› 3vig

X-ray diffraction
0.99Å resolution

Crystal structure of beta-glucosidase from termite Neotermes koshunensis in complex with 1-deoxynojirimycin

Released:
DOI: 10.2210/pdb3vig/pdb
PDB entry 3vig coloured by chain, front view.
PDB entry 3vig coloured by chain, side view.
PDB entry 3vig coloured by chain, top view.
Source organism: Neotermes koshunensis
Primary publication:
High-resolution structures of Neotermes koshunensis β-glucosidase mutants provide insights into the catalytic mechanism and the synthesis of glucoconjugates.
Jeng WY, Wang NC, Lin CT, Chang WJ, Liu CI, Wang AH
Acta Crystallogr D Biol Crystallogr 68 829-38 (2012)
PMID: 22751668

Function and Biology Details

Reaction catalysed: 
Hydrolysis of terminal, non-reducing beta-D-glucosyl residues with release of beta-D-glucose
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-186121 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Beta-glucosidase Chain: A
Molecule details ›
Chain: A
Length: 487 amino acids
Theoretical weight: 55.63 KDa
Source organism: Neotermes koshunensis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8T0W7 (Residues: 21-498; Coverage: 100%)
Gene name: NkBG
Sequence domains: Glycosyl hydrolase family 1
Structure domains: Glycosidases

Ligands and Environments

5 bound ligands:
Ligand NOJ 1 x NOJ
Ligand EPE 1 x EPE
Ligand GOL 1 x GOL
Ligand NA 1 x NA
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: C2
Unit cell:
a: 93.108Å b: 68.559Å c: 75.144Å
α: 90° β: 95.54° γ: 90°
R-values:
R R work R free
0.131 0.13 0.146
Expression system: Escherichia coli

Quick links

Citations

12 citation in other articles

Oligomerization as a strategy for cold adaptation: Structure and dynamics of the GH1 β-glucosidase from Exiguobacterium antarcticum B7.
Zanphorlin et al. (2016)
11 more

3 mentions without citation

En Route to the Transformation of Glycoscience: A Chemist's Perspective on Internal and External Crossroads in Glycochemistry.
Crich D. (2021)
2 more