title: Acyldepsipeptide antibiotics induce the formation of a structured axial channel in ClpP: A model for the ClpX/ClpA-bound state of ClpP.
abstract: In ClpXP and ClpAP complexes, ClpA and ClpX use the energy of ATP hydrolysis to unfold proteins and translocate them into the self-compartmentalized ClpP protease. ClpP requires the ATPases to degrade folded or unfolded substrates, but binding of acyldepsipeptide antibiotics (ADEPs) to ClpP bypasses this requirement with unfolded proteins. We present the crystal structure of Escherichia coli ClpP bound to ADEP1 and report the structural changes underlying ClpP activation. ADEP1 binds in the hydrophobic groove that serves as the primary docking site for ClpP ATPases. Binding of ADEP1 locks the N-terminal loops of ClpP in a β-hairpin conformation, generating a stable pore through which extended polypeptides can be threaded. This structure serves as a model for ClpP in the holoenzyme ClpAP and ClpXP complexes and provides critical information to further develop this class of antibiotics.
authors.affiliation: Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.
authors.forename: Dominic Him Shun
authors.initials: DH
authors.lastname: Li
authors.forename: Yu Seon
authors.initials: YS
authors.lastname: Chung
authors.forename: Melanie
authors.initials: M
authors.lastname: Gloyd
authors.forename: Ebenezer
authors.initials: E
authors.lastname: Joseph
authors.forename: Rodolfo
authors.initials: R
authors.lastname: Ghirlando
authors.forename: Gerard D
authors.initials: GD
authors.lastname: Wright
authors.forename: Yi-Qiang
authors.initials: YQ
authors.lastname: Cheng
authors.forename: Michael R
authors.initials: MR
authors.lastname: Maurizi
authors.forename: Alba
authors.initials: A
authors.lastname: Guarné
authors.forename: Joaquin
authors.initials: J
authors.lastname: Ortega
mesh_terms: D000074183:ATPases Associated with Diverse Cellular Activities; D000251:Adenosine Triphosphatases / Q000737:chemistry / Q000378:metabolism; D000900:Anti-Bacterial Agents / Q000737:chemistry*; D047630:Depsipeptides / Q000737:chemistry*; D049071:Endopeptidase Clp / Q000737:chemistry* / Q000378:metabolism; D004926:Escherichia coli / Q000201:enzymology; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000378:metabolism; D007700:Kinetics; D008958:Models, Molecular; D018832:Molecular Chaperones / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D013379:Substrate Specificity
chemical_list: D000900:Anti-Bacterial Agents; D047630:Depsipeptides; D029968:Escherichia coli Proteins; D018832:Molecular Chaperones; C483568:ClpA protease, E coli; C483572:ClpP protease, E coli; D049071:Endopeptidase Clp; D000251:Adenosine Triphosphatases; C088072:ClpX protein, E coli; D000074183:ATPases Associated with Diverse Cellular Activities