3KTI

Structure of ClpP in complex with ADEP1

Summary for 3KTI

• Entry DOI: 10.2210/pdb3kti/pdb
• Related: 3KTG 3KTH 3KTJ 3KTK
• Related PRD ID: PRD_000503
• Descriptor: ATP-dependent Clp protease proteolytic subunit, Acyldepsipeptide 1, DIMETHYL SULFOXIDE, ... (5 entities in total)
• Functional Keywords: hydrolase, protease, serine protease, stress response, a54556a, enopeptin, depsipeptide, antibiotics, hydrolase-antibiotic complex, hydrolase/antibiotic
• Biological source: Bacillus subtilis; More
• Cellular location: Cytoplasm (By similarity): P80244
• Total number of polymer chains: 14
• Total formula weight: 161087.51

Authors

Lee, B.-G.,Brotz-Oesterhelt, H.,Song, H.K. (deposition date: 2009-11-25, release date: 2010-03-23, Last modification date: 2025-03-26)

Primary citation

Lee, B.-G.,Park, E.Y.,Lee, K.-E.,Jeon, H.,Sung, K.H.,Paulsen, H.,Rubsamen-Schaeff, H.,Brotz-Oesterhelt, H.,Song, H.K.
Structures of ClpP in complex with acyldepsipeptide antibiotics reveal its activation mechanism
Nat.Struct.Mol.Biol., 17:471-478, 2010

PubMed 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.

PubMed: 20305655
DOI: 10.1038/nsmb.1787

Experimental method

X-RAY DIFFRACTION (2 Å)