasomes. Biochem. J. 332, 749– 754 (1998).

    Article  Google Scholar 

  19. Stern, L. J. & Wiley, D. C. Antigenic peptide binding by class I and class II histocompatibility proteins. Structure 2, 245–251 (1994).

    Article  CAS  Google Scholar 

  20. Gaczynska, M., Goldberg, A. L., Tanaka, K., Hendil, K. B. & Rock, K. L. Proteasome subunits X and Y alter peptidase activities in opposite ways to the interferon-γ-induced subunits LMP2 and LMP7. J. Biol. Chem. 271, 17275–17280 (1996).

    Article  CAS  Google Scholar 

  21. Kisselev, A. F., Akopian, T. N., Woo, K. M. & Goldberg, A. L. The sizes of peptides generated from protein by mammalian 26 and 20S proteasomes. Implications for understanding the degradative mechanism and antigen presentation. J. Biol. Chem. 274, 3363– 3371 (1999).

    Article  CAS  Google Scholar 

  22. Nussbaum, A. K. et al. Cleavage motifs of the yeast 20S proteasome beta subunits deduced from digests of enolase 1. Proc. Natl Acad. Sci. USA 95, 125024–125029 (1998 ).

    Article  Google Scholar 

  23. Craiu, A., Akopian, T., Goldberg, A. & Rock, K. L. Two distinct proteolytic processes in the generation of a major histocompatibility class I-presented peptide. Proc. Natl Acad. Sci. USA 94, 10850–10855 (1997).

    Article  ADS  CAS  Google Scholar 

  24. Rubin, D. M. et al. Identification of the gal4 suppressor Sug1 as a subunit of the yeast 26S proteasome. Nature 379, 655–657 (1996).

    Article  ADS  CAS  Google Scholar 

  25. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 ( 1997).

    Article  CAS  Google Scholar 

  26. Collaborative Computing Project No. 4.. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760–763 ( 1994).

    Article  Google Scholar 

  27. Navaza, J. AMoRe: an automated package for molecular replacement. Acta Crystallogr. A 50, 157–163 ( 1994).

    Article  Google Scholar 

  28. Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119 (1991).

    Article  Google Scholar 

  29. Cowtan, K. & Main, P. Miscellaneous algorithms for density modification. Acta Crystallogr. D 54, 487 –493 (1998).

    Article  CAS  Google Scholar 

  30. Brünger, A. T. X-PLOR Version 3.843, a System for X-ray Crystallography and NMR (Yale Univ., New Haven, Connecticut, 1996).

    Google Scholar 

Download references

Acknowledgements

We thank P. Brown, N.-L. Chan, B. Howard and M. Mathews for assistance with data collection; D. Finley for Saccharomyces cerevisae strain SUB459, K. Alexander for assistance with protein purification; and W. Sundquist and M. Rechesteiner for comments on the manuscript. This work was supported by grants from the NIH and based on research conducted at the Stanford Synchrotron Radiation Laboratory (SSRL), which is funded by the Department of Energy (BES, BER) and the NIH (NCRR, NIGMS). Preliminary structure determination was performed with data collected from small crystals at Beamline X25 of the National Synchrotron Light Source, which is supported by the Office of Basic Energy Research of the US Department of Energy and by the NIH.

Author information

Author notes

  1. Frank G. Whitby, Eugene I. Masters, Yi Yao and Ching C. Wang: These authors contributed euqally to this work

Authors and Affiliations

  1. Biochemistry Department, University of Utah, 50 N Medical Drive, Salt Lake City, 84132, Utah, USA

    Frank G. Whitby, Eugene I. Masters, Larissa Kramer, J. Randolph Knowlton & Christopher P. Hill

  2. Department of Pharmaceutical Chemistry University of California, San Francisco, 94143-0446, California, USA

    Yi Yao & Ching C. Wang

Authors
  1. Frank G. Whitby
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Eugene I. Masters
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Larissa Kramer
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. J. Randolph Knowlton
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yi Yao
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Ching C. Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Christopher P. Hill
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Christopher P. Hill.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Whitby, F., Masters, E., Kramer, L. et al. Structural basis for the activation of 20S proteasomes by 11S regulators . Nature 408, 115–120 (2000). https://doi.org/10.1038/35040607

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/35040607

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

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