A New Conformation for K48 Ubiquitin Chains Revealed by the hRpn2:Rpn13:K48-Diubiquitin Structure

Rpn13/Adrm1 is recruited to the proteasome by PSMD1/Rpn2, where it serves as a substrate receptor that binds preferentially to K48-linked ubiquitin chains, an established signal for protein proteolysis. Here, we use NMR to solve the structure of hRpn13 Pru:hRpn2 (940-953):K48-diubiquitin. Surprisingly, hRpn2-bound hRpn13 selects a new conformation of K48-diubiquitin that is more extended and unique from previously determined structures. NMR experiments on free K48-diubiquitin demonstrate the presence of the reported ‘closed’ conformation observed by crystallography, but also this more extended state, in which the hRpn13-binding surface is exposed. This new K48-diubiquitin conformation is defined by interactions between L73 from G76-linked (distal) ubiquitin and a Y59-centered surface of K48-linked (proximal) ubiquitin. Furthermore, hRpn13 exchanges between the two ubiquitins within 100 ms, although prefers the proximal ubiquitin due to interactions with the K48 linker region. Altogether, these data lead to a new model of how ubiquitinated substrates interact with the proteasome.

Keywords: Proteasome, ubiquitin signaling, NMR, Rpn13, Rpn2

Suggested Citation: Suggested Citation

Lu, Xiuxiu and Ebelle, Danielle and Matsuo, Hiroshi and Walters, Kylie J., A New Conformation for K48 Ubiquitin Chains Revealed by the hRpn2:Rpn13:K48-Diubiquitin Structure. Available at SSRN: https://ssrn.com/abstract=3508886 or http://dx.doi.org/10.2139/ssrn.3508886

This version of the paper has not been formally peer reviewed.