Towards improved understanding of intersubunit interactions in modular polyketide biosynthesis: docking in the enacyloxin IIa polyketide synthase.

Risser F, Collin S, Dos Santos-Morais R, Gruez A, Chagot B, Weissman KJ, J Struct Biol :107581 (2020) Europe PMC

SASDJL2 – Artificial fusion protein of the beta-ketoacyl synthase Bamb_5925 C-terminal docking domain and the beta-ketoacyl synthase Bamb_5924 N-terminal docking domain

Beta-ketoacyl synthase Bamb_5925 CDD/Bamb_5924 NDD artificial protein fusion
MWexperimental 23 kDa
MWexpected 18 kDa
VPorod 47 nm3
log I(s) 3.42×10-2 3.42×10-3 3.42×10-4 3.42×10-5
Beta-ketoacyl synthase Bamb_5925 CDD/Bamb_5924 NDD artificial protein fusion small angle scattering data  s, nm-1
ln I(s)
Beta-ketoacyl synthase Bamb_5925 CDD/Bamb_5924 NDD artificial protein fusion Guinier plot ln 3.42×10-2 Rg: 2.1 nm 0 (2.1 nm)-2 s2
(sRg)2I(s)/I(0)
Beta-ketoacyl synthase Bamb_5925 CDD/Bamb_5924 NDD artificial protein fusion Kratky plot 1.104 0 √3 sRg
p(r)
Beta-ketoacyl synthase Bamb_5925 CDD/Bamb_5924 NDD artificial protein fusion pair distance distribution function Rg: 2.2 nm 0 Dmax: 9.6 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Beta-ketoacyl synthase Bamb_5925 CDD/Bamb_5924 NDD artificial protein fusion PDB (PROTEIN DATA BANK) model
log I(s)
 s, nm-1
Beta-ketoacyl synthase Bamb_5925 CDD/Bamb_5924 NDD artificial protein fusion PDB (PROTEIN DATA BANK) model
Synchrotron SAXS data from solutions of the Bamb_5925 CDD/Bamb_5924 NDD protein fusion in 20 mM Tris-HCl, 200 mM NaCl, 5% glycerol, pH 7.5 were collected on the SWING beam line at SOLEIL (Saint-Aubin, France) using a AVIEX PCCD170170 detector at a sample-detector distance of 1.8 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 50.00 μl sample at 8 mg/ml was injected at a 0.10 ml/min flow rate onto a Agilent Bio SEC-3, 100 Å column at 15°C. 100 successive 0.750 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 protein samples were injected using the online automatic sample changer into a pre-equilibrated HPLC-coupled size-exclusion chromatography column.

Beta-ketoacyl synthase Bamb_5925 CDD/Bamb_5924 NDD artificial protein fusion (5925/5424 fusion)
Mol. type   Protein
Organism   Burkholderia ambifaria
Olig. state   Dimer
Mon. MW   9.1 kDa
Sequence   FASTA
 
PDB ID   6TDN