Toxin:antitoxin ratio sensing autoregulation of the Vibrio cholerae parDE2 module.

Garcia-Rodriguez G, Girardin Y, Kumar Singh R, Volkov AN, Van Dyck J, Muruganandam G, Sobott F, Charlier D, Loris R, Sci Adv 10(1):eadj2403 (2024) Europe PMC

SASDPL3 – Vibrio cholerae ParD2:ParE2 complex bound to 31-bp DNA operator box

Antitoxin ParD
Toxin
31-bp DNA operator box
MWexperimental 97 kDa
MWexpected 98 kDa
VPorod 160 nm3
log I(s) 3.84×101 3.84×100 3.84×10-1 3.84×10-2
Antitoxin ParD Toxin 31-bp DNA operator box small angle scattering data  s, nm-1
ln I(s)
Antitoxin ParD Toxin 31-bp DNA operator box Guinier plot ln 3.84×101 Rg: 3.3 nm 0 (3.3 nm)-2 s2
(sRg)2I(s)/I(0)
Antitoxin ParD Toxin 31-bp DNA operator box Kratky plot 1.104 0 √3 sRg
Dmax: 10.5 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Antitoxin ParD Toxin 31-bp DNA operator box CUSTOM IN-HOUSE model
Antitoxin ParD Toxin 31-bp DNA operator box CUSTOM IN-HOUSE model
Antitoxin ParD Toxin 31-bp DNA operator box CUSTOM IN-HOUSE model
Antitoxin ParD Toxin 31-bp DNA operator box CUSTOM IN-HOUSE model
Antitoxin ParD Toxin 31-bp DNA operator box CUSTOM IN-HOUSE model
Synchrotron SAXS data from solutions of Vibrio cholerae ParD2:ParE2 complex bound to 31-bp DNA operator box in 20 mM Tris, 150 mM NaCl, 1 mM TCEP, pH 8 were collected on the SWING beam line at SOLEIL (Saint-Aubin, France) using a Eiger 4M detector at a sample-detector distance of 2 m and at a wavelength of λ = 0.103 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 75.00 μl sample at 10 mg/ml was injected at a 0.75 ml/min flow rate onto a GE Superdex 200 Increase 10/300 column at 19°C. 700 successive 2.990 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

Antitoxin ParD (ParD2)
Mol. type   Protein
Organism   Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Olig. state   Hexamer
Mon. MW   9.0 kDa
 
UniProt   P58093 (1-80)
Sequence   FASTA
 
Toxin (ParE2)
Mol. type   Protein
Organism   Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Olig. state   Other
Mon. MW   12.4 kDa
 
UniProt   Q9KMJ0 (1-99)
Sequence   FASTA
 
31-bp DNA operator box (DNA operator)
Mol. type   DNA
Organism   Vibrio cholerae O1
Olig. state   Monomer
Mon. MW   19.2 kDa
Sequence   FASTA
 
PDB ID   7R5A
 
PDB ID   7R5A
 
PDB ID   7R5A
 
PDB ID   7R5A
 
PDB ID   7R5A