7KGY | pdb_00007kgy

Beta-glucuronidase from Faecalibacterium prausnitzii bound to the inhibitor UNC10201652-glucuronide

PDB DOI: https://doi.org/10.2210/pdb7KGY/pdb

Classification: HYDROLASE/INHIBITOR
Organism(s): Faecalibacterium prausnitzii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-10-19 Released: 2021-11-10
Deposition Author(s): Simpson, J.B., Redinbo, M.R.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.193 (Depositor)
R-Value Work:
0.147 (Depositor)
R-Value Observed:
0.147 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Microbial enzymes induce colitis by reactivating triclosan in the mouse gastrointestinal tract.

Zhang, J., Walker, M.E., Sanidad, K.Z., Zhang, H., Liang, Y., Zhao, E., Chacon-Vargas, K., Yeliseyev, V., Parsonnet, J., Haggerty, T.D., Wang, G., Simpson, J.B., Jariwala, P.B., Beaty, V.V., Yang, J., Yang, H., Panigrahy, A., Minter, L.M., Kim, D., Gibbons, J.G., Liu, L., Li, Z., Xiao, H., Borlandelli, V., Overkleeft, H.S., Cloer, E.W., Major, M.B., Goldfarb, D., Cai, Z., Redinbo, M.R., Zhang, G.

(2022) Nat Commun 13: 136-136

PubMed: 35013263 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-021-27762-y
Primary Citation Related Structures:
7KGY, 7KGZ

PubMed Abstract:
Emerging research supports that triclosan (TCS), an antimicrobial agent found in thousands of consumer products, exacerbates colitis and colitis-associated colorectal tumorigenesis in animal models. While the intestinal toxicities of TCS require the presence of gut microbiota, the molecular mechanisms involved have not been defined. Here we show that intestinal commensal microbes mediate metabolic activation of TCS in the colon and drive its gut toxicology. Using a range of in vitro, ex vivo, and in vivo approaches, we identify specific microbial β-glucuronidase (GUS) enzymes involved and pinpoint molecular motifs required to metabolically activate TCS in the gut. Finally, we show that targeted inhibition of bacterial GUS enzymes abolishes the colitis-promoting effects of TCS, supporting an essential role of specific microbial proteins in TCS toxicity. Together, our results define a mechanism by which intestinal microbes contribute to the metabolic activation and gut toxicity of TCS, and highlight the importance of considering the contributions of the gut microbiota in evaluating the toxic potential of environmental chemicals.

Organizational Affiliation

Department of Food Science, University of Massachusetts, Amherst, MA, USA.

Departments of Chemistry, Biochemistry, Microbiology and Genomics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.

State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, SAR, China.

Department of Occupational and Environmental Health, School of Public Health, Qingdao University, Qingdao, China.

Massachusetts Host-Microbiota Center, Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.

Department of Medicine and Department of Health Research and Policy, Stanford University, Stanford, CA, USA.

School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China.

Department of Entomology and Nematology, University of California, Davis, CA, USA.

Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA, USA.

Department of Mathematics and Statistics, University of Massachusetts, Amherst, MA, USA.

Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA, USA.

Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands.

Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.

Department of Cell Biology and Physiology, and Department of Otolaryngology, Washington University, St. Louis, MO, USA.

Department of Cell Biology and Physiology, Institute for Informatics, Washington University, St. Louis, MO, USA.

State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, SAR, China. zwcai@hkbu.edu.hk.

Departments of Chemistry, Biochemistry, Microbiology and Genomics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. redinbo@unc.edu.

Department of Food Science, University of Massachusetts, Amherst, MA, USA. zhanggd@nus.edu.sg.

Department of Food Science and Technology, National University of Singapore, Singapore, Singapore. zhanggd@nus.edu.sg.

Macromolecule Content

Total Structure Weight: 279.05 kDa
Atom Count: 20,821
Modeled Residue Count: 2,367
Deposited Residue Count: 2,432
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-glucuronidase	A, B, C, D	608	Faecalibacterium prausnitzii	Mutation(s): 0 Gene Names: uidA, ERS852426_02720 EC: 3.2.1.31

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
I9G (Subject of Investigation/LOI) Query on I9G Download:Ideal Coordinates CCD File SDF format, chain J [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain J [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain J [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], J [auth D]	8-(4-beta-D-glucopyranuronosylpiperazin-1-yl)-5-(morpholin-4-yl)-1,2,3,4-tetrahydro[1,2,3]triazino[4',5':4,5]thieno[2,3 -c]isoquinoline C₂₆ H₃₃ N₇ O₇ S AQRGEQSNANJABA-WFFUTXBBSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain J [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain J [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain K [auth D] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain K [auth D] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], K [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth D]