5F1M

Crystal structure of Serine/threonine phosphatase Stp1 from Staphylococcus aureus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structure-Based Identification of a Potent Inhibitor Targeting Stp1-Mediated Virulence Regulation in Staphylococcus aureus

Zheng, W.Cai, X.Xie, M.Liang, Y.Wang, T.Li, Z.

(2016) Cell Chem Biol 23: 1002-1013

  • DOI: https://doi.org/10.1016/j.chembiol.2016.06.014
  • Primary Citation of Related Structures:  
    5F1M

  • PubMed Abstract: 

    The increasing threats of antibiotic resistance urge the need for developing new strategies against bacterial infections. Targeting eukaryotic-like Ser/Thr phosphatase Stp1-mediated virulence regulation represents a promising approach for combating staphylococcal infection yet to be explored. Here, we report the 2.32-Å resolution crystal structure of Stp1. Stp1 binds an unexpected fourth metal ion, which is important for Stp1's enzymatic activity as demonstrated by amino acid substitution studies. Inspired by the structural details of Stp1, we identified a potent and selective Stp1 inhibitor, aurintricarboxylic acid (ATA). Transcriptome analysis and biochemical studies supported Stp1 as the target of ATA inhibition within the pathogen, preventing upregulation of virulence genes. Notably, ATA did not affect in vitro growth of Staphylococcus aureus, while simultaneously attenuating staphylococcal virulence in mice. Our findings demonstrate that ATA is a potent anti-virulence compound against staphylococcal infection, laying the foundation for further developing new scaffolds for Stp1-targeted small molecules.


  • Organizational Affiliation

    Key Lab of Chemical Genomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen 518055, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphorylated protein phosphatase268Staphylococcus aureusMutation(s): 0 
Gene Names: prpCAS858_01330BN1321_240063EQ80_005655ER12_005650ERS093009_00664
EC: 3.1.3.16
UniProt
Find proteins for Q9RL81 (Staphylococcus aureus)
Explore Q9RL81 
Go to UniProtKB:  Q9RL81
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RL81
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.77α = 90
b = 77.35β = 90
c = 85.36γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
iMOSFLMdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
MOSTChina2013CB911501
SZSTIChinaJCYJ20150331100849958

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-24
    Type: Initial release
  • Version 1.1: 2016-09-14
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description