Controlled modulation of the dynamics of the Deinococcus grandis Dps N-terminal tails by divalent metals.

Guerra JPL, Blanchet CE, Vieira BJC, Waerenborgh JC, Jones NC, Hoffmann SV, Pereira AS, Tavares P, Protein Sci :e4567 (2023) Europe PMC

SASDQY4 – DNA-binding protein from starved cells: DgrDpsWT + 24 Zn2+ in 50 mM MOPS pH 7.0, 230 mM NaCl, 5 mM EDTA

DNA protection during starvation, DPS (Ferritin superfamily)
MWexperimental 319 kDa
MWexpected 270 kDa
VPorod 453 nm3
log I(s) 1.02×104 1.02×103 1.02×102 1.02×101
DNA protection during starvation, DPS (Ferritin superfamily) small angle scattering data  s, nm-1
ln I(s)
DNA protection during starvation, DPS (Ferritin superfamily) Guinier plot ln 1.03×104 Rg: 4.5 nm 0 (4.5 nm)-2 s2
(sRg)2I(s)/I(0)
DNA protection during starvation, DPS (Ferritin superfamily) Kratky plot 1.104 0 3 sRg
p(r)
DNA protection during starvation, DPS (Ferritin superfamily) pair distance distribution function Rg: 4.6 nm 0 Dmax: 19.5 nm

Data validation


Fits and models


log I(s)
 s, nm-1
DNA protection during starvation, DPS (Ferritin superfamily) GASBOR model

Synchrotron SAXS data from solutions of DgrDpsWT + 24 Zn2+ in 50 mM MOPS pH 7.0, 230 mM NaCl, 5 mM EDTA were collected on the EMBL P12 beam line at PETRA III (DESY, Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 6 m and at a wavelength of λ = 0.124 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 50.00 μl sample at 10 mg/ml was injected at a 0.50 ml/min flow rate onto a GE Superdex 200 Increase 5/150 column at 25°C. 10 successive 1 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.

The gene sequence used in this project was NCBI Reference Sequence: WP_058978256.1, which lacks the initial 10 amino acids of UniProt sequence A0A100HLL5. https://www.ncbi.nlm.nih.gov/protein/WP_058978256.1

DNA protection during starvation, DPS (Ferritin superfamily) (DgrDpsWT)
Mol. type   Protein
Organism   Deinococcus grandis
Olig. state   Dodecamer
Mon. MW   22.5 kDa
 
UniProt   A0A100HLL5 (10-214)
Sequence   FASTA