Acyldepsipeptide Antibiotics Induce the Formation of a Structured Axial Channel in CIpP: A Model for the CIpX/CIpA-Bound State of CIpP

In CIpXP and CIpAP complexes, CIpA and CIpX use the energy of ATP hydrolysis to unfold proteins and translocate them into the self-compartmentalized CIpP protease. CIpP requires the ATPases to degrade folded or unfolded substrates, but binding of acyldepsipeptide antibiotics (ADEPs) to CIpP bypasses this requirement with unfolded proteins. We present the crystal structure of Escherichia coli CIpP bound to ADEP1 and report the structural changes underlying CIpP activation. ADEP1 binds in the hydrophobic groove that serves as the primary docking site for CIpP ATPases. Binding of ADEP1 locks the N-terminal loops of CIpP in a beta-hairpin conformation, generating a stable pore through which extended polypeptides can be threaded. This structure serves as a model for CIpP in the holoenzyme CIpAP and CIpXP complexes and provides critical information to further develop this class of antibiotics.