› 6i02

X-ray diffraction
2.45Å resolution

Structure of human D-glucuronyl C5 epimerase in complex with product

Released:
DOI: 10.2210/pdb6i02/pdb
PDB entry 6i02 coloured by chain, front view.
PDB entry 6i02 coloured by chain, side view.
PDB entry 6i02 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Substrate binding mode and catalytic mechanism of human heparan sulfate d-glucuronyl C5 epimerase.
Debarnot C, Monneau YR, Roig-Zamboni V, Delauzun V, Le Narvor C, Richard E, Hénault J, Goulet A, Fadel F, Vivès RR, Priem B, Bonnaffé D, Lortat-Jacob H, Bourne Y
Proc Natl Acad Sci U S A 116 6760-6765 (2019)
PMID: 30872481

Function and Biology Details

Reaction catalysed: 
Epimerization of D-glucuronate in heparosan-N-sulfate to L-iduronate.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-131793 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (8 distinct):
D-glucuronyl C5-epimerase Chains: A, B
Molecule details ›
Chains: A, B
Length: 527 amino acids
Theoretical weight: 60.29 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O94923 (Residues: 98-617; Coverage: 84%)
Gene names: GLCE, KIAA0836
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: GNS, IDR
Carbohydrate polymer
Carbohydrate polymer : NEW Components: GNS, IDR
Carbohydrate polymer
5 bound ligands:
Ligand CA 2 x CA
Ligand NAG 1 x NAG
Ligand GOL 11 x GOL
Ligand MES 1 x MES
Ligand P6G 1 x P6G
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P61
Unit cell:
a: 99.811Å b: 99.811Å c: 260.488Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.175 0.173 0.218
Expression system: Homo sapiens

Quick links

Citations

3 review citations

Heparan Sulfate Proteoglycans Biosynthesis and Post Synthesis Mechanisms Combine Few Enzymes and Few Core Proteins to Generate Extensive Structural and Functional Diversity.
Annaval et al. (2020)
2 more

1 mention without citation

Substrate binding mode and catalytic mechanism of human heparan sulfate d-glucuronyl C5 epimerase.
Debarnot et al. (2019)