Identification and characterization of endo-α-, exo-α-, and exo-β-d-arabinofuranosidases degrading lipoarabinomannan and arabinogalactan of mycobacteria

Shimokawa M, Ishiwata A, Kashima T, Nakashima C, Li J, Fukushima R, Sawai N, Nakamori M, Tanaka Y, Kudo A, Morikami S, Iwanaga N, Akai G, Shimizu N, Arakawa T, Yamada C, Kitahara K, Tanaka K, Ito Y, Fushinobu S, Fujita K, Nature Communications 14(1) (2023) DOI

SASDQQ8 – Endo-D-arabinanase, 54 kDa, dimer, Microbacterium arabinogalactanolyticum

Endo-D-arabinanase
MWI(0) 111 kDa
MWexpected 107 kDa
VPorod 131 nm3
log I(s) 8.54×10-2 8.54×10-3 8.54×10-4 8.54×10-5
Endo-D-arabinanase small angle scattering data  s, nm-1
ln I(s)
Endo-D-arabinanase Guinier plot ln 8.54×10-2 Rg: 3.1 nm 0 (3.1 nm)-2 s2
(sRg)2I(s)/I(0)
Endo-D-arabinanase Kratky plot 1.104 0 √3 sRg
p(r)
Endo-D-arabinanase pair distance distribution function Rg: 3.1 nm 0 Dmax: 10.4 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Endo-D-arabinanase REFMAC model
log I(s)
 s, nm-1
Endo-D-arabinanase DAMMIN model
Synchrotron SAXS data from solutions of Endo-D-arabinanase,20 mM Tris-HCl, 200 mM NaCl, pH 7.5 were collected on the BL-10C beam line at the Photon Factory (PF), High Energy Accelerator Research Organization (KEK; Tsukuba, Japan) using a Pilatus3 2M detector at a sample-detector distance of 2.1 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 130.00 μl sample at 2.4 mg/ml was injected at a 0.02 ml/min flow rate onto a Shodex KW403 column at 20°C. 247 successive 20 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.

Endo-D-arabinanase (EndoMA1)
Mol. type   Protein
Organism   Microbacterium arabinogalactanolyticum
Olig. state   Dimer
Mon. MW   53.7 kDa
Sequence   FASTA
 
PDB ID   8HHV