Ubiquitin docking at the proteasome through a novel pleckstrin-homology domain interaction

Abstract

The 26S proteasome is a multisubunit complex that selectively degrades ubiquitin conjugated proteins. Two studies show that a known component of the proteasome, Rpn13 functions as a novel ubiquitin binding receptor. Structural studies reveal a novel mode of ubiquitin recognition. Rpn 13 is also a receptor for a deubiquitinating enzyme, suggesting a linkage between ubiquitin chain recognition and disassembly. The 26S proteasome is a multisubunit complex that selectively degrades ubiquitin conjugated proteins. Two studies (this Letter and the Article Dikic doi:10.1038/nature06926) show that a known component of the proteasome, Rpn13, functions as a novel ubiquitin binding receptor, and structural studies reveal a novel mode of ubiquitin recognition. Rpn13 is also a receptor for a deubiquitinating enzyme, suggesting a linkage between ubiquitin chain recognition and disassembly. Targeted protein degradation is largely performed by the ubiquitin–proteasome pathway, in which substrate proteins are marked by covalently attached ubiquitin chains that mediate recognition by the proteasome. It is currently unclear how the proteasome recognizes its substrates, as the only established ubiquitin receptor intrinsic to the proteasome is Rpn10/S5a (ref. 1), which is not essential for ubiquitin-mediated protein degradation in budding yeast2. In the accompanying manuscript we report that Rpn13 (refs 3–7), a component of the nine-subunit proteasome base, functions as a ubiquitin receptor8, complementing its known role in docking de-ubiquitinating enzyme Uch37/UCHL5 (refs 4–6) to the proteasome. Here we merge crystallography and NMR data to describe the ubiquitin-binding mechanism of Rpn13. We determine the structure of Rpn13 alone and complexed with ubiquitin. The co-complex reveals a novel ubiquitin-binding mode in which loops rather than secondary structural elements are used to capture ubiquitin. Further support for the role of Rpn13 as a proteasomal ubiquitin receptor is demonstrated by its ability to bind ubiquitin and proteasome subunit Rpn2/S1 simultaneously. Finally, we provide a model structure of Rpn13 complexed to diubiquitin, which provides insights into how Rpn13 as a ubiquitin receptor is coupled to substrate deubiquitination by Uch37.