› 6i01

X-ray diffraction
2.1Å resolution

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

Released:
DOI: 10.2210/pdb6i01/pdb
PDB entry 6i01 coloured by chain, front view.
PDB entry 6i01 coloured by chain, side view.
PDB entry 6i01 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 (6 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, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: BDP, GNS
Carbohydrate polymer
4 bound ligands:
Ligand NAG 1 x NAG
Ligand GOL 14 x GOL
Ligand ACT 1 x ACT
Ligand CA 2 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID30B
Spacegroup: P61
Unit cell:
a: 99.675Å b: 99.675Å c: 258.823Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.164 0.162 0.195
Expression system: Homo sapiens

Quick links

Citations

1 review citation

Heparan Sulfate Biosynthesis and Sulfation Profiles as Modulators of Cancer Signalling and Progression.
Marques et al. (2021)
5 other articles

2 mentions without citation

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)
1 more