6ZI1

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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

Bertelsen, M.B.Senissar, M.Nielsen, M.H.Bisiak, F.Cunha, M.V.Molinaro, A.L.Daines, D.A.Brodersen, D.E.

(2021) Structure 29: 139

  • DOI: https://doi.org/10.1016/j.str.2020.10.002
  • Primary Citation of Related Structures:  
    6ZI0, 6ZI1, 6ZN8

  • 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.


  • Organizational Affiliation

    Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endoribonuclease VapDA [auth AAA],
B [auth BBB]
102Haemophilus influenzae 86-028NPMutation(s): 1 
Gene Names: vapDNTHI0577
EC: 3.1
UniProt
Find proteins for Q4QN95 (Haemophilus influenzae (strain 86-028NP))
Explore Q4QN95 
Go to UniProtKB:  Q4QN95
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4QN95
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.214 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.38α = 90
b = 84.38β = 90
c = 49.48γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Novo Nordisk FoundationDenmarkNNF18OC0030646

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-14
    Type: Initial release
  • Version 1.1: 2020-11-04
    Changes: Database references
  • Version 1.2: 2021-02-17
    Changes: Database references