Crossref journal-article
Proceedings of the National Academy of Sciences
Proceedings of the National Academy of Sciences (341)
Abstract

Significance In eukaryotic cells the 26S proteasome is responsible for the regulated degradation of intracellular proteins. The function of this large macromolecular machine is regulated by many cofactors, most notably the deubiquitylating enzyme ubiquitin C-terminal hydrolase 6 (Ubp6). Here, we investigate the structure of Ubp6 bound to the 26S proteasome and explore its influence on the conformational landscape of the 26S proteasome. Our structure reveals that Ubp6’s active site may contribute to a large composite active site, also formed by the mouth of the proteasomal ATPase ring and the active site of deubiquitylating enzyme regulatory particle non-ATPase 11. Moreover, Ubp6 modulates the conformational landscape of the proteasome, favoring an intermediate state, which may explain the effects of Ubp6 on proteasomal degradation.

Bibliography

Aufderheide, A., Beck, F., Stengel, F., Hartwig, M., Schweitzer, A., Pfeifer, G., Goldberg, A. L., Sakata, E., Baumeister, W., & Förster, F. (2015). Structural characterization of the interaction of Ubp6 with the 26S proteasome. Proceedings of the National Academy of Sciences, 112(28), 8626–8631.

Authors 10
  1. Antje Aufderheide (first)
  2. Florian Beck (additional)
  3. Florian Stengel (additional)
  4. Michaela Hartwig (additional)
  5. Andreas Schweitzer (additional)
  6. Günter Pfeifer (additional)
  7. Alfred L. Goldberg (additional)
  8. Eri Sakata (additional)
  9. Wolfgang Baumeister (additional)
  10. Friedrich Förster (additional)
References 40 Referenced 104
  1. A Hershko, A Ciechanover, The ubiquitin system. Annu Rev Biochem 67, 425–479 (1998). (10.1146/annurev.biochem.67.1.425) / Annu Rev Biochem / The ubiquitin system by Hershko A (1998)
  2. D Voges, P Zwickl, W Baumeister, The 26S proteasome: A molecular machine designed for controlled proteolysis. Annu Rev Biochem 68, 1015–1068 (1999). (10.1146/annurev.biochem.68.1.1015) / Annu Rev Biochem / The 26S proteasome: A molecular machine designed for controlled proteolysis by Voges D (1999)
  3. F Förster, P Unverdorben, P Sledź, W Baumeister, Unveiling the long-held secrets of the 26S proteasome. Structure 21, 1551–1562 (2013). (10.1016/j.str.2013.08.010) / Structure / Unveiling the long-held secrets of the 26S proteasome by Förster F (2013)
  4. J Löwe, , Crystal structure of the 20S proteasome from the archaeon T. acidophilum at 3.4 A resolution. Science 268, 533–539 (1995). (10.1126/science.7725097) / Science / Crystal structure of the 20S proteasome from the archaeon T. acidophilum at 3.4 A resolution by Löwe J (1995)
  5. M Groll, , Structure of 20S proteasome from yeast at 2.4 A resolution. Nature 386, 463–471 (1997). (10.1038/386463a0) / Nature / Structure of 20S proteasome from yeast at 2.4 A resolution by Groll M (1997)
  6. F Beck, , Near-atomic resolution structural model of the yeast 26S proteasome. Proc Natl Acad Sci USA 109, 14870–14875 (2012). (10.1073/pnas.1213333109) / Proc Natl Acad Sci USA / Near-atomic resolution structural model of the yeast 26S proteasome by Beck F (2012)
  7. GC Lander, , Complete subunit architecture of the proteasome regulatory particle. Nature 482, 186–191 (2012). (10.1038/nature10774) / Nature / Complete subunit architecture of the proteasome regulatory particle by Lander GC (2012)
  8. S Nickell, , Insights into the molecular architecture of the 26S proteasome. Proc Natl Acad Sci USA 106, 11943–11947 (2009). (10.1073/pnas.0905081106) / Proc Natl Acad Sci USA / Insights into the molecular architecture of the 26S proteasome by Nickell S (2009)
