6VHD

FphF, Staphylococcus aureus fluorophosphonate-binding serine hydrolases F, KT129 bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

wwPDB Validation 3D Report Full Report



Literature

Structural basis for the inhibitor and substrate specificity of the unique Fph serine hydrolases of Staphylococcus aureus.

Fellner, M.Lentz, C.S.Jamieson, S.A.Brewster, J.L.Chen, L.Bogyo, M.Mace, P.D.

(2020) ACS Infect Dis 

  • DOI: 10.1021/acsinfecdis.0c00503
  • Primary Citation of Related Structures:  
    6VHE, 6VHD, 6VH9, 6WCX

  • PubMed Abstract: 
  • Staphylococcus aureus is a prevalent bacterial pathogen in both community and hospital settings, and its treatment is made particularly difficult by resilience within biofilms. Within this niche, serine hydrolase enzymes play a key role in generating ...

    Staphylococcus aureus is a prevalent bacterial pathogen in both community and hospital settings, and its treatment is made particularly difficult by resilience within biofilms. Within this niche, serine hydrolase enzymes play a key role in generating and maintaining the biofilm matrix. Activity-based profiling has previously identified a family of serine hydrolases, designated fluorophosphonate-binding hydrolases (Fphs), some of which contribute to the virulence of S. aureus in vivo. These ten Fph proteins have limited annotation, and have few, if any, characterized bacterial or mammalian homologs. This suggests unique hydrolase functions even within bacterial species. Here we report structures of one of the most abundant Fph family members, FphF. Our structures capture FphF alone, covalently bound to a substrate analog, and bound to small molecule inhibitors that occupy the hydrophobic substrate-binding pocket. In line with these findings, we show that FphF has promiscuous esterase activity towards hydrophobic lipid substrates. We present docking studies that characterize interactions of inhibitors and substrates within the active site environment, which can be extended to other Fph family members. Comparison of FphF to other esterases and the wider Fph protein family suggest that FphF forms a new esterase subfamily. Our data suggest that other Fph enzymes, including the virulence factor FphB, are likely to have more restricted substrate profiles than FphF. This work demonstrates a clear molecular rationale for the specificity of fluorophosphonate probes that target FphF and provides a structural template for the design of enhanced probes and inhibitors of the Fph family of serine hydrolases.


    Organizational Affiliation

    Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Esterase family proteinA, B, C, D255Staphylococcus aureusMutation(s): 0 
Gene Names: 
EC: 3.1.2.12
Find proteins for A0A0D6GS23 (Staphylococcus aureus)
Explore A0A0D6GS23 
Go to UniProtKB:  A0A0D6GS23
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6WG
Query on 6WG

Download CCD File 
A, B, C, D
(2~{R})-2-phenylpiperidine-1-carbaldehyde
C12 H15 N O
MUZIXORETQNNBG-GFCCVEGCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.202α = 90
b = 87.202β = 90
c = 455.197γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-09-16
    Type: Initial release