9EKQ | pdb_00009ekq

Inhibiting the Virulence of Gut Bacteria through Blocking the Activation of a Two-component Lanthipeptide Toxin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 
    0.186 (Depositor), 0.183 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

Starting Model: in silico
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Combatting virulent gut bacteria by inhibiting the biosynthesis of a two-component lanthipeptide toxin.

Moreira, R.Chakraborty, B.Yang, Y.Padhi, C.Gilmore, M.S.Nair, S.K.van der Donk, W.A.

(2025) Nat Commun 16: 6936-6936

  • DOI: https://doi.org/10.1038/s41467-025-62161-7
  • Primary Citation of Related Structures:  
    9EKQ

  • PubMed Abstract: 

    The enterococcal cytolysin is a toxic, two-component ribosomally synthesized and post-translationally modified peptide (RiPP) produced by pathogenic Enterococcus faecalis. Cytolysin-producing (C+) E. faecalis resides in the gut microbiome in a commensal role, but results in negative clinical outcomes in alcoholic hepatitis patients. To potentially combat cytolysin virulence, we report inhibitors of its maturation. An extracellular serine protease CylA that is essential for toxin activation is chosen as target. A series of α-aminopeptide boronic acids are designed and synthesized that block cytolysin maturation at low micromolar to nanomolar concentrations in vitro. A crystal structure of CylA provides insights into substrate recognition, autocatalytic activation of the enzyme, and toxin maturation. The inhibitors block hemolytic activity, reduce the amount of cytolysin, and attenuate expression of the cytolysin biosynthetic gene cluster without impeding cell growth. These studies provide a potential route to the development of treatments for cytolysin-induced disease states.


  • Organizational Affiliation
    • Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lantibiotic leader peptide processing serine protease CylA402Enterococcus faecalisMutation(s): 0 
Gene Names: P018_02818
EC: 3.4.21
UniProt
Find proteins for A0A2P6AWB8 (Enterococcus faecalis)
Explore A0A2P6AWB8 
Go to UniProtKB:  A0A2P6AWB8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2P6AWB8
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free:  0.186 (Depositor), 0.183 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.442α = 90
b = 56.922β = 102.47
c = 50.824γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata processing
Aimlessdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R35GM151874-01

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-25
    Type: Initial release
  • Version 1.1: 2025-09-03
    Changes: Database references