› 2bfg

X-ray diffraction
2.4Å resolution

crystal structure of beta-xylosidase (fam GH39) in complex with dinitrophenyl-beta-xyloside and covalently bound xyloside

Released:
DOI: 10.2210/pdb2bfg/pdb
PDB entry 2bfg coloured by chain, front view.
PDB entry 2bfg coloured by chain, side view.
PDB entry 2bfg coloured by chain, top view.
Source organism: Geobacillus stearothermophilus
Primary publication:
Enzyme-substrate complex structures of a GH39 beta-xylosidase from Geobacillus stearothermophilus.
Czjzek M, Ben David A, Bravman T, Shoham G, Henrissat B, Shoham Y
J Mol Biol 353 838-46 (2005)
PMID: 16212978

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-195634 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Beta-xylosidase Chains: A, B, C, D, E, F, G, H
Molecule details ›
Chains: A, B, C, D, E, F, G, H
Length: 503 amino acids
Theoretical weight: 58 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q9ZFM2 (Residues: 1-447, 448-504; Coverage: 100%)
Gene name: xynB
Sequence domains: Glycosyl hydrolases family 39
Structure domains:

Ligands and Environments

5 bound ligands:
Ligand NA 8 x NA
Ligand ANX 2 x ANX
Ligand XYP 2 x XYP
Ligand XYS 8 x XYS
Ligand SO4 8 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: P212121
Unit cell:
a: 88.95Å b: 162.16Å c: 308.2Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.198 0.194 0.27
Expression system: Escherichia coli BL21

Quick links

Citations

4 review citations

Biotransformation of ginsenosides by hydrolyzing the sugar moieties of ginsenosides using microbial glycosidases.
Park et al. (2010)
3 more

5 mentions without citation

β-Xylosidases: Structural Diversity, Catalytic Mechanism, and Inhibition by Monosaccharides.
Rohman et al. (2019)
4 more