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Lys11-linked ubiquitin chains adopt compact conformations and are preferentially hydrolyzed by the deubiquitinase Cezanne

Nature Structural & Molecular Biology volume 17, pages 939947 (2010) | Download Citation

Abstract

Ubiquitin is a versatile cellular signaling molecule that can form polymers of eight different linkages, and individual linkage types have been associated with distinct cellular functions. Though little is currently known about Lys11-linked ubiquitin chains, recent data indicate that they may be as abundant as Lys48 linkages and may be involved in vital cellular processes. Here we report the generation of Lys11-linked polyubiquitin in vitro, for which the Lys11-specific E2 enzyme UBE2S was fused to a ubiquitin binding domain. Crystallographic and NMR analyses of Lys11-linked diubiquitin reveal that Lys11-linked chains adopt compact conformations in which Ile44 is solvent exposed. Furthermore, we identify the OTU family deubiquitinase Cezanne as the first deubiquitinase with Lys11-linkage preference. Our data highlight the intrinsic specificity of the ubiquitin system that extends to Lys11-linked chains and emphasize that differentially linked polyubiquitin chains must be regarded as independent post-translational modifications.

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Acknowledgements

We would like to thank E. Stephens, S. Peak-Chew and F. Begum for MS analysis, M. Allen for help with isotope labeling, T. Nicholson (ENZO LifeSciences) for providing ubiquitin mutants, P. Cohen (Univ. of Dundee), S. Urbe, M. Clague (Univ. of Liverpool), K.D. Wilkinson (Emory Univ.), S. Todi (Univ. Of Michigan) and B. Kessler (Oxford Univ.) for constructs, T. Tenno (Kobe Univ.) and M. Shirakawa (Kyoto Univ.) for kindly providing NMR data for Lys48- and Lys63-linked diubiquitin and members of the Komander lab, especially Y. Kulathu, Y. Ye, M. Akutsu, S. Virdee and A. Eslambolchi for providing reagents and many discussions. A.B. is a MRC Career Development Fellow.

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  1. Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.

    • Anja Bremm
    • , Stefan M V Freund
    •  & David Komander

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Contributions

A.B. designed, performed and analyzed all experiments; S.M.V.F. performed solution measurements and analyzed the data; D.K. designed research, analyzed the data and wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to David Komander.

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https://doi.org/10.1038/nsmb.1873

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