Structural, Thermodynamic and Enzymatic Characterization of N,N-Diacetylchitobiose Deacetylase from Pyrococcus chitonophagus.

Biniek-Antosiak K, Bejger M, Śliwiak J, Baranowski D, Mohammed ASA, Svergun DI, Rypniewski W, Int J Mol Sci 23(24) (2022) Europe PMC

SASDMA9 – Diacetylchitobiose deacetylase (isolated hexamer from SEC-SAXS)

Diacetylchitobiose deacetylase
MWexperimental 185 kDa
MWexpected 186 kDa
VPorod 317 nm3
log I(s) 7.72×103 7.72×102 7.72×101 7.72×100
Diacetylchitobiose deacetylase small angle scattering data  s, nm-1
ln I(s)
Diacetylchitobiose deacetylase Guinier plot ln 7.72×103 Rg: 3.6 nm 0 (3.6 nm)-2 s2
(sRg)2I(s)/I(0)
Diacetylchitobiose deacetylase Kratky plot 1.104 0 √3 sRg
p(r)
Diacetylchitobiose deacetylase pair distance distribution function Rg: 3.6 nm 0 Dmax: 11.2 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Diacetylchitobiose deacetylase PYMOL model
Synchrotron SAXS data from solutions of diacetylchitobiose deacetylase in 20 mM TRIS, 200 mM NaCl, pH 7.4 were collected on the EMBL P12 beam line at PETRA III (DESY, Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 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 30.00 μl sample at 4.7 mg/ml was injected at a 0.35 ml/min flow rate onto a GE Superdex 200 Increase 5/150 column at 20°C. 2880 successive 0.250 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.

Diacetylchitobiose deacetylase (Dac-74)
Mol. type   Protein
Organism   Thermococcus chitonophagus
Olig. state   Hexamer
Mon. MW   30.9 kDa
 
UniProt   A0A160VQZ8 (1-267)
Sequence   FASTA
 
PDB ID   8BGN