  9. S Bohn, , Structure of the 26S proteasome from Schizosaccharomyces pombe at subnanometer resolution. Proc Natl Acad Sci USA 107, 20992–20997 (2010). (10.1073/pnas.1015530107) / Proc Natl Acad Sci USA / Structure of the 26S proteasome from Schizosaccharomyces pombe at subnanometer resolution by Bohn S (2010)
  10. R Verma, , Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome. Science 298, 611–615 (2002). (10.1126/science.1075898) / Science / Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome by Verma R (2002)
  11. T Yao, RE Cohen, A cryptic protease couples deubiquitination and degradation by the proteasome. Nature 419, 403–407 (2002). (10.1038/nature01071) / Nature / A cryptic protease couples deubiquitination and degradation by the proteasome by Yao T (2002)
  12. E Sakata, , Localization of the proteasomal ubiquitin receptors Rpn10 and Rpn13 by electron cryomicroscopy. Proc Natl Acad Sci USA 109, 1479–1484 (2012). (10.1073/pnas.1119394109) / Proc Natl Acad Sci USA / Localization of the proteasomal ubiquitin receptors Rpn10 and Rpn13 by electron cryomicroscopy by Sakata E (2012)
  13. P Unverdorben, , Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome. Proc Natl Acad Sci USA 111, 5544–5549 (2014). (10.1073/pnas.1403409111) / Proc Natl Acad Sci USA / Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome by Unverdorben P (2014)
  14. P Śledź, , Structure of the 26S proteasome with ATP-γS bound provides insights into the mechanism of nucleotide-dependent substrate translocation. Proc Natl Acad Sci USA 110, 7264–7269 (2013). (10.1073/pnas.1305782110) / Proc Natl Acad Sci USA / Structure of the 26S proteasome with ATP-γS bound provides insights into the mechanism of nucleotide-dependent substrate translocation by Śledź P (2013)
  15. ME Matyskiela, GC Lander, A Martin, Conformational switching of the 26S proteasome enables substrate degradation. Nat Struct Mol Biol 20, 781–788 (2013). (10.1038/nsmb.2616) / Nat Struct Mol Biol / Conformational switching of the 26S proteasome enables substrate degradation by Matyskiela ME (2013)
  16. DS Leggett, , Multiple associated proteins regulate proteasome structure and function. Mol Cell 10, 495–507 (2002). (10.1016/S1097-2765(02)00638-X) / Mol Cell / Multiple associated proteins regulate proteasome structure and function by Leggett DS (2002)
  17. R Verma, , Proteasomal proteomics: Identification of nucleotide-sensitive proteasome-interacting proteins by mass spectrometric analysis of affinity-purified proteasomes. Mol Biol Cell 11, 3425–3439 (2000). (10.1091/mbc.11.10.3425) / Mol Biol Cell / Proteasomal proteomics: Identification of nucleotide-sensitive proteasome-interacting proteins by mass spectrometric analysis of affinity-purified proteasomes by Verma R (2000)
  18. X Wang, L Huang, Identifying dynamic interactors of protein complexes by quantitative mass spectrometry. Mol Cell Proteomics 7, 46–57 (2008). (10.1074/mcp.M700261-MCP200) / Mol Cell Proteomics / Identifying dynamic interactors of protein complexes by quantitative mass spectrometry by Wang X (2008)
  19. HC Besche, W Haas, SP Gygi, AL Goldberg, Isolation of mammalian 26S proteasomes and p97/VCP complexes using the ubiquitin-like domain from HHR23B reveals novel proteasome-associated proteins. Biochemistry 48, 2538–2549 (2009). (10.1021/bi802198q) / Biochemistry / Isolation of mammalian 26S proteasomes and p97/VCP complexes using the ubiquitin-like domain from HHR23B reveals novel proteasome-associated proteins by Besche HC (2009)
  20. E Sakata, , The catalytic activity of Ubp6 enhances maturation of the proteasomal regulatory particle. Mol Cell 42, 637–649 (2011). (10.1016/j.molcel.2011.04.021) / Mol Cell / The catalytic activity of Ubp6 enhances maturation of the proteasomal regulatory particle by Sakata E (2011)
