› 2yfn

X-ray diffraction
1.45Å resolution

galactosidase domain of alpha-galactosidase-sucrose kinase, AgaSK

Released:
DOI: 10.2210/pdb2yfn/pdb
PDB entry 2yfn coloured by chain, front view.
PDB entry 2yfn coloured by chain, side view.
PDB entry 2yfn coloured by chain, top view.
Source organism: [Ruminococcus] gnavus E1
Primary publication:
α-Galactosidase/sucrose kinase (AgaSK), a novel bifunctional enzyme from the human microbiome coupling galactosidase and kinase activities.
Bruel L, Sulzenbacher G, Cervera Tison M, Pujol A, Nicoletti C, Perrier J, Galinier A, Ropartz D, Fons M, Pompeo F, Giardina T
J Biol Chem 286 40814-23 (2011)
PMID: 21931163

Function and Biology Details

Reaction catalysed: 
Hydrolysis of terminal, non-reducing alpha-D-galactose residues in alpha-D-galactosides, including galactose oligosaccharides, galactomannans and galactolipids
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-124448 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Bifunctional alpha-galactosidase/sucrose kinase AgaSK Chain: A
Molecule details ›
Chain: A
Length: 720 amino acids
Theoretical weight: 81.33 KDa
Source organism: [Ruminococcus] gnavus E1
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: G4T4R7 (Residues: 1-720; Coverage: 77%)
Gene names: RUGNEv3_61222, agaSK
Sequence domains:
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand GOL 2 x GOL
Ligand EDO 1 x EDO
Ligand PO4 1 x PO4
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: I222
Unit cell:
a: 105.058Å b: 111.65Å c: 154.886Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.131 0.13 0.15
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

8 review citations

Microbiota and gut-liver axis: their influences on obesity and obesity-related liver disease.
Vajro et al. (2013)
7 more

5 mentions without citation

Ruminococcus gnavus: friend or foe for human health.
Crost et al. (2023)
4 more