› 5yaq

X-ray diffraction
1.99Å resolution

Crystal structure of scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity complexed with scyllo-inosose

Released:
DOI: 10.2210/pdb5yaq/pdb
PDB entry 5yaq coloured by chain, front view.
PDB entry 5yaq coloured by chain, side view.
PDB entry 5yaq coloured by chain, top view.
Source organism: Paracoccus laeviglucosivorans
Primary publication:
Structural basis of L-glucose oxidation by scyllo-inositol dehydrogenase: Implications for a novel enzyme subfamily classification.
Fukano K, Ozawa K, Kokubu M, Shimizu T, Ito S, Sasaki Y, Nakamura A, Yajima S
OpenAccess logo PLoS One 13 e0198010 (2018)
PMID: 29799855

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-125636 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 380 amino acids
Theoretical weight: 41.4 KDa
Source organism: Paracoccus laeviglucosivorans
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: K7ZP76 (Residues: 1-372; Coverage: 100%)
Gene names: SAMN06265221_102142, lgdA
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand NAD 4 x NAD
Ligand ISE 3 x ISE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P212121
Unit cell:
a: 86.55Å b: 121.243Å c: 140.395Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.181 0.18 0.194
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 citation in other articles

Anaerobic peroxisomes in Entamoeba histolytica metabolize myo-inositol.
Verner et al. (2021)
1 more

2 mentions without citation

Identification, functional characterization, and crystal structure determination of bacterial levoglucosan dehydrogenase.
Sugiura et al. (2018)
1 more