› 3khu

X-ray diffraction
2.3Å resolution

Crystal structure of human UDP-glucose dehydrogenase Glu161Gln, in complex with thiohemiacetal intermediate

Released:
DOI: 10.2210/pdb3khu/pdb
PDB entry 3khu coloured by chain, front view.
PDB entry 3khu coloured by chain, side view.
PDB entry 3khu coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural and kinetic evidence that catalytic reaction of human UDP-glucose 6-dehydrogenase involves covalent thiohemiacetal and thioester enzyme intermediates.
Egger S, Chaikuad A, Klimacek M, Kavanagh KL, Oppermann U, Nidetzky B
OpenAccess logo J Biol Chem 287 2119-29 (2012)
PMID: 22123821

Function and Biology Details

Reaction catalysed: 
UDP-glucose + 2 NAD(+) + H(2)O = UDP-glucuronate + 2 NADH
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-130073 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
UDP-glucose 6-dehydrogenase Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 467 amino acids
Theoretical weight: 52.08 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O60701 (Residues: 1-466; Coverage: 94%)
Gene name: UGDH
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand UPG 12 x UPG
Ligand EDO 17 x EDO
Ligand EPE 1 x EPE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P21212
Unit cell:
a: 203.54Å b: 207.34Å c: 93.4Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.195 0.195 0.225
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Integration of Sugar Metabolism and Proteoglycan Synthesis by UDP-glucose Dehydrogenase.
Zimmer et al. (2021)
1 more

10 mentions without citation

Defined PEG smears as an alternative approach to enhance the search for crystallization conditions and crystal-quality improvement in reduced screens.
Chaikuad et al. (2015)
9 more