8QNL | pdb_00008qnl

Structure of the toxin-antitoxin NatRT complex from Pseudomonas aeruginosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 
    0.250 (Depositor), 0.251 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 8QNL

This is version 1.1 of the entry. See complete history

Literature

Toxin-mediated depletion of NAD and NADP drives persister formation in a human pathogen.

Santi, I.Dias Teixeira, R.Manfredi, P.Hernandez Gonzalez, H.Spiess, D.C.Mas, G.Klotz, A.Kaczmarczyk, A.Zamboni, N.Hiller, S.Jenal, U.

(2024) EMBO J 43: 5211-5236

  • DOI: https://doi.org/10.1038/s44318-024-00248-5
  • Primary Citation Related Structures: 
    8QNL, 8QNQ

  • PubMed Abstract: 

    Toxin-antitoxin (TA) systems are widespread in bacteria and implicated in genome stability, virulence, phage defense, and persistence. TA systems have diverse activities and cellular targets, but their physiological roles and regulatory mechanisms are often unclear. Here, we show that the NatR-NatT TA system, which is part of the core genome of the human pathogen Pseudomonas aeruginosa, generates drug-tolerant persisters by specifically depleting nicotinamide dinucleotides. While actively growing P. aeruginosa cells compensate for NatT-mediated NAD + deficiency by inducing the NAD + salvage pathway, NAD depletion generates drug-tolerant persisters under nutrient-limited conditions. Our structural and biochemical analyses propose a model for NatT toxin activation and autoregulation and indicate that NatT activity is subject to powerful metabolic feedback control by the NAD + precursor nicotinamide. Based on the identification of natT gain-of-function alleles in patient isolates and on the observation that NatT increases P. aeruginosa virulence, we postulate that NatT modulates pathogen fitness during infections. These findings pave the way for detailed investigations into how a toxin-antitoxin system can promote pathogen persistence by disrupting essential metabolic pathways.


  • Organizational Affiliation
    • Biozentrum, University of Basel, Basel, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 116.8 kDa 
  • Atom Count: 7,855 
  • Modeled Residue Count: 980 
  • Deposited Residue Count: 1,044 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Antitoxin Xre/MbcA/ParS-like toxin-binding domain-containing protein
A, B, D, E
129Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: PA1029
UniProt
Find proteins for Q9I4U5 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I4U5 
Go to UniProtKB:  Q9I4U5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I4U5
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
RES domain-containing protein
C, F
264Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: PA1030
UniProt
Find proteins for Q9I4U4 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I4U4 
Go to UniProtKB:  Q9I4U4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I4U4
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free:  0.250 (Depositor), 0.251 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.18α = 90
b = 106.922β = 104.21
c = 93.499γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland310030_189253
Swiss National Science FoundationSwitzerland51NF40_180541

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-02
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Database references, Structure summary