8GET | pdb_00008get

R. hominis 2 beta-glucuronidase bound to norquetiapine-glucuronide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.269 (Depositor), 0.271 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8GET

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Gut microbial beta-glucuronidases influence endobiotic homeostasis and are modulated by diverse therapeutics.

Simpson, J.B.Walker, M.E.Sekela, J.J.Ivey, S.M.Jariwala, P.B.Storch, C.M.Kowalewski, M.E.Graboski, A.L.Lietzan, A.D.Walton, W.G.Davis, K.A.Cloer, E.W.Borlandelli, V.Hsiao, Y.C.Roberts, L.R.Perlman, D.H.Liang, X.Overkleeft, H.S.Bhatt, A.P.Lu, K.Redinbo, M.R.

(2024) Cell Host Microbe 32: 925-944.e10

  • DOI: https://doi.org/10.1016/j.chom.2024.04.018
  • Primary Citation Related Structures: 
    8GEN, 8GEO, 8GEQ, 8GER, 8GES, 8GET

  • PubMed Abstract: 

    Hormones and neurotransmitters are essential to homeostasis, and their disruptions are connected to diseases ranging from cancer to anxiety. The differential reactivation of endobiotic glucuronides by gut microbial β-glucuronidase (GUS) enzymes may influence interindividual differences in the onset and treatment of disease. Using multi-omic, in vitro, and in vivo approaches, we show that germ-free mice have reduced levels of active endobiotics and that distinct gut microbial Loop 1 and FMN GUS enzymes drive hormone and neurotransmitter reactivation. We demonstrate that a range of FDA-approved drugs prevent this reactivation by intercepting the catalytic cycle of the enzymes in a conserved fashion. Finally, we find that inhibiting GUS in conventional mice reduces free serotonin and increases its inactive glucuronide in the serum and intestines. Our results illuminate the indispensability of gut microbial enzymes in sustaining endobiotic homeostasis and indicate that therapeutic disruptions of this metabolism promote interindividual response variabilities.


  • Organizational Affiliation
    • Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA.

Macromolecule Content 

  • Total Structure Weight: 347.28 kDa 
  • Atom Count: 20,670 
  • Modeled Residue Count: 2,565 
  • Deposited Residue Count: 3,028 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
beta-galactosidase
A, B, C, D
757Roseburia hominisMutation(s): 0 
Gene Names: DWX93_05255
UniProt
Find proteins for A0A395V8I7 (Roseburia hominis)
Explore A0A395V8I7 
Go to UniProtKB:  A0A395V8I7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A395V8I7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZG5

Query on ZG5



Download:Ideal Coordinates CCD File
M [auth C]11-(4-beta-D-glucopyranuronosylpiperazin-1-yl)dibenzo[b,f][1,4]thiazepine
C23 H25 N3 O6 S
UKCFGNFADWVWOZ-SXFAUFNYSA-N
FMN

Query on FMN



Download:Ideal Coordinates CCD File
G [auth A],
L [auth B],
P [auth C]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
BDP

Query on BDP



Download:Ideal Coordinates CCD File
F [auth A],
K [auth B],
Q [auth D]
beta-D-glucopyranuronic acid
C6 H10 O7
AEMOLEFTQBMNLQ-QIUUJYRFSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A]
H [auth B]
I [auth B]
J [auth B]
N [auth C]
E [auth A],
H [auth B],
I [auth B],
J [auth B],
N [auth C],
O [auth C],
R [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.269 (Depositor), 0.271 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.466α = 90
b = 146.29β = 90
c = 281.432γ = 90
Software Package:
Software NamePurpose
phenix.refinerefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM135218

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-20
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Database references
  • Version 1.2: 2024-06-26
    Changes: Database references