An AAA Motor-Driven Mechanical Switch in Rpn11 Controls Deubiquitination at the 26S Proteasome

• Published in: Molecular cell 2017-09, Vol.67 (5), p.799-811.e8
• Main Authors: Worden, Evan J., Dong, Ken C., Martin, Andreas
• Format: Article
• Language: English
• Subjects: 26S proteasome; AAA ATPase; Binding Sites; Crystallography, X-Ray; deubiquitination; DUB; Endopeptidases - chemistry; Endopeptidases - genetics; Endopeptidases - metabolism; energy-dependent protein degradation; mechanochemical coupling; Models, Molecular; Mutation; Proteasome Endopeptidase Complex - chemistry; Proteasome Endopeptidase Complex - genetics; Proteasome Endopeptidase Complex - metabolism; Protein Binding; Protein Conformation; Protein Unfolding; Proteolysis; Rpn11; Saccharomyces cerevisiae - enzymology; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae Proteins - chemistry; Saccharomyces cerevisiae Proteins - genetics; Saccharomyces cerevisiae Proteins - metabolism; Structure-Activity Relationship; ubiquitin; Ubiquitin - chemistry; Ubiquitin - metabolism; Ubiquitination
• ISSN: 1097-2765; 1097-4164
• DOI: 10.1016/j.molcel.2017.07.023

Poly-ubiquitin chains direct protein substrates to the 26S proteasome, where they are removed by the deubiquitinase Rpn11 during ATP-dependent substrate degradation. Rapid deubiquitination is required for efficient degradation but must be restricted to committed substrates that are engaged with the ATPase motor to prevent premature ubiquitin chain removal and substrate escape. Here we reveal the ubiquitin-bound structure of Rpn11 from S. cerevisiae and the mechanisms for mechanochemical coupling of substrate degradation and deubiquitination. Ubiquitin binding induces a conformational switch of Rpn11’s Insert-1 loop from an inactive closed state to an active β hairpin. This switch is rate-limiting for deubiquitination and strongly accelerated by mechanical substrate translocation into the AAA+ motor. Deubiquitination by Rpn11 and ubiquitin unfolding by the ATPases are in direct competition. The AAA+ motor-driven acceleration of Rpn11 is therefore important to ensure that poly-ubiquitin chains are removed only from committed substrates and fast enough to prevent their co-degradation. [Display omitted] •Proteasomal substrate degradation and deubiquitination are mechanochemically coupled•Ubiquitin binding to the proteasomal DUB Rpn11 induces a conformational switch•This switch is rate-limiting for ubiquitin chain removal from a substrate•Substrate translocation by the AAA ATPase motor accelerates the Rpn11 switch Poly-ubiquitin modifications target protein substrates for degradation to the 26S proteasome, where they need to be removed for efficient substrate processing. Worden et al. reveal how degradation and deubiquitination are mechanochemically coupled through a conformational switch in the de-ubiquitinating subunit Rpn11, which is driven by the mechanical pulling of substrate into the proteasomal ATPase motor.