Structural, biophysical and biochemical studies of CAZYmes involved in exopolysaccharides degradation of microbial biofilms

Amanda Freitas Cruz, Universidade de São Paulo Master's thesis (2025) URL

SASDXY4 – Serratia marcescens truncated Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB

Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB
MWexperimental 66 kDa
MWexpected 69 kDa
VPorod 102 nm3
log I(s) 1.75×101 1.75×100 1.75×10-1 1.75×10-2
Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB small angle scattering data  s, nm-1
ln I(s)
Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB Guinier plot ln 1.76×101 Rg: 2.8 nm 0 (2.8 nm)-2 s2
(sRg)2I(s)/I(0)
Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB Kratky plot 1.104 0 √3 sRg
p(r)
Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB pair distance distribution function Rg: 2.8 nm 0 Dmax: 9.0 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB ALPHAFOLD model
Synchrotron SAXS data from solutions of truncated PgaB in phosphate-buffered saline, pH 7.4 were collected on the BL4-2 beam line at the Stanford Synchrotron Radiation Lightsource (SSRL; Menlo Park, CA, USA) using a Pilatus3 X 1M detector at a sample-detector distance of 1.7 m and at a wavelength of λ = 0.1127 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 0.05 μl sample at 8 mg/ml was injected at a 0.05 ml/min flow rate onto a GE Superdex 200 Increase 10/300 column at 20°C. Four successive 0.100 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.

Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB
Mol. type   Protein
Organism   Serratia marcescens
Olig. state   Monomer
Mon. MW   69.1 kDa
 
UniProt   A0A2V4FWX5 (40-653)
Sequence   FASTA