Proteasome subunit Rpn13 is a novel ubiquitin receptor

Abstract

Proteasomal receptors that recognize ubiquitin chains attached to substrates are key mediators of selective protein degradation in eukaryotes. Here we report the identification of a new ubiquitin receptor, Rpn13/ARM1, a known component of the proteasome. Rpn13 binds ubiquitin through a conserved amino-terminal region termed the pleckstrin-like receptor for ubiquitin (Pru) domain, which binds K48-linked diubiquitin with an affinity of approximately 90 nM. Like proteasomal ubiquitin receptor Rpn10/S5a, Rpn13 also binds ubiquitin-like (UBL) domains of UBL-ubiquitin-associated (UBA) proteins. In yeast, a synthetic phenotype results when specific mutations of the ubiquitin binding sites of Rpn10 and Rpn13 are combined, indicating functional linkage between these ubiquitin receptors. Because Rpn13 is also the proteasomal receptor for Uch37, a deubiquitinating enzyme, our findings suggest a coupling of chain recognition and disassembly at the proteasome.

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Figure 1: Murine Rpn13 binds ubiquitin chains.
Figure 2: Rpn13 contributes to recognition of ubiquitin conjugates by the proteasome.
Figure 3: Rpn13 uses loops to bind ubiquitin.
Figure 4: Rpn13 binds to ubiquitin and UBLs of proteasomal receptors.
Figure 5: An Rpn13 mutant specifically defective in ubiquitin chain binding.
Figure 6: Phenotypic effects of the loss of ubiquitin receptor function by Rpn13.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

The structures of full-length scRpn13 are deposited in Protein Data Bank under accession number 2Z4D.

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Acknowledgements

We thank members of our laboratories, as well as D. Hoeller, G. Dittmar, J. Lipscomb and M. Schmidt, for discussions, comments and reading of the manuscript. We also thank the University of Minnesota’s NMR facility, Minnesota Supercomputing Institutes’s Basic Sciences Computing Laboratory and E. Arriaga for allowing us to use his spectrofluorometer. We thank G. Zapart for the initial Y2H ubiquitin screening, and M. Groll and P. Schneider for allowing us to use the mRpn13–ubiquitin coordinates to generate Fig. 5c. This work was supported by grants from Deutsche Forschungsgemeinschaft (DI 931/3-1), the Cluster of Excellence ‘Macromolecular Complexes’ of the Goethe University Frankfurt (EXC115) (I.D.) and the National Institutes of Health (CA097004 to K.J.W.; GM043601 to D.F.; GM008700-CBITG to L.R.).

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Correspondence to Kylie J. Walters or Daniel Finley or Ivan Dikic.

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The file contains Supplementary Methods and Supplementary Figures 1-7 with Legends. (PDF 767 kb)

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Husnjak, K., Elsasser, S., Zhang, N. et al. Proteasome subunit Rpn13 is a novel ubiquitin receptor. Nature 453, 481–488 (2008). https://doi.org/10.1038/nature06926

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