Structural basis of DNA binding by YdaT, a functional equivalent of the CII repressor in the cryptic prophage CP-933P from Escherichia coli O157:H7

Prolič-Kalinšek M, Volkov A, Hadži S, Van Dyck J, Bervoets I, Charlier D, Loris R, Acta Crystallographica Section D Structural Biology 79(3):245-258 (2023) DOI

SASDQE9 – YdaT_toxin domain-containing protein bound to 30 base pair dsDNA

YdaT_toxin domain-containing protein
Om 30 base pair dsDNA
MWexperimental 102 kDa
MWexpected 111 kDa
VPorod 190 nm3
log I(s) 5.77×101 5.77×100 5.77×10-1 5.77×10-2
YdaT_toxin domain-containing protein Om 30 base pair dsDNA small angle scattering data  s, nm-1
ln I(s)
YdaT_toxin domain-containing protein Om 30 base pair dsDNA Guinier plot ln 5.78×101 Rg: 4.2 nm 0 (4.2 nm)-2 s2
(sRg)2I(s)/I(0)
YdaT_toxin domain-containing protein Om 30 base pair dsDNA Kratky plot 1.104 0 √3 sRg
p(r)
YdaT_toxin domain-containing protein Om 30 base pair dsDNA pair distance distribution function Rg: 4.2 nm 0 Dmax: 12.8 nm

Data validation

Fits and models

log I(s)
 s, nm-1
YdaT_toxin domain-containing protein Om 30 base pair dsDNA OTHER model
YdaT_toxin domain-containing protein Om 30 base pair dsDNA OTHER model
YdaT_toxin domain-containing protein Om 30 base pair dsDNA OTHER model
YdaT_toxin domain-containing protein Om 30 base pair dsDNA OTHER model
YdaT_toxin domain-containing protein Om 30 base pair dsDNA OTHER model
YdaT_toxin domain-containing protein Om 30 base pair dsDNA OTHER model
YdaT_toxin domain-containing protein Om 30 base pair dsDNA OTHER model
YdaT_toxin domain-containing protein Om 30 base pair dsDNA OTHER model
YdaT_toxin domain-containing protein Om 30 base pair dsDNA OTHER model
YdaT_toxin domain-containing protein Om 30 base pair dsDNA OTHER model
Synchrotron SAXS data from solutions of YdaT_toxin domain-containing protein bound to 30 base pair DNA in 20 mM Tris-HCl, 200 mM NaCl, pH 8 were collected on the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus3 2M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.099 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 45.00 μl sample at 8 mg/ml was injected at a 0.16 ml/min flow rate onto a Agilent AdvanceBio SEC 300Å, 4.6 x 150 mm column at 15°C. 13 successive 2 second frames were collected through the sample elution peak. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

The models presented above show several protein-DNA complex ensembles.

YdaT_toxin domain-containing protein (YdaT)
Mol. type   Protein
Organism   Escherichia coli O157:H7
Olig. state   Tetramer
Mon. MW   18.5 kDa
 
UniProt   A0A6M7H0F8 (2-141)
Sequence   FASTA
 
Om 30 base pair dsDNA (Om)
Mol. type   DNA
Olig. state   Dimer
Mon. MW   18.6 kDa
Sequence   FASTA