9JVZ

CryoEM structure of M. tuberculosis ClpP1P2 bound to bortezomib

Summary for 9JVZ

• Entry DOI: 10.2210/pdb9jvz/pdb
• EMDB information: 61847
• Descriptor: ATP-dependent Clp protease proteolytic subunit 1, ATP-dependent Clp protease proteolytic subunit 2, N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE (3 entities in total)
• Functional Keywords: mycobacterium tuberculosis, caseinolytic protease system, activation, hydrolase
• Biological source: Mycobacterium tuberculosis H37Rv; More
• Total number of polymer chains: 14
• Total formula weight: 291073.97

Authors

Zhou, B.,Zhao, H.,Gao, Y.,Chen, W.,Zhang, T.,He, J.,Xiong, X. (deposition date: 2024-10-09, release date: 2025-03-19, Last modification date: 2026-04-08)

Primary citation

Zhou, B.,Gao, Y.,Zhao, H.,Liu, B.,Zhang, H.,Fang, C.,Yuan, H.,Wang, J.,Li, Z.,Zhao, Y.,Huang, X.,Wang, X.,Oliveira, A.S.F.,Spencer, J.,Mulholland, A.J.,Burston, S.G.,Hu, J.,Su, N.,Chen, X.,He, J.,Zhang, T.,Xiong, X.
Structural Insights into Bortezomib-Induced Activation of the Caseinolytic Chaperone-Protease System in Mycobacterium tuberculosis.
Nat Commun, 16:3466-3466, 2025

PubMed Abstract: The caseinolytic protease (Clp) system has recently emerged as a promising anti-tuberculosis target. The anti-cancer drug bortezomib exhibits potent anti-mycobacterial activity and binds to Mycobacterium tuberculosis (Mtb) Clp protease complexes. We determine cryo-EM structures of Mtb ClpP1P2, ClpC1P1P2 and ClpXP1P2 complexes bound to bortezomib in different conformations. Structural and biochemical data indicate that sub-stoichiometric binding by bortezomib to the protease active sites orthosterically activates the MtbClpP1P2 complex. Bortezomib activation of MtbClpP1P2 induces structural changes promoting the recruitment of the chaperone-unfoldases, MtbClpC1 or MtbClpX, facilitating holoenzyme formation. The structures of the MtbClpC1P1P2 holoenzyme indicate that MtbClpC1 motion, induced by ATP rebinding at the MtbClpC1 spiral seam, translocates the substrate. In the MtbClpXP1P2 holoenzyme structure, we identify a specialized substrate channel gating mechanism involving the MtbClpX pore-2 loop and MtbClpP2 N-terminal domains. Our results provide insights into the intricate regulation of the Mtb Clp system and suggest that bortezomib can disrupt this regulation by sub-stoichiometric binding at the Mtb Clp protease sites.

PubMed: 40216758
DOI: 10.1038/s41467-025-58410-4

Experimental method

ELECTRON MICROSCOPY (2.56 Å)