› 6ldb

X-ray diffraction
1.65Å resolution

Structure of Bifidobacterium dentium beta-glucuronidase complexed with uronic isofagomine

Released:
DOI: 10.2210/pdb6ldb/pdb
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PDB entry 6ldb coloured by chain, front view.
PDB entry 6ldb coloured by chain, side view.
PDB entry 6ldb coloured by chain, top view.
Source organism: Bifidobacterium dentium Bd1
Primary publication:
Entropy-driven binding of gut bacterial β-glucuronidase inhibitors ameliorates irinotecan-induced toxicity.
Lin HY, Chen CY, Lin TC, Yeh LF, Hsieh WC, Gao S, Burnouf PA, Chen BM, Hsieh TJ, Dashnyam P, Kuo YH, Tu Z, Roffler SR, Lin CH
OpenAccess logo Commun Biol 4 280 (2021)
PMID: 33664385

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-112399 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Beta-glucuronidase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 670 amino acids
Theoretical weight: 74.59 KDa
Source organism: Bifidobacterium dentium Bd1
Expression system: Escherichia coli
UniProt:
  • Canonical: D2Q7B1 (Residues: 1-668; Coverage: 100%)
Gene names: BDP_2112, lacZ1
Sequence domains:

Ligands and Environments

1 bound ligand:
Ligand SJ5 4 x SJ5
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE BL13C1
Spacegroup: P21
Unit cell:
a: 92.69Å b: 104.64Å c: 160.504Å
α: 90° β: 91.29° γ: 90°
R-values:
R R work R free
0.156 0.156 0.183
Expression system: Escherichia coli

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Citations

5 review citations

Cancer pharmacomicrobiomics: targeting microbiota to optimise cancer therapy outcomes.
Ting et al. (2022)
4 more

2 mentions without citation

A New Paradigm in the Relationship between Gut Microbiota and Breast Cancer: β-glucuronidase Enzyme Identified as Potential Therapeutic Target.
Fernández-Murga et al. (2023)
1 more

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