6ED1 image
Entry Detail
PDB ID:
6ED1
Keywords:
Title:
Bacteroides dorei Beta-glucuronidase
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2018-08-08
Release Date:
2019-02-13
Method Details:
Experimental Method:
Resolution:
2.90 Å
R-Value Free:
0.26
R-Value Work:
0.17
R-Value Observed:
0.18
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Glycosyl hydrolase family 2, sugar binding domain protein
Chain IDs:A, B, C, D
Chain Length:879
Number of Molecules:4
Biological Source:Bacteroides dorei
Ligand Molecules
Primary Citation
Structure, function, and inhibition of drug reactivating human gut microbial beta-glucuronidases.
Sci Rep 9 825 825 (2019)
PMID: 30696850 DOI: 10.1038/s41598-018-36069-w

Abstact

Bacterial β-glucuronidase (GUS) enzymes cause drug toxicity by reversing Phase II glucuronidation in the gastrointestinal tract. While many human gut microbial GUS enzymes have been examined with model glucuronide substrates like p-nitrophenol-β-D-glucuronide (pNPG), the GUS orthologs that are most efficient at processing drug-glucuronides remain unclear. Here we present the crystal structures of GUS enzymes from human gut commensals Lactobacillus rhamnosus, Ruminococcus gnavus, and Faecalibacterium prausnitzii that possess an active site loop (Loop 1; L1) analogous to that found in E. coli GUS, which processes drug substrates. We also resolve the structure of the No Loop GUS from Bacteroides dorei. We then compare the pNPG and diclofenac glucuronide processing abilities of a panel of twelve structurally diverse GUS proteins, and find that the new L1 GUS enzymes presented here process small glucuronide substrates inefficiently compared to previously characterized L1 GUS enzymes like E. coli GUS. We further demonstrate that our GUS inhibitors, which are effective against some L1 enzymes, are not potent towards all. Our findings pinpoint active site structural features necessary for the processing of drug-glucuronide substrates and the inhibition of such processing.

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Primary Citation of related structures