Structural Basis for Toxin Inhibition in the VapXD Toxin-Antitoxin System

Structure. 2021 Feb 4;29(2):139-150.e3. doi: 10.1016/j.str.2020.10.002. Epub 2020 Oct 22.


Bacterial type II toxin-antitoxin (TA) modules encode a toxic protein that downregulates metabolism and a specific antitoxin that binds and inhibits the toxin during normal growth. In non-typeable Haemophilus influenzae, a common cause of infections in humans, the vapXD locus was found to constitute a functional TA module and contribute to pathogenicity; however, the mode of action of VapD and the mechanism of inhibition by the VapX antitoxin remain unknown. Here, we report the structure of the intact H. influenzae VapXD complex, revealing an unusual 2:1 TA molecular stoichiometry where a Cas2-like homodimer of VapD binds a single VapX antitoxin. VapX consists of an oligonucleotide/oligosaccharide-binding domain that docks into an asymmetrical cavity on the toxin dimer. Structures of isolated VapD further reveal how a symmetrical toxin homodimer adapts to interacting with an asymmetrical antitoxin and suggest how a primordial TA system evolved to become part of CRISPR-Cas immunity systems.

Keywords: CRISPR-Cas; Cas2; Haemophilus influenzae; OB fold; RNase; VapD.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / metabolism
  • Bacterial Toxins / chemistry*
  • Bacterial Toxins / metabolism
  • Binding Sites
  • Haemophilus influenzae / chemistry
  • Haemophilus influenzae / enzymology
  • Membrane Glycoproteins / chemistry*
  • Membrane Glycoproteins / metabolism
  • Molecular Docking Simulation
  • Protein Domains
  • Toxin-Antitoxin Systems*


  • Bacterial Proteins
  • Bacterial Toxins
  • Membrane Glycoproteins
  • VapD protein, Bacteria