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Nat Commun. 2015 Feb 19;6:6320. doi: 10.1038/ncomms7320.

AAA+ chaperones and acyldepsipeptides activate the ClpP protease via conformational control.

Author information

1
Department of Chemistry and Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany.
2
Institute for Pharmaceutical Biology and Biotechnology, University of Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany.
3
1] Department of Chemistry and Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany [2] Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.
4
AiCuris GmbH &Co. KG, Friedrich-Ebert-Straße 475, 42117 Wuppertal, Germany.
5
1] Department of Chemistry and Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany [2] Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany [3] Institute of Molecular Biology &Biochemistry, Center of Molecular Medicine, Medical University of Graz, 8010 Graz, Austria.

Abstract

The Clp protease complex degrades a multitude of substrates, which are engaged by a AAA+ chaperone such as ClpX and subsequently digested by the dynamic, barrel-shaped ClpP protease. Acyldepsipeptides (ADEPs) are natural product-derived antibiotics that activate ClpP for chaperone-independent protein digestion. Here we show that both protein and small-molecule activators of ClpP allosterically control the ClpP barrel conformation. We dissect the catalytic mechanism with chemical probes and show that ADEP in addition to opening the axial pore directly stimulates ClpP activity through cooperative binding. ClpP activation thus reaches beyond active site accessibility and also involves conformational control of the catalytic residues. Moreover, we demonstrate that substoichiometric amounts of ADEP potently prevent binding of ClpX to ClpP and, at the same time, partially inhibit ClpP through conformational perturbance. Collectively, our results establish the hydrophobic binding pocket as a major conformational regulatory site with implications for both ClpXP proteolysis and ADEP-based anti-bacterial activity.

PMID:
25695750
DOI:
10.1038/ncomms7320
[Indexed for MEDLINE]

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