Structure of Bifidobacterium dentium beta-glucuronidase complexed with C6-hexyl uronic isofagomine

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.201 

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Entropy-driven binding of gut bacterial beta-glucuronidase inhibitors ameliorates irinotecan-induced toxicity.

Lin, H.Y.Chen, C.Y.Lin, T.C.Yeh, L.F.Hsieh, W.C.Gao, S.Burnouf, P.A.Chen, B.M.Hsieh, T.J.Dashnyam, P.Kuo, Y.H.Tu, Z.Roffler, S.R.Lin, C.H.

(2021) Commun Biol 4: 280-280

  • DOI: https://doi.org/10.1038/s42003-021-01815-w
  • Primary Citation of Related Structures:  
    6LD0, 6LD6, 6LDB, 6LDC, 6LDD, 6LEG, 6LEJ, 6LEL, 6LEM

  • PubMed Abstract: 

    Irinotecan inhibits cell proliferation and thus is used for the primary treatment of colorectal cancer. Metabolism of irinotecan involves incorporation of β-glucuronic acid to facilitate excretion. During transit of the glucuronidated product through the gastrointestinal tract, an induced upregulation of gut microbial β-glucuronidase (GUS) activity may cause severe diarrhea and thus force many patients to stop treatment. We herein report the development of uronic isofagomine (UIFG) derivatives that act as general, potent inhibitors of bacterial GUSs, especially those of Escherichia coli and Clostridium perfringens. The best inhibitor, C6-nonyl UIFG, is 23,300-fold more selective for E. coli GUS than for human GUS (K i  = 0.0045 and 105 μM, respectively). Structural evidence indicated that the loss of coordinated water molecules, with the consequent increase in entropy, contributes to the high affinity and selectivity for bacterial GUSs. The inhibitors also effectively reduced irinotecan-induced diarrhea in mice without damaging intestinal epithelial cells.

  • Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LacZ1 Beta-galactosidase
A, B, C, D
670Bifidobacterium dentium Bd1Mutation(s): 0 
Gene Names: lacZ1BDP_2112
Find proteins for D2Q7B1 (Bifidobacterium dentium (strain ATCC 27534 / DSM 20436 / JCM 1195 / Bd1))
Explore D2Q7B1 
Go to UniProtKB:  D2Q7B1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD2Q7B1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.914α = 90
b = 105.395β = 91.16
c = 162.293γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
Blu-Icedata collection

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Science and Technology (Taiwan)Taiwan108-2113-M-001 -001

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-27
    Type: Initial release
  • Version 1.1: 2021-08-11
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Refinement description