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

Byung Gil Lee, Eun Young Park, Kyung Eun Lee, Hyesung Jeon, Kwang Hoon Sung, Holger Paulsen, Helga Rübsamen-Schaeff, Heike Brötz-Oesterhelt, Hyun Kyu Song

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175 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)471-478
Number of pages8
JournalNature Structural and Molecular Biology
Issue number4
Publication statusPublished - 2010 Apr

Bibliographical note

Funding Information:
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.

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology


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