› 2eae

X-ray diffraction
1.8Å resolution

Crystal structure of 1,2-a-L-fucosidase from Bifidobacterium bifidum in complexes with products

Released:
DOI: 10.2210/pdb2eae/pdb
PDB entry 2eae coloured by chain, front view.
PDB entry 2eae coloured by chain, side view.
PDB entry 2eae 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 Chain: A
Molecule details ›
Chain: A
Length: 898 amino acids
Theoretical weight: 96.8 KDa
Source organism: Bifidobacterium bifidum
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q6JV24 (Residues: 577-1474; Coverage: 47%)
Gene name: afcA
Sequence domains:
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: GLC, GAL
Carbohydrate polymer
3 bound ligands:
Ligand FUC 1 x FUC
Ligand FUL 1 x FUL
Ligand CA 2 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P212121
Unit cell:
a: 64.519Å b: 70.878Å c: 170.979Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.182 0.18 0.219
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

15 review citations

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

3 mentions without citation

Glycan complexity dictates microbial resource allocation in the large intestine.
Rogowski et al. (2015)
2 more