› 3wkx

X-ray diffraction
2Å resolution

Crystal structure of GH127 beta-L-arabinofuranosidase HypBA1 from Bifidobacterium longum arabinose complex form

Released:
DOI: 10.2210/pdb3wkx/pdb
PDB entry 3wkx coloured by chain, front view.
PDB entry 3wkx coloured by chain, side view.
PDB entry 3wkx coloured by chain, top view.
Source organism: Bifidobacterium longum subsp. longum JCM 1217
Primary publication:
Crystal structure of glycoside hydrolase family 127 β-l-arabinofuranosidase from Bifidobacterium longum.
Ito T, Saikawa K, Kim S, Fujita K, Ishiwata A, Kaeothip S, Arakawa T, Wakagi T, Beckham GT, Ito Y, Fushinobu S
Biochem Biophys Res Commun 447 32-7 (2014)
PMID: 24680821

Function and Biology Details

Reaction catalysed: 
Beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranose + H(2)O = 2 beta-L-arabinofuranose
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-123108 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Non-reducing end beta-L-arabinofuranosidase Chain: A
Molecule details ›
Chain: A
Length: 669 amino acids
Theoretical weight: 74.46 KDa
Source organism: Bifidobacterium longum subsp. longum JCM 1217
Expression system: Escherichia coli
UniProt:
  • Canonical: E8MGH8 (Residues: 1-658; Coverage: 100%)
Gene names: BLLJ_0211, hypBA1
Sequence domains:

Ligands and Environments

2 bound ligands:
Ligand FUB 1 x FUB
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P3221
Unit cell:
a: 77.726Å b: 77.726Å c: 252.668Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.229 0.226 0.279
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Plant Glycan Metabolism by Bifidobacteria.
Kelly et al. (2021)
2 more

3 mentions without citation

Structure and evolution of the bifidobacterial carbohydrate metabolism proteins and enzymes.
Fushinobu et al. (2021)
2 more