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Structural basis for the recognition of K48-linked Ub chain by proteasomal receptor Rpn13

By Zhu Liu, Xu Dong, Hua-Wei Yi, Ju Yang, Zhou Gong, Yi Wang, Kan Liu, Wei-Ping Zhang, Chun Tang

Posted 29 Jan 2019
bioRxiv DOI: 10.1101/533331 (published DOI: 10.1038/s41421-019-0089-7)

The interaction between K48-linked ubiquitin (Ub) chain and Rpn13 is important for proteasomal degradation of ubiquitinated substrate proteins. Only the complex structure between the N-terminal domain of Rpn13 (Rpn13 NTD) and Ub monomer has been characterized, and it remains unclear how Rpn13 specifically recognizes K48-linked Ub chain. Using single-molecule FRET, here we show that K48-linked diubiquitin (K48-diUb) fluctuates among three distinct conformational states, and a preexisting compact state is selectively enriched by Rpn13 NTD. The same binding mode is observed for full-length Rpn13 and longer K48-linked Ub chain. Using solution NMR spectroscopy, we have solved the complex structure between Rpn13 NTD and K48-diUb. In the structure, Rpn13 NTD simultaneously interacts with proximal and distal Ub subunits of K48-diUb that remain associated in the complex, thus corroborating smFRET findings. The proximal Ub interacts with Rpn13 NTD similarly as the Ub monomer in the known Rpn13 NTD:Ub structure, while the distal Ub binds to a largely electrostatic surface of Rpn13 NTD. Thus, a charge reversal mutation in Rpn13 NTD can weaken the interaction between Rpn13 and K48-linked Ub chain, causing accumulation of ubiquitinated proteins. Moreover, blockage of the access of the distal Ub to Rpn13 NTD with a proximity attached Ub monomer can also disrupt the interaction between Rpn13 and K48-diUb. Together, the bivalent interaction of K48-linked Ub chain with Rpn13 provides the structural basis for Rpn13 linkage selectivity, which opens a new window for modulating proteasomal function.

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