6ZI1

Crystal structure of the isolated H. influenzae VapD toxin (D7N mutant)

This is a non-PDB format compatible entry.

Summary for 6ZI1

• Entry DOI: 10.2210/pdb6zi1/pdb
• Descriptor: Endoribonuclease VapD (2 entities in total)
• Functional Keywords: toxin-antitoxin, vapxd, rnase, nucleic-acid binding protein, hydrolase, toxin
• Biological source: Haemophilus influenzae 86-028NP
• Total number of polymer chains: 2
• Total formula weight: 23738.70

Authors

Bertelsen, M.B.,Senissar, M.,Nielsen, M.H.,Bisiak, F.,Cunha, M.V.,Molinaro, A.L.,Daines, D.A.,Brodersen, D.E. (deposition date: 2020-06-24, release date: 2020-10-14, Last modification date: 2024-05-01)

Primary citation

Bertelsen, M.B.,Senissar, M.,Nielsen, M.H.,Bisiak, F.,Cunha, M.V.,Molinaro, A.L.,Daines, D.A.,Brodersen, D.E.
Structural Basis for Toxin Inhibition in the VapXD Toxin-Antitoxin System.
Structure, 29:139-, 2021

PubMed Abstract: 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.

PubMed: 33096014
DOI: 10.1016/j.str.2020.10.002

Experimental method

X-RAY DIFFRACTION (2.2 Å)