Structures of ClpP in complex with acyldepsipeptide antibiotics reveal its activation mechanism

Abstract

Clp-family proteins are prototypes for studying the mechanism of ATP-dependent proteases because the proteolytic activity of the ClpP core is tightly regulated by activating Clp-ATPases. Nonetheless, the proteolytic activation mechanism has remained elusive because of the lack of a complex structure. Acyldepsipeptides (ADEPs), a recently discovered class of antibiotics, activate and disregulate ClpP. Here we have elucidated the structural changes underlying the ClpP activation process by ADEPs. We present the structures of Bacillus subtilis ClpP alone and in complex with ADEP1 and ADEP2. The structures show the closed-to-open-gate transition of the ClpP N-terminal segments upon activation as well as conformational changes restricted to the upper portion of ClpP. The direction of the conformational movement and the hydrophobic clustering that stabilizes the closed structure are markedly different from those of other ATP-dependent proteases, providing unprecedented insights into the activation of ClpP.

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Figure 1: Structure of the BsClpP–ADEP1 complex and model of the ClpX hexamer.
Figure 2: Entrance pore of BsClpP.
Figure 3: Superposition of free and ADEP1-complexed BsClpP structures.
Figure 4: Interaction between ClpP and ADEPs.
Figure 5: Biochemical results with BsClpP mutants.
Figure 6: Proposed model for ClpP activation.

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Acknowledgements

We thank the staff at 4A beamline, Pohang Accelerator Laboratory, Korea and NW12 beamline, Photon Factory, Japan for help with data collection, B. Hinzen and S. Raddatz (Bayer HealthCare) for the synthesis of ADEPs, M.J. Eck (Dana Farber Cancer Institute) for critical comments on the manuscript and the Advanced Analysis Center in Korea Institute of Science and Technology for providing a transmission electron microscope. This work was supported by the 21C Frontier Functional Proteomics Project (FPR08B2-270), a Korea Research Foundation Grant (KRF-2007-314-C00176), the World Class University project (R33-10108) and the Plant Signaling Network Research Center. This work was also supported by a Korea Institute of Science and Technology Institutional Grant, by the Systems Biology Infrastructure Establishment Grant provided by Gwangju Institute of Science & Technology to H.J. and by a grant of the Deutsche Forschungsgemeinschaft (FOR854) to H.B.-O. B.-G.L. was supported by a Seoul Science Fellowship and a Korean Student Aid Foundation Science Graduate Research Scholarship.

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B.-G.L. and H.K.S. performed X-ray studies; K.-E.L. and H.J. performed electron microscopy studies; B.-G.L. and E.Y.P. performed biochemical studies; K.H.S., H.P. and H.R.-S. performed additional experiments; B.-G.L., H.B.-O. and H.K.S. analyzed data and wrote the manuscript.

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Correspondence to Hyun Kyu Song.

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Lee, BG., Park, E., Lee, KE. et al. Structures of ClpP in complex with acyldepsipeptide antibiotics reveal its activation mechanism. Nat Struct Mol Biol 17, 471–478 (2010). https://doi.org/10.1038/nsmb.1787

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