› 5bxs

X-ray diffraction
2.2Å resolution

LNBase in complex with LNB-NHAcCAS

Released:
DOI: 10.2210/pdb5bxs/pdb
PDB entry 5bxs coloured by chain, front view.
PDB entry 5bxs coloured by chain, side view.
PDB entry 5bxs coloured by chain, top view.
Source organism: Bifidobacterium bifidum JCM 1254
Primary publication:
Gaining insight into the catalysis by GH20 lacto-N-biosidase using small molecule inhibitors and structural analysis.
Hattie M, Ito T, Debowski AW, Arakawa T, Katayama T, Yamamoto K, Fushinobu S, Stubbs KA
Chem Commun (Camb) 51 15008-11 (2015)
PMID: 26312778

Function and Biology Details

Reaction catalysed: 
Beta-D-Gal-(1->3)-beta-D-GlcNAc-(1->3)-beta-D-Gal-(1->4)-D-Glc + H(2)O = beta-D-Gal-(1->3)-D-GlcNAc + beta-D-Gal-(1->4)-D-Glc
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-109913 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lacto-N-biosidase Chains: A, B
Molecule details ›
Chains: A, B
Length: 644 amino acids
Theoretical weight: 71.89 KDa
Source organism: Bifidobacterium bifidum JCM 1254
Expression system: Escherichia coli
UniProt:
  • Canonical: B3TLD6 (Residues: 41-663; Coverage: 58%)
Gene name: lnbB
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand GAL 2 x GAL
Ligand GC2 2 x GC2
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NE3A
Spacegroup: P21212
Unit cell:
a: 116.678Å b: 131.699Å c: 104.531Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.193 0.191 0.238
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Host-derived glycans serve as selected nutrients for the gut microbe: human milk oligosaccharides and bifidobacteria.
Katayama T. (2016)
1 more