Structure of the drug target ClpC1 unfoldase in action provides insights on antibiotic mechanism of action

• Published in: The Journal of biological chemistry Vol. 298; no. 11; p. 102553
• Main Authors: Weinhäupl, Katharina, Gragera, Marcos, Bueno-Carrasco, M. Teresa, Arranz, Rocío, Krandor, Olga, Akopian, Tatos, Soares, Raquel, Rubin, Eric, Felix, Jan, Fraga, Hugo
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.11.2022; American Society for Biochemistry and Molecular Biology
• Subjects: Anti-Bacterial Agents - metabolism; Anti-Bacterial Agents - pharmacology; antibiotics; Bacterial Proteins - metabolism; chaperone; cryo-electron microscopy; Humans; Molecular Chaperones - metabolism; Mycobacterium tuberculosis; Mycobacterium tuberculosis - metabolism; protein degradation; Tuberculosis; NPAs; Mycobacterium tuberculosis; chaperone; ArgP; MD; Mtb; antibiotics; protein degradation; TB; cryo-electron microscopy; NTD; PDB
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1016/j.jbc.2022.102553

The unfoldase ClpC1 is one of the most exciting drug targets against tuberculosis. This AAA+ unfoldase works in cooperation with the ClpP1P2 protease and is the target of at least four natural product antibiotics: cyclomarin, ecumicin, lassomycin, and rufomycin. Although these molecules are promising starting points for drug development, their mechanisms of action remain largely unknown. Taking advantage of a middle domain mutant, we determined the first structure of Mycobacterium tuberculosis ClpC1 in its apo, cyclomarin-, and ecumicin-bound states via cryo-EM. The obtained structure displays features observed in other members of the AAA+ family and provides a map for further drug development. While the apo and cyclomarin-bound structures are indistinguishable and have N-terminal domains that are invisible in their respective EM maps, around half of the ecumicin-bound ClpC1 particles display three of their six N-terminal domains in an extended conformation. Our structural observations suggest a mechanism where ecumicin functions by mimicking substrate binding, leading to ATPase activation and changes in protein degradation profile.