  21. S Elsasser, , Proteasome subunit Rpn1 binds ubiquitin-like protein domains. Nat Cell Biol 4, 725–730 (2002). (10.1038/ncb845) / Nat Cell Biol / Proteasome subunit Rpn1 binds ubiquitin-like protein domains by Elsasser S (2002)
  22. R Rosenzweig, V Bronner, D Zhang, D Fushman, MH Glickman, Rpn1 and Rpn2 coordinate ubiquitin processing factors at proteasome. J Biol Chem 287, 14659–14671 (2012). (10.1074/jbc.M111.316323) / J Biol Chem / Rpn1 and Rpn2 coordinate ubiquitin processing factors at proteasome by Rosenzweig R (2012)
  23. A Borodovsky, , A novel active site-directed probe specific for deubiquitylating enzymes reveals proteasome association of USP14. EMBO J 20, 5187–5196 (2001). (10.1093/emboj/20.18.5187) / EMBO J / A novel active site-directed probe specific for deubiquitylating enzymes reveals proteasome association of USP14 by Borodovsky A (2001)
  24. M Hu, , Structure and mechanisms of the proteasome-associated deubiquitinating enzyme USP14. EMBO J 24, 3747–3756 (2005). (10.1038/sj.emboj.7600832) / EMBO J / Structure and mechanisms of the proteasome-associated deubiquitinating enzyme USP14 by Hu M (2005)
  25. J Hanna, , Deubiquitinating enzyme Ubp6 functions noncatalytically to delay proteasomal degradation. Cell 127, 99–111 (2006). (10.1016/j.cell.2006.07.038) / Cell / Deubiquitinating enzyme Ubp6 functions noncatalytically to delay proteasomal degradation by Hanna J (2006)
  26. BH Lee, , Enhancement of proteasome activity by a small-molecule inhibitor of USP14. Nature 467, 179–184 (2010). (10.1038/nature09299) / Nature / Enhancement of proteasome activity by a small-molecule inhibitor of USP14 by Lee BH (2010)
  27. A Peth, HC Besche, AL Goldberg, Ubiquitinated proteins activate the proteasome by binding to Usp14/Ubp6, which causes 20S gate opening. Mol Cell 36, 794–804 (2009). (10.1016/j.molcel.2009.11.015) / Mol Cell / Ubiquitinated proteins activate the proteasome by binding to Usp14/Ubp6, which causes 20S gate opening by Peth A (2009)
  28. A Peth, N Kukushkin, M Bossé, AL Goldberg, Ubiquitinated proteins activate the proteasomal ATPases by binding to Usp14 or Uch37 homologs. J Biol Chem 288, 7781–7790 (2013). (10.1074/jbc.M112.441907) / J Biol Chem / Ubiquitinated proteins activate the proteasomal ATPases by binding to Usp14 or Uch37 homologs by Peth A (2013)
  29. T Walzthoeni, , False discovery rate estimation for cross-linked peptides identified by mass spectrometry. Nat Methods 9, 901–903 (2012). (10.1038/nmeth.2103) / Nat Methods / False discovery rate estimation for cross-linked peptides identified by mass spectrometry by Walzthoeni T (2012)
  30. GR Pathare, , Crystal structure of the proteasomal deubiquitylation module Rpn8-Rpn11. Proc Natl Acad Sci USA 111, 2984–2989 (2014). (10.1073/pnas.1400546111) / Proc Natl Acad Sci USA / Crystal structure of the proteasomal deubiquitylation module Rpn8-Rpn11 by Pathare GR (2014)
  31. EJ Worden, C Padovani, A Martin, Structure of the Rpn11-Rpn8 dimer reveals mechanisms of substrate deubiquitination during proteasomal degradation. Nat Struct Mol Biol 21, 220–227 (2014). (10.1038/nsmb.2771) / Nat Struct Mol Biol / Structure of the Rpn11-Rpn8 dimer reveals mechanisms of substrate deubiquitination during proteasomal degradation by Worden EJ (2014)
  32. B Crosas, , Ubiquitin chains are remodeled at the proteasome by opposing ubiquitin ligase and deubiquitinating activities. Cell 127, 1401–1413 (2006). (10.1016/j.cell.2006.09.051) / Cell / Ubiquitin chains are remodeled at the proteasome by opposing ubiquitin ligase and deubiquitinating activities by Crosas B (2006)
