› 3uet

X-ray diffraction
2.1Å resolution

Crystal structure of alpha-1,3/4-fucosidase from Bifidobacterium longum subsp. infantis D172A/E217A mutant complexed with lacto-N-fucopentaose II

Released:
DOI: 10.2210/pdb3uet/pdb
PDB entry 3uet coloured by chain, front view.
PDB entry 3uet coloured by chain, side view.
PDB entry 3uet coloured by chain, top view.
Source organism: Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088
Primary publication:
1,3-1,4-α-L-fucosynthase that specifically introduces Lewis a/x antigens into type-1/2 chains.
Sakurama H, Fushinobu S, Hidaka M, Yoshida E, Honda Y, Ashida H, Kitaoka M, Kumagai H, Yamamoto K, Katayama T
J Biol Chem 287 16709-19 (2012)
PMID: 22451675

Function and Biology Details

Reaction catalysed: 
Hydrolysis of (1->3)-linkages between alpha-L-fucose and N-acetylglucosamine residues in glycoproteins
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-110471 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
F5/8 type C domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 478 amino acids
Theoretical weight: 52.99 KDa
Source organism: Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088
Expression system: Escherichia coli
UniProt:
  • Canonical: B7GNN8 (Residues: 1-478; Coverage: 100%)
Gene name: Blon_2336
Sequence domains:
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, GAL, FUC
Carbohydrate polymer
2 bound ligands:
Ligand NA 2 x NA
Ligand EDO 2 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P212121
Unit cell:
a: 82.588Å b: 105.971Å c: 120.715Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.175 0.173 0.223
Expression system: Escherichia coli

Quick links

Citations

13 review citations

Varied Pathways of Infant Gut-Associated Bifidobacterium to Assimilate Human Milk Oligosaccharides: Prevalence of the Gene Set and Its Correlation with Bifidobacteria-Rich Microbiota Formation.
Sakanaka et al. (2019)
12 more

7 mentions without citation

Conformations of the type-1 lacto-N-biose I unit in protein complex structures.
Fushinobu S. (2018)
6 more