› 3vnz

X-ray diffraction
1.8Å resolution

Crystal structure of beta-glucuronidase from Acidobacterium capsulatum in complex with D-glucuronic acid

Released:
DOI: 10.2210/pdb3vnz/pdb
PDB entry 3vnz coloured by chain, front view.
PDB entry 3vnz coloured by chain, side view.
PDB entry 3vnz coloured by chain, top view.
Source organism: Acidobacterium capsulatum ATCC 51196
Primary publication:
Structural and biochemical characterization of glycoside hydrolase family 79 β-glucuronidase from Acidobacterium capsulatum.
Michikawa M, Ichinose H, Momma M, Biely P, Jongkees S, Yoshida M, Kotake T, Tsumuraya Y, Withers SG, Fujimoto Z, Kaneko S
J Biol Chem 287 14069-77 (2012)
PMID: 22367201

Function and Biology Details

Reaction catalysed: 
A beta-D-glucuronoside + H(2)O = D-glucuronate + an alcohol
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-111104 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Beta-glucuronidase C-terminal domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 488 amino acids
Theoretical weight: 52.34 KDa
Source organism: Acidobacterium capsulatum ATCC 51196
Expression system: Escherichia coli
UniProt:
  • Canonical: C1F2K5 (Residues: 1-475; Coverage: 100%)
Gene name: ACP_2665
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand BDP 1 x BDP
Ligand PO4 1 x PO4
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NE3A
Spacegroup: I4122
Unit cell:
a: 101.271Å b: 101.271Å c: 217.768Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.201 0.199 0.23
Expression system: Escherichia coli

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Citations

4 review citations

Uronic polysaccharide degrading enzymes.
Garron et al. (2014)
3 more

4 mentions without citation

Kinetic analysis and molecular modeling of the inhibition mechanism of roneparstat (SST0001) on human heparanase.
Pala et al. (2016)
3 more