6BO6

Eubacterium eligens beta-glucuronidase bound to UNC4917 glucuronic acid conjugate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.801 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.258 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Gut Microbial beta-Glucuronidase Inhibition via Catalytic Cycle Interception.

Pellock, S.J.Creekmore, B.C.Walton, W.G.Mehta, N.Biernat, K.A.Cesmat, A.P.Ariyarathna, Y.Dunn, Z.D.Li, B.Jin, J.James, L.I.Redinbo, M.R.

(2018) ACS Cent Sci 4: 868-879

  • DOI: 10.1021/acscentsci.8b00239
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Microbial β-glucuronidases (GUSs) cause severe gut toxicities that limit the efficacy of cancer drugs and other therapeutics. Selective inhibitors of bacterial GUS have been shown to alleviate these side effects. Using structural and chemical biology ...

    Microbial β-glucuronidases (GUSs) cause severe gut toxicities that limit the efficacy of cancer drugs and other therapeutics. Selective inhibitors of bacterial GUS have been shown to alleviate these side effects. Using structural and chemical biology, mass spectrometry, and cell-based assays, we establish that piperazine-containing GUS inhibitors intercept the glycosyl-enzyme catalytic intermediate of these retaining glycosyl hydrolases. We demonstrate that piperazine-based compounds are substrate-dependent GUS inhibitors that bind to the GUS-GlcA catalytic intermediate as a piperazine-linked glucuronide (GlcA, glucuronic acid). We confirm the GUS-dependent formation of inhibitor-glucuronide conjugates by LC-MS and show that methylated piperazine analogs display significantly reduced potencies. We further demonstrate that a range of approved piperazine- and piperidine-containing drugs from many classes, including those for the treatment of depression, infection, and cancer, function by the same mechanism, and we confirm through gene editing that these compounds selectively inhibit GUS in living bacterial cells. Together, these data reveal a unique mechanism of GUS inhibition and show that a range of therapeutics may impact GUS activities in the human gut.


    Organizational Affiliation

    Department of Chemistry, Center for Integrated Chemical Biology and Drug Discovery, Eshelman School of Pharmacy, and Integrated Program for Biological and Genome Sciences, and Departments of Biochemistry and Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycoside Hydrolase Family 2 candidate b-glucuronidase
A
611Eubacterium eligens (strain ATCC 27750 / VPI C15-48)Mutation(s): 0 
Find proteins for C4Z6Z2 (Eubacterium eligens (strain ATCC 27750 / VPI C15-48))
Go to UniProtKB:  C4Z6Z2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
E0V
Query on E0V

Download SDF File 
Download CCD File 
A
4-(4-beta-D-glucopyranuronosylpiperazin-1-yl)-2,7-bis(methylamino)pyrido[3',2':4,5]thieno[3,2-d]pyrimidine
C21 H27 N7 O6 S
FTTVFXSMHOJZPZ-KVMGVCFTSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.801 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.258 
  • Space Group: P 64 2 2
Unit Cell:
Length (Å)Angle (°)
a = 179.443α = 90.00
b = 179.443β = 90.00
c = 133.778γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States--

Revision History 

  • Version 1.0: 2018-07-25
    Type: Initial release
  • Version 1.1: 2019-02-06
    Type: Data collection, Database references
  • Version 1.2: 2019-02-20
    Type: Author supporting evidence, Data collection