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Structural basis for the recognition of N-end rule substrates by the UBR box of ubiquitin ligases

Nature Structural & Molecular Biology volume 17, pages 1175–1181 (2010)Cite this article

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Abstract

The N-end rule pathway is a regulated proteolytic system that targets proteins containing destabilizing N-terminal residues (N-degrons) for ubiquitination and proteasomal degradation in eukaryotes. The N-degrons of type 1 substrates contain an N-terminal basic residue that is recognized by the UBR box domain of the E3 ubiquitin ligase UBR1. We describe structures of the UBR box of Saccharomyces cerevisiae UBR1 alone and in complex with N-degron peptides, including that of the cohesin subunit Scc1, which is cleaved and targeted for degradation at the metaphase-anaphase transition. The structures reveal a previously unknown protein fold that is stabilized by a novel binuclear zinc center. N-terminal arginine, lysine or histidine side chains of the N-degron are coordinated in a multispecific binding pocket. Unexpectedly, the structures together with our in vitro biochemical and in vivo pulse-chase analyses reveal a previously unknown modulation of binding specificity by the residue at position 2 of the N-degron.

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Figure 1: Structure of the UBR box.
Figure 2: Effect of the residue at position 2 of N-degrons.
Figure 3: Binding affinities of the UBR box to peptides of different residues at position 2.
Figure 4: Details of UBR domain recognition of residues at position 2.
Figure 5: A schematic view of the interactions between the UBR box and the N-degron peptide.

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Acknowledgements

We thank the staff at the 4A and 6B beamlines, Pohang Accelerator Laboratory, Korea, and the NW12 beamline, Photon Factory, Japan, for help with the data collection. We also thank Y.T. Kwon (University of Pittsburgh) for providing us with unpublished data of UBR fragments and A. Varshavsky (California Institute of Technology) for yeast strains and plasmids used for the in vivo study. This work was supported by a Basic Science Research Program through the National Research Foundation of Korea (NRF 2007-0055395), the 21C Frontier Functional Proteomics Project (FPR08B2-270), World-Class University Project (R33-10108), the Plant Signaling Network Research Center and the Korea Healthcare Technology R&D Project, Ministry for Health, Welfare & Family Affairs, Republic of Korea (A092006).

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Authors and Affiliations

  1. School of Life Sciences and Biotechnology, Korea University, Anam-Dong, Korea

    Woo Suk Choi, Byung-Cheon Jeong, Yoo Jin Joo, Myeong-Ryeol Lee, Joon Kim & Hyun Kyu Song

  2. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, USA

    Michael J Eck

  3. Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA

    Michael J Eck

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Contributions

W.S.C., B.-C.J., M.-R.L. and H.K.S. performed structural studies; W.S.C. and B.-C.J. performed biochemical studies; Y.J.J. and J.K. performed in vivo assay; W.S.C., M.J.E. & H.K.S. designed experiments, analyzed data and wrote the manuscript.

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Correspondence to Hyun Kyu Song.

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Choi, W., Jeong, BC., Joo, Y. et al. Structural basis for the recognition of N-end rule substrates by the UBR box of ubiquitin ligases. Nat Struct Mol Biol 17, 1175–1181 (2010). https://doi.org/10.1038/nsmb.1907

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