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Published October 29, 2002 | Published
Journal Article Open

Pairs of dipeptides synergistically activate the binding of substrate by ubiquitin ligase through dissociation of its autoinhibitory domain


Protein degradation by the ubiquitin (Ub) system controls the concentrations of many regulatory proteins. The degradation signals (degrons) of these proteins are recognized by the system's Ub ligases (complexes of E2 and E3 enzymes). Two substrate-binding sites of UBR1, the E3 of the Wend rule pathway in the yeast Saccharomyces cerevisiae, recognize basic (type 1) and bulky hydrophobic (type 2) N-terminal residues of proteins or short peptides. A third substrate-binding site of UBR1 targets CUP9, a transcriptional repressor of the peptide transporter PTR2, through an internal (non-N-terminal) degron of CUP9. Previous work demonstrated that dipeptides with destabilizing N-terminal residues allosterically activate UBR1, leading to accelerated in vivo degradation of CUP9 and the induction of PTR2 expression. Through this positive feedback, S. cerevisiae can sense the presence of extracellular peptides and react by accelerating their uptake. Here, we show that dipeptides with destabilizing N-terminal residues cause dissociation of the C-terminal autoinhibitory domain of UBR1 from its N-terminal region that contains all three substrate-binding sites. This dissociation, which allows the interaction between UBR1 and CUP9, is strongly increased only if both type 1- and type 2-binding sites of UBR1 are occupied by dipeptides. An aspect of autoinhibition characteristic of yeast UBR1 also was observed with mammalian (mouse) UBR1. The discovery of autoinhibition in Ub ligases of the UBR family indicates that this regulatory mechanism may also control the activity of other Ub ligases.

Additional Information

© 2002 by the National Academy of Sciences. Contributed by Alexander Varshavsky, August 29, 2002. Published online before print October 21, 2002, 10.1073/pnas.172527399. We thank S. A. Johnston, S. W. Stevens, and A. Webster for strains and plasmids, S. Horvath and her colleagues for the synthesis of peptides, and G. C. Turner, A. Webster, and M. Ghislain for permission to cite unpublished data. We thank former and current members of the Varshavsky laboratory, particularly G. C. Turner and H. Rao, for discussions and advice, and G. C. Turner for his comments on the manuscript. This work was supported by National Institutes of Health Grants DK39520 and GM31530 (to A.V.). F.N.-G. was supported by postdoctoral fellowships from the Spanish Ministry of Education, the Fulbright Foundation, and the Del Amo-UCM Foundation.

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