› 2ead

X-ray diffraction
1.89Å resolution

Crystal structure of 1,2-a-L-fucosidase from Bifidobacterium bifidum in complex with substrate

Released:
DOI: 10.2210/pdb2ead/pdb
PDB entry 2ead coloured by chain, front view.
PDB entry 2ead coloured by chain, side view.
PDB entry 2ead coloured by chain, top view.
Source organism: Bifidobacterium bifidum
Primary publication:
Structural basis of the catalytic reaction mechanism of novel 1,2-alpha-L-fucosidase from Bifidobacterium bifidum.
Nagae M, Tsuchiya A, Katayama T, Yamamoto K, Wakatsuki S, Kato R
J Biol Chem 282 18497-18509 (2007)
PMID: 17459873

Function and Biology Details

Reaction catalysed: 
Methyl-2-alpha-L-fucopyranosyl-beta-D-galactoside + H(2)O = L-fucose + methyl beta-D-galactoside
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-179824 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
BIG2 domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 899 amino acids
Theoretical weight: 96.91 KDa
Source organism: Bifidobacterium bifidum
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q6JV24 (Residues: 576-1474; Coverage: 47%)
Gene name: afcA
Sequence domains:
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: BGC, GAL, FUC
Carbohydrate polymer
2 bound ligands:
Ligand CA 4 x CA
Ligand MES 1 x MES
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-6A
Spacegroup: P21
Unit cell:
a: 88.448Å b: 72.743Å c: 129.207Å
α: 90° β: 96.68° γ: 90°
R-values:
R R work R free
0.162 0.159 0.21
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

14 review citations

Mucin glycan foraging in the human gut microbiome.
Tailford et al. (2015)
13 more

3 mentions without citation

Structure and function of microbial α-l-fucosidases: a mini review.
Wu et al. (2023)
2 more