Crystal structure and activity of a de novo enzyme, ferric enterobactin esterase Syn-F4.

Kurihara K, Umezawa K, Donnelly AE, Sperling B, Liao G, Hecht MH, Arai R, Proc Natl Acad Sci U S A 120(38):e2218281120 (2023) Europe PMC

SASDRJ8 – A de novo enzyme, ferric enterobactin esterase Syn-F4

De novo enterobactin esterase Syn-F4 (K4T)
MWexperimental 24 kDa
MWexpected 25 kDa
VPorod 40 nm3
log I(s) 5.45×10-2 5.45×10-3 5.45×10-4 5.45×10-5
De novo enterobactin esterase Syn-F4 (K4T) small angle scattering data  s, nm-1
ln I(s)
De novo enterobactin esterase Syn-F4 (K4T) Guinier plot ln 5.45×10-2 Rg: 2.5 nm 0 (2.5 nm)-2 s2
(sRg)2I(s)/I(0)
De novo enterobactin esterase Syn-F4 (K4T) Kratky plot 1.104 0 √3 sRg
p(r)
De novo enterobactin esterase Syn-F4 (K4T) pair distance distribution function Rg: 2.7 nm 0 Dmax: 10 nm

Data validation

Fits and models

log I(s)
 s, nm-1
De novo enterobactin esterase Syn-F4 (K4T) DAMMIN model
log I(s)
 s, nm-1
De novo enterobactin esterase Syn-F4 (K4T) OTHER model
Synchrotron SAXS data from solutions of the de novo enzyme ferric enterobactin esterase Syn-F4 in 25 mM MES, 100 mM NaCl, 10% glycerol, 200 mM Arg-HCl, pH 6.5 were collected on the BL-10C beam line at the Photon Factory (PF), High Energy Accelerator Research Organization (KEK; Tsukuba, Japan) using a Pilatus3 2M detector at a sample-detector distance of 1.0 m and at a wavelength of λ = 0.12 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 4.50 mg/ml was measured at 20°C. 30 successive 5 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.

Experimental errors are severely overestimated.

De novo enterobactin esterase Syn-F4 (K4T) (Syn-F4 (K4T))
Mol. type   Protein
Organism   synthetic construct
Olig. state   Dimer
Mon. MW   12.5 kDa
Sequence   FASTA