› 5zqx

X-ray diffraction
2Å resolution

Crystal structure of beta-xylosidase mutant (E186Q) from Bacillus pumilus

Released:
DOI: 10.2210/pdb5zqx/pdb
PDB entry 5zqx coloured by chain, front view.
PDB entry 5zqx coloured by chain, side view.
PDB entry 5zqx coloured by chain, top view.
Source organism: Bacillus pumilus
Primary publication:
Structure-based protein engineering of bacterial β-xylosidase to increase the production yield of xylobiose from xylose.
Hong S, Kyung M, Jo I, Kim YR, Ha NC
Biochem Biophys Res Commun 501 703-710 (2018)
PMID: 29752942

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 analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-139394 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Beta-xylosidase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 541 amino acids
Theoretical weight: 62.09 KDa
Source organism: Bacillus pumilus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P07129 (Residues: 1-535; Coverage: 100%)
Gene name: xynB
Sequence domains:
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: XYP
Carbohydrate polymer
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 7A (6B, 6C1)
Spacegroup: P21
Unit cell:
a: 103.259Å b: 104.776Å c: 113.163Å
α: 90° β: 111.13° γ: 90°
R-values:
R R work R free
0.172 0.17 0.214
Expression system: Escherichia coli BL21(DE3)

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Citations

3 review citations

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

1 mention without citation

Biochemical and Structural Characterization of Thermostable GH159 Glycoside Hydrolases Exhibiting α-L-Arabinofuranosidase Activity.
Baudrexl et al. (2022)