Alternative dimerization is required for activity and inhibition of the HEPN ribonuclease RnlA

Garcia-Rodriguez G, Charlier D, Wilmaerts D, Michiels J, Loris R, Nucleic Acids Research 49(12):7164-7178 (2021) DOI

SASDKL2 – NRD-HEPN - mRNA endoribonuclease toxin LS from Escherichia coli (strain K12)

NRD-HEPN truncated variant of RnlA endoribonuclease
MWexperimental 57 kDa
MWexpected 62 kDa
VPorod 88 nm3
log I(s) 7.79×10-2 7.79×10-3 7.79×10-4 7.79×10-5
NRD-HEPN truncated variant of RnlA endoribonuclease small angle scattering data  s, nm-1
ln I(s)
NRD-HEPN truncated variant of RnlA endoribonuclease Guinier plot ln 7.80×10-2 Rg: 3.0 nm 0 (3.0 nm)-2 s2
(sRg)2I(s)/I(0)
NRD-HEPN truncated variant of RnlA endoribonuclease Kratky plot 1.104 0 3 sRg
p(r)
NRD-HEPN truncated variant of RnlA endoribonuclease pair distance distribution function Rg: 3.0 nm 0 Dmax: 10.4 nm

Data validation


Fits and models


log I(s)
 s, nm-1
NRD-HEPN truncated variant of RnlA endoribonuclease MULTIFOXS model

Synchrotron SAXS data from solutions of NRD-HEPN - mRNA endoribonuclease toxin LS from Escherichia coli (strain K12) in 20 mM Tris, 150 mM NaCl, 1 mM TCEP, pH 8 were collected on the SWING beam line at the SOLEIL storage ring (Saint-Aubin, France) using a Eiger 4M detector at a wavelength of λ = 1.033 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 60.00 μl sample at 24 mg/ml was injected at a 0.20 ml/min flow rate onto a Agilent Bio SEC-3, 300 Å column at 16°C. 480 successive 0.990 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.

The sample in the previously defined buffer (after Ni-NTA and gel filtration purification) was flash-frozen in (l)N2. Once at the beamline the sample was quickly thawed, spun down and concentration checked before being applied onto an HPLC column connected to a quartz capillary for measurement.

NRD-HEPN truncated variant of RnlA endoribonuclease (NRD-HEPN)
Mol. type   Protein
Organism   Escherichia coli
Olig. state   Dimer
Mon. MW   31.1 kDa
 
UniProt   P52129 (87-357)
Sequence   FASTA