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Structural basis of substrate recognition and specificity in the N-end rule pathway

Abstract

The N-end rule links the half-life of a protein to the identity of its N-terminal residue. Destabilizing N-terminal residues are recognized by E3 ubiquitin ligases, termed N-recognins. A conserved structural domain called the UBR box is responsible for their specificity. Here we report the crystal structures of the UBR boxes of the human N-recognins UBR1 and UBR2, alone and in complex with an N-end rule peptide, Arg-Ile-Phe-Ser. These structures show that the UBR box adopts a previously undescribed fold stabilized through the binding of three zinc ions to form a binding pocket for type 1 N-degrons. NMR experiments reveal a preference for N-terminal arginine. Peptide binding is abrogated by N-terminal acetylation of the peptide or loss of the positive charge of the N-terminal residue. These results rationalize and refine the empirical rules for the classification of type 1 N-degrons. We also confirm that a missense mutation in UBR1 that is responsible for Johanson-Blizzard syndrome leads to UBR box unfolding and loss of function.

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Figure 1: Global fold of the UBR boxes from UBR1 and UBR2.
Figure 2: Structure of the UBR box–N-degron complex.
Figure 3: UBR box binding of type 1 N-degrons.

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Acknowledgements

We thank J.-F. Trempe and M. Ménade for technical assistance and helpful discussions. E.M.C. is funded by the Canadian Institutes of Health Research (CIHR) and McGill University. Data acquisition at the Macromolecular Diffraction (MacCHESS) facility at the Cornell High Energy Synchrotron Source (CHESS) was supported by US National Science Foundation award DMR 0225180 and US National Institutes of Health award RR-01646. This study was funded by CIHR grant MOP-14219.

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Correspondence to Kalle Gehring.

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Matta-Camacho, E., Kozlov, G., Li, F. et al. Structural basis of substrate recognition and specificity in the N-end rule pathway. Nat Struct Mol Biol 17, 1182–1187 (2010). https://doi.org/10.1038/nsmb.1894

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