› 2eac

X-ray diffraction
2.1Å resolution

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

Released:
DOI: 10.2210/pdb2eac/pdb
PDB entry 2eac coloured by chain, front view.
PDB entry 2eac coloured by chain, side view.
PDB entry 2eac 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
Macromolecule:
BIG2 domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 899 amino acids
Theoretical weight: 96.97 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

2 bound ligands:
Ligand CA 4 x CA
Ligand DFU 2 x DFU
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P21
Unit cell:
a: 90.668Å b: 111.702Å c: 98.346Å
α: 90° β: 95.31° γ: 90°
R-values:
R R work R free
0.153 0.15 0.198
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

15 review citations

Nursing our microbiota: molecular linkages between bifidobacteria and milk oligosaccharides.
Sela et al. (2010)
14 more

3 mentions without citation

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