7-Deazaguanines in DNA: functional and structural elucidation of a DNA modification system.

Gedara SH, Wood E, Gustafson A, Liang C, Hung SH, Savage J, Phan P, Luthra A, de Crécy-Lagard V, Dedon P, Swairjo MA, Iwata-Reuyl D, Nucleic Acids Res (2023) Europe PMC

SASDQ59 – Mutant 7-deazapurine in DNA protein A (D95A)

DNA-guanine transglycosylase - D95A mutant
MWexperimental 48 kDa
MWexpected 50 kDa
VPorod 67 nm3
log I(s) 1.03×101 1.03×100 1.03×10-1 1.03×10-2
DNA-guanine transglycosylase - D95A mutant small angle scattering data  s, nm-1
ln I(s)
DNA-guanine transglycosylase - D95A mutant Guinier plot ln 1.04×101 Rg: 2.7 nm 0 (2.7 nm)-2 s2
(sRg)2I(s)/I(0)
DNA-guanine transglycosylase - D95A mutant Kratky plot 1.104 0 √3 sRg
p(r)
DNA-guanine transglycosylase - D95A mutant pair distance distribution function Rg: 2.7 nm 0 Dmax: 10.1 nm

Data validation

Fits and models

log I(s)
 s, nm-1
DNA-guanine transglycosylase - D95A mutant GROMACS model
Synchrotron SAXS data from solutions of mutant 7-deazapurine in DNA protein A (D95A) in 100 mM KCl, 50 mM Tris pH 7.0, 1 mM DTT, pH 7 were collected on the 12.3.1 (SIBYLS) beam line at the Advanced Light Source (ALS; Berkeley, CA, USA) using a Pilatus3 X 2M detector at a sample-detector distance of 1.5 m and at a wavelength of λ = 0.1 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 sample at 3 mg/ml was injected at a 0.50 ml/min flow rate onto a Shodex PROTEIN KW-802.5 size exclusion column (8.0 mm I.D. x 300 mm) at 24.9°C. Scattering images were collected with 3-s exposures per frame over the course of 40 minutes. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

Sample injection volume = UNKNOWN

DNA-guanine transglycosylase - D95A mutant (DpdA(D95A))
Mol. type   Protein
Organism   Salmonella enterica subsp. enterica serovar Montevideo
Olig. state   Monomer
Mon. MW   50.4 kDa
 
UniProt   P0DW33 (2-416)
Sequence   FASTA