Unveiling the role of novel carbohydrate-binding modules in laminarin interaction of multimodular proteins from marine Bacteroidota during phytoplankton blooms.

Zühlke MK, Ficko-Blean E, Bartosik D, Terrapon N, Jeudy A, Jam M, Wang F, Welsch N, Dürwald A, Martin LT, Larocque R, Jouanneau D, Eisenack T, Thomas F, Trautwein-Schult A, Teeling H, Becher D, Schweder T, Czjzek M, Environ Microbiol 26(5):e16624 (2024) Europe PMC

SASDU93 – multimodular GH16_3 containing a CBM and a catalytic domain

Glycosyl hydrolase, family 16
MWI(0) 56 kDa
MWexpected 58 kDa
VPorod 76 nm3
log I(s) 1.31×10-1 1.31×10-2 1.31×10-3 1.31×10-4
Glycosyl hydrolase, family 16 small angle scattering data  s, nm-1
ln I(s)
Glycosyl hydrolase, family 16 Guinier plot ln 1.32×10-1 Rg: 3.8 nm 0 (3.8 nm)-2 s2
(sRg)2I(s)/I(0)
Glycosyl hydrolase, family 16 Kratky plot 1.104 0 3 sRg
p(r)
Glycosyl hydrolase, family 16 pair distance distribution function Rg: 3.8 nm 0 Dmax: 12.9 nm

Data validation


Fits and models


log I(s)
 s, nm-1
Glycosyl hydrolase, family 16 DADIMODO model

Synchrotron SAXS data from solutions of multimodular GH16_3 containing a CBM and a catalytic domain in 10 mM MOPS, 100 mM NaCl, pH 7.8 were collected on the SWING beam line at the SOLEIL storage ring (Saint-Aubin, France) using a AVIEX PCCD170170 detector at a sample-detector distance of 2.4 m and at a wavelength of λ = 1.033 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle) resulting in a scattering vector q-range of 0.017 – 0.504 Å-1. In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 70.00 μl sample at 8.2 mg/ml was injected at a 0.20 ml/min flow rate onto a Agilent Bio SEC-3, 300 Å column at 17°C. 250 successive 1.5 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.

The protein construct used for SAXS contains a N-terminal polyhistidine tag MGSSHHHHHHGS. Protein samples were centrifuged prior to analyses to remove putative aggregates. SAXS measurements were coupled with prefixed SEC. The SEC column was equilibrated in buffer C (100 mM NaCl, 10 mM MOPS pH 7.8), which was used for protein purification. The Guinier equation was used to calculate the forward scattering I(0) and the radius of gyration Rg. The distance distribution function P(r) and the maximum particle dimension Dmax were calculated by Fourier inversion of the scattering intensity I(q) using GNOM integrated in the PRIMUS software (ATSAS 3.1.3)

Glycosyl hydrolase, family 16 (Cf-GH16_3)
Mol. type   Protein
Organism   Christiangramia forsetii (strain DSM 17595 / CGMCC 1.15422 / KT0803)
Olig. state   Monomer
Mon. MW   57.8 kDa
 
UniProt   A0M710-1 (29-538)
Sequence   FASTA