› 2exk

X-ray diffraction
2.2Å resolution

Structure of the family43 beta-Xylosidase E187G from geobacillus stearothermophilus in complex with xylobiose

Released:
DOI: 10.2210/pdb2exk/pdb
PDB entry 2exk coloured by chain, front view.
PDB entry 2exk coloured by chain, side view.
PDB entry 2exk coloured by chain, top view.
Source organism: Geobacillus stearothermophilus
Primary publication:
The structure of an inverting GH43 beta-xylosidase from Geobacillus stearothermophilus with its substrate reveals the role of the three catalytic residues.
Brüx C, Ben-David A, Shallom-Shezifi D, Leon M, Niefind K, Shoham G, Shoham Y, Schomburg D
J Mol Biol 359 97-109 (2006)
PMID: 16631196

Function and Biology Details

Reaction catalysed: 
Hydrolysis of (1->4)-beta-D-xylans, to remove successive D-xylose residues from the non-reducing termini
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-170833 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Beta-xylosidase C-terminal Concanavalin A-like domain-containing protein Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 535 amino acids
Theoretical weight: 61.9 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q09LX0 (Residues: 1-535; Coverage: 100%)
Gene name: xynB3
Sequence domains:
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: XYS
Carbohydrate polymer
3 bound ligands:
Ligand CA 4 x CA
Ligand MES 3 x MES
Ligand GOL 4 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X13
Spacegroup: P43212
Unit cell:
a: 139.87Å b: 139.87Å c: 232.025Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.188 0.185 0.238
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

β-xylosidases and α-L-arabinofuranosidases: accessory enzymes for arabinoxylan degradation.
Lagaert et al. (2014)
3 more

2 mentions without citation

Crystal structure of an Exo-1,5-{alpha}-L-arabinofuranosidase from Streptomyces avermitilis provides insights into the mechanism of substrate discrimination between exo- and endo-type enzymes in glycoside hydrolase family 43.
Fujimoto et al. (2010)
1 more