  33. Y Lu, BH Lee, RW King, D Finley, MW Kirschner, Substrate degradation by the proteasome: A single-molecule kinetic analysis. Science 348, 1250834 (2015). (10.1126/science.1250834) / Science / Substrate degradation by the proteasome: A single-molecule kinetic analysis by Lu Y (2015)
  34. DM Smith, H Fraga, C Reis, G Kafri, AL Goldberg, ATP binds to proteasomal ATPases in pairs with distinct functional effects, implying an ordered reaction cycle. Cell 144, 526–538 (2011). (10.1016/j.cell.2011.02.005) / Cell / ATP binds to proteasomal ATPases in pairs with distinct functional effects, implying an ordered reaction cycle by Smith DM (2011)
  35. MJ Lee BH Lee J Hanna RW King D Finley Trimming of ubiquitin chains by proteasome-associated deubiquitinating enzymes. Mol Cell Proteomics 10(5):R110 003871–003875. (2011). (10.1074/mcp.R110.003871)
  36. A Leitner, T Walzthoeni, R Aebersold, Lysine-specific chemical cross-linking of protein complexes and identification of cross-linking sites using LC-MS/MS and the xQuest/xProphet software pipeline. Nat Protoc 9, 120–137 (2014). (10.1038/nprot.2013.168) / Nat Protoc / Lysine-specific chemical cross-linking of protein complexes and identification of cross-linking sites using LC-MS/MS and the xQuest/xProphet software pipeline by Leitner A (2014)
  37. Scheres SH Nunez-Ramirez R Sorzano CO Carazo JM Marabini R (2008) Image processing for electron microscopy single-particle analysis using XMIPP. Nat Protoc 3(6):977–990. (10.1038/nprot.2008.62)
  38. Nickell S et al. (2005) TOM software toolbox: Acquisition and analysis for electron tomography. J Struct Biol 149(3):227–234. (10.1016/j.jsb.2004.10.006)
  39. Hrabe T et al. (2012) PyTom: A python-based toolbox for localization of macromolecules in cryo-electron tomograms and subtomogram analysis. J Struct Biol 178(2):177–188. (10.1016/j.jsb.2011.12.003)
  40. Goddard TD Huang CC Ferrin TE (2007) Visualizing density maps with UCSF Chimera. J Struct Biol 157:281–287. (10.1016/j.jsb.2006.06.010)
Dates
Type When
Created 10 years, 1 month ago (July 1, 2015, 12:42 a.m.)
Deposited 3 years, 2 months ago (June 7, 2022, 8:52 a.m.)
Indexed 2 weeks, 5 days ago (Aug. 2, 2025, 12:55 a.m.)
Issued 10 years, 1 month ago (June 30, 2015)
Published 10 years, 1 month ago (June 30, 2015)
Published Online 10 years, 1 month ago (June 30, 2015)
Published Print 10 years, 1 month ago (July 14, 2015)
Funders 3
  1. Ludwig-Maximilians-Universität München 10.13039/501100005722

    Region: Europe

    gov (Local government)

    Labels3
    1. Ludwig Maximilians University Munich
    2. LMU Munich
    3. LMU
    Awards1
    1. CIPSM
  2. Deutsche Forschungsgemeinschaft 10.13039/501100001659

    Region: Europe

    gov (National government)

    Labels3
    1. German Research Association
    2. German Research Foundation
    3. DFG
    Awards1
    1. SFB-1035
  3. Deutsche Forschungsgemeinschaft 10.13039/501100001659

    Region: Europe

    gov (National government)

    Labels3
    1. German Research Association
    2. German Research Foundation
    3. DFG
    Awards1
    1. SFB-969

@article{Aufderheide_2015, title={Structural characterization of the interaction of Ubp6 with the 26S proteasome}, volume={112}, ISSN={1091-6490}, url={http://dx.doi.org/10.1073/pnas.1510449112}, DOI={10.1073/pnas.1510449112}, number={28}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Aufderheide, Antje and Beck, Florian and Stengel, Florian and Hartwig, Michaela and Schweitzer, Andreas and Pfeifer, Günter and Goldberg, Alfred L. and Sakata, Eri and Baumeister, Wolfgang and Förster, Friedrich}, year={2015}, month=jun, pages={8626–8631} }