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

SASDJF2 – Beta-ketoacyl synthase (Bamb_5924) N-terminal docking domain

Beta-ketoacyl synthase Bamb_5924
MWexperimental 10 kDa
MWexpected 10 kDa
VPorod 22 nm3
log I(s) 3.10×10-2 3.10×10-3 3.10×10-4 3.10×10-5
Beta-ketoacyl synthase Bamb_5924 small angle scattering data  s, nm-1
ln I(s)
Beta-ketoacyl synthase Bamb_5924 Guinier plot ln 3.10×10-2 Rg: 1.9 nm 0 (1.9 nm)-2 s2
(sRg)2I(s)/I(0)
Beta-ketoacyl synthase Bamb_5924 Kratky plot 1.104 0 √3 sRg
p(r)
Beta-ketoacyl synthase Bamb_5924 pair distance distribution function Rg: 1.9 nm 0 Dmax: 7.5 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Beta-ketoacyl synthase Bamb_5924 DAMFILT model
log I(s)
 s, nm-1
Beta-ketoacyl synthase Bamb_5924 PDB (PROTEIN DATA BANK) model
log I(s)
 s, nm-1
Beta-ketoacyl synthase Bamb_5924 PDB (PROTEIN DATA BANK) model
Synchrotron SAXS data from solutions of Bamb_5924 NDD 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 28 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 sample was injected using the online automatic sample changer into a pre-equilibrated HPLC-coupled size-exclusion chromatography column.

Beta-ketoacyl synthase Bamb_5924 (Bamb_5924 NDD)
Mol. type   Protein
Organism   Burkholderia ambifaria
Olig. state   Dimer
Mon. MW   5.0 kDa
 
UniProt   Q0B304 (1-41)
Sequence   FASTA
 
PDB ID   6TDD