8UWM | pdb_00008uwm

FphE, Staphylococcus aureus fluorophosphonate-binding serine hydrolases E, borolane-based compound Q41 bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 
    0.204 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.168 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 
    0.170 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Identification of covalent inhibitors of Staphylococcus aureus serine hydrolases important for virulence and biofilm formation.

Upadhyay, T.Woods, E.C.Dela Ahator, S.Julin, K.Faucher, F.F.Uddin, M.J.Hollander, M.J.Pedowitz, N.J.Abegg, D.Hammond, I.Eke, I.E.Wang, S.Chen, S.Bennett, J.M.Jo, J.Lentz, C.S.Adibekian, A.Fellner, M.Bogyo, M.

(2025) Nat Commun 16: 5046-5046

  • DOI: https://doi.org/10.1038/s41467-025-60367-3
  • Primary Citation of Related Structures:  
    8TAV, 8TFW, 8UGM, 8UIX, 8UWM

  • PubMed Abstract: 

    Staphylococcus aureus is a leading cause of bacteria-associated mortality worldwide. New tools are needed to both image and treat this pathogen. We previously identified a group of S. aureus serine hydrolases (Fphs), which regulate aspects of virulence and lipid metabolism. However, due to high structural and functional similarities, it remains challenging to distinguish the specific roles of members of this family. Here, we apply a high-throughput screening approach using a library of covalent electrophiles to identify inhibitors for FphB, FphE, and FphH. We identify selective covalent inhibitors for each target without the need for extensive medicinal chemistry optimization. Structural and biochemical analysis identify novel binding modes for several of the inhibitors. Functional studies using the inhibitors suggest that all three hydrolases likely play distinct functional roles in biofilm formation and virulence. This approach has the potential to be applied to target hydrolases in other diverse pathogens or higher eukaryotes.


  • Organizational Affiliation
    • Department of Pathology, Stanford School of Medicine, Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.

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 Q2FV39 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FV39 
Go to UniProtKB:  Q2FV39
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FV39
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free:  0.204 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.168 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 0.170 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.887α = 90
b = 77.993β = 90
c = 110.457γ = 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: 2024-11-20 
  • 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: 2024-11-20
    Type: Initial release
  • Version 1.1: 2025-06-25
    Changes: Database references, Source and taxonomy