8ZSF

CryoEM Helical Structure of KomC

Summary for 8ZSF

• Entry DOI: 10.2210/pdb8zsf/pdb
• EMDB information: 60413
• Descriptor: Sir2 family NAD-dependent protein deacetylase (1 entity in total)
• Functional Keywords: nadase, filament, cryoem, immune system
• Biological source: Escherichia coli
• Total number of polymer chains: 12
• Total formula weight: 367870.67

Authors

Feng, H.,Shao, K.,Luo, M. (deposition date: 2024-06-05, release date: 2025-12-10, Last modification date: 2026-06-24)

Primary citation

Feng, H.,Shao, K.,Zeng, Z.,Tan, E.Y.J.,Hu, Z.,Zhao, R.,Rao, J.,Shi, J.,Chen, Z.,Redondo, R.P.,Wu, B.,Han, W.,Luo, M.
Filament-mediated repurposing of toxic dITP for immunity in the Kongming system.
Mol.Cell, 86:1148-1163.e5, 2026

PubMed Abstract: Abortive infection systems protect bacteria by triggering self-destruction in response to phage attack. Most known systems rely on stable cyclic nucleotides that accumulate to stoichiometric levels to activate effectors; the Kongming (Kom) system employs the toxic metabolite deoxyinosine triphosphate (dITP) as its signaling molecule. Here, we show that the Escherichia coli KomB-KomC (KomBC) complex forms a preassembled filament that remains inactive until dITP binding induces cooperative allosteric activation. KomB, a homolog of the nucleotide-hydrolyzing enzyme HAM1, has lost catalytic activity but evolved a high-affinity, hydrolysis-resistant binding pocket for dITP. Interestingly, substoichiometric dITP binding is sufficient to activate adjacent KomC NADase domains, which propagate activation cooperatively along the filament. This filament-based architecture enables ultrasensitive, long-range allosteric signaling in response to a low-abundance and short-lived metabolite. Our findings reveal an ultrasensitive immune strategy that transforms a toxic byproduct into a robust antiviral trigger, expanding the known repertoire of bacterial defense strategies.

PubMed: 41638214
DOI: 10.1016/j.molcel.2026.01.027

Experimental method

ELECTRON MICROSCOPY (3.24 Å)