The SspB adaptor drives structural changes in the AAA+ ClpXP protease during ssrA-tagged substrate delivery

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 120; no. 6; p. e2219044120
• Main Authors: Ghanbarpour, Alireza, Fei, Xue, Baker, Tania A, Davis, Joseph H, Sauer, Robert T
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 07.02.2023
• Subjects: Adapters; Adenosine Triphosphatases - metabolism; ATPases Associated with Diverse Cellular Activities - genetics; ATPases Associated with Diverse Cellular Activities - metabolism; Biodegradation; Biological Sciences; Carrier Proteins - metabolism; Degradation; E coli; Endopeptidase Clp - genetics; Endopeptidase Clp - metabolism; Escherichia coli - genetics; Escherichia coli - metabolism; Escherichia coli Proteins - metabolism; Homeostasis; Organelles; Polypeptides; Protease; Proteins; Substrate Specificity; Substrates; Tethering; TmRNA; Translocation; adaptor-mediated proteolysis; AAA+ proteases; tethering adaptors; cryo-EM structure
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.2219044120

Energy-dependent protein degradation by the AAA+ ClpXP protease helps maintain protein homeostasis in bacteria and eukaryotic organelles of bacterial origin. In  and many other proteobacteria, the SspB adaptor assists ClpXP in degrading ssrA-tagged polypeptides produced as a consequence of tmRNA-mediated ribosome rescue. By tethering these incomplete ssrA-tagged proteins to ClpXP, SspB facilitates their efficient degradation at low substrate concentrations. How this process occurs structurally is unknown. Here, we present a cryo-EM structure of the SspB adaptor bound to a GFP-ssrA substrate and to ClpXP. This structure provides evidence for simultaneous contacts of SspB and ClpX with the ssrA tag within the tethering complex, allowing direct substrate handoff concomitant with the initiation of substrate translocation. Furthermore, our structure reveals that binding of the substrate·adaptor complex induces unexpected conformational changes within the spiral structure of the AAA+ ClpX hexamer and its interaction with the ClpP tetradecamer.