9MK5

Crystal structure of Neisseria meningitidis ClpP protease complex with small molecule activator, Dioctatin

This is a non-PDB format compatible entry.

Summary for 9MK5

• Entry DOI: 10.2210/pdb9mk5/pdb
• Descriptor: ATP-dependent Clp protease proteolytic subunit, N-{(3S)-3-[(3S)-3-aminooctanamido]octanoyl}glycine (3 entities in total)
• Functional Keywords: small molecule, inhibitor, activator, metabolite, hydrolase
• Biological source: Neisseria meningitidis
• Total number of polymer chains: 14
• Total formula weight: 345555.77

Authors

Mabanglo, M.F.,Houry, W.A. (deposition date: 2024-12-16, release date: 2025-09-03, Last modification date: 2025-10-15)

Primary citation

Barghash, M.M.,Mabanglo, M.F.,Hoff, S.E.,Brozdnychenko, D.,Wong, K.S.,Binepal, G.,Ip, P.,Shen, J.,Furukawa, T.,Katayama, H.,Trudel, V.,Tan, J.,Yudin, A.K.,Gray-Owen, S.D.,Sakuda, S.,Batey, R.A.,Vahidi, S.,Bonomi, M.,Houry, W.A.
Small molecule dysregulation of ClpP activity via bidirectional allosteric pathways.
Structure, 33:1700-, 2025

PubMed Abstract: The bacterial ClpP protease is essential for the virulence and infectivity of many human pathogens and has emerged as a novel antibacterial drug target. Several classes of small molecules dysregulate or activate ClpP, leading to uncontrolled protein degradation and cell death. Here, we investigate the mechanism of ClpP activation by these compounds using an integrative approach combining structural, biochemical, and computational tools. We identified small molecules that activate ClpP through binding at internal catalytic sites where peptide bond hydrolysis occurs. Combined with knowledge of ClpP activation by small molecules that bind to external hydrophobic sites, this work sheds light on the mechanisms governing ClpP allostery and identifies a common molecular pathway utilized by site-specific effectors to achieve allosteric activation. We propose a consensus, bidirectional ClpP activation mechanism causing protease dysregulation.

PubMed: 40795847
DOI: 10.1016/j.str.2025.07.013

Experimental method

X-RAY DIFFRACTION (1.9 Å)