8T88

FphE, Staphylococcus aureus fluorophosphonate-binding serine hydrolases E, Oxadiazolone JJ004 bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Development of Oxadiazolone Activity-Based Probes Targeting FphE for Specific Detection of Staphylococcus aureus Infections.

Jo, J.Upadhyay, T.Woods, E.C.Park, K.W.Pedowitz, N.J.Jaworek-Korjakowska, J.Wang, S.Valdez, T.A.Fellner, M.Bogyo, M.

(2024) J Am Chem Soc 146: 6880-6892

  • DOI: https://doi.org/10.1021/jacs.3c13974
  • Primary Citation of Related Structures:  
    8T87, 8T88

  • PubMed Abstract: 

    Staphylococcus aureus ( S. aureus ) is a major human pathogen that is responsible for a wide range of systemic infections. Since its propensity to form biofilms in vivo poses formidable challenges for both detection and treatment, tools that can be used to specifically image S. aureus biofilms are highly valuable for clinical management. Here, we describe the development of oxadiazolone-based activity-based probes to target the S. aureus -specific serine hydrolase FphE. Because this enzyme lacks homologues in other bacteria, it is an ideal target for selective imaging of S. aureus infections. Using X-ray crystallography, direct cell labeling, and mouse models of infection, we demonstrate that oxadiazolone-based probes enable specific labeling of S. aureus bacteria through the direct covalent modification of the FphE active site serine. These results demonstrate the utility of the oxadizolone electrophile for activity-based probes and validate FphE as a target for the development of imaging contrast agents for the rapid detection of S. aureus infections.


  • Organizational Affiliation

    Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fluorophosphonate-binding serine hydrolase E
A, B
279Staphylococcus aureus USA300-0114Mutation(s): 0 
Gene Names: SAUSA300_2518
EC: 3
UniProt
Find proteins for Q2FDS6 (Staphylococcus aureus (strain USA300))
Explore Q2FDS6 
Go to UniProtKB:  Q2FDS6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FDS6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.743α = 90
b = 74.271β = 91.7
c = 73.638γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2024-03-06 
  • Deposition Author(s): Fellner, M.

Funding OrganizationLocationGrant Number
Capability Build Funding - New Zealand Synchrotron Group LtdNew Zealand--

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-06
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Database references