Abstract
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.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 51 print issues and online access
$199.00 per year
only $3.90 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Deveraux, Q., Ustrell, V., Pickart, C. & Rechsteiner, M. A 26 S protease subunit that binds ubiquitin conjugates. J. Biol. Chem. 269, 7059–7061 (1994)
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)
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)
Yao, T. et al. Proteasome recruitment and activation of the Uch37 deubiquitinating enzyme by Adrm1. Nature Cell Biol. 8, 994–1002 (2006)
Hamazaki, J. et al. A novel proteasome interacting protein recruits the deubiquitinating enzyme UCH37 to 26S proteasomes. EMBO J. 25, 4524–4536 (2006)
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)
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)
Husnjak, K. et al. Proteasome subunit Rpn13 is a novel ubiquitin receptor. Nature 10.1038/nature06926 (this issue) (2008)
Hirano, S. et al. Structural basis of ubiquitin recognition by mammalian Eap45 GLUE domain. Nature Struct. Mol. Biol. 13, 1031–1032 (2006)
Kang, R. S. et al. Solution structure of a CUE-ubiquitin complex reveals a conserved mode of ubiquitin binding. Cell 113, 621–630 (2003)
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)
Ito, T. et al. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci. USA 98, 4569–4574 (2001)
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)
Chau, V. et al. A multiubiquitin chain is confined to specific lysine in a targeted short-lived protein. Science 243, 1576–1583 (1989)
Finley, D. et al. Inhibition of proteolysis and cell cycle progression in a multiubiquitination-deficient yeast mutant. Mol. Cell. Biol. 14, 5501–5509 (1994)
Lemmon, M. A. Pleckstrin homology domains: not just for phosphoinositides. Biochem. Soc. Trans. 32, 707–711 (2004)
Fisher, R. D. et al. Structure and ubiquitin binding of the ubiquitin-interacting motif. J. Biol. Chem. 278, 28976–28984 (2003)
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)
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)
Lee, S. et al. Structural basis for ubiquitin recognition and autoubiquitination by Rabex-5. Nature Struct. Mol. Biol. 13, 264–271 (2006)
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)
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)
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)
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)
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)
Hanna, J. et al. Deubiquitinating enzyme Ubp6 functions noncatalytically to delay proteasomal degradation. Cell 127, 99–111 (2006)
Verma, R. et al. Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome. Science 298, 611–615 (2002)
Yao, T. & Cohen, R. E. A cryptic protease couples deubiquitination and degradation by the proteasome. Nature 419, 403–407 (2002)
Crosas, B. et al. Ubiquitin chains are remodeled at the proteasome by opposing ubiquitin ligase and deubiquitinating activities. Cell 127, 1401–1413 (2006)
Acknowledgements
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.
Author information
Authors and Affiliations
Corresponding authors
Supplementary information
Supplementary information
The file contains Supplementary Notes with additional references, Supplementary Tables S1-S2 and Supplementary Figures 1-9 with Legends. (PDF 876 kb)
Rights and permissions
About this article
Cite this article
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). https://doi.org/10.1038/nature06924
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1038/nature06924
This article is cited by
-
Downregulation of pro-surfactant protein B contributes to the recurrence of early-stage non-small cell lung cancer by activating PGK1-mediated Akt signaling
Experimental Hematology & Oncology (2023)
-
A context-dependent and disordered ubiquitin-binding motif
Cellular and Molecular Life Sciences (2022)
-
Proteomic analysis identifies mechanism(s) of overcoming bortezomib resistance via targeting ubiquitin receptor Rpn13
Leukemia (2021)
-
Structure-guided bifunctional molecules hit a DEUBAD-lacking hRpn13 species upregulated in multiple myeloma
Nature Communications (2021)
-
The ubiquitin–proteasome system in regulation of the skeletal muscle homeostasis and atrophy: from basic science to disorders
The Journal of Physiological Sciences (2020)
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.