Crystal structure of bacterial serine phosphatase bound with phosphorylated peptide

Experimental Data Snapshot

  • Resolution: 1.57 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Structural Insight into the Mechanism of Staphylococcus aureus Stp1 Phosphatase.

Yang, T.Liu, T.Gan, J.Yu, K.Chen, K.Xue, W.Lan, L.Yang, S.Yang, C.G.

(2019) ACS Infect Dis 5: 841-850

  • DOI: https://doi.org/10.1021/acsinfecdis.8b00316
  • Primary Citation of Related Structures:  
    6IHL, 6IHR, 6IHS, 6IHT, 6IHU, 6IHV, 6IHW

  • PubMed Abstract: 

    Staphylococcus aureus Stp1, which belongs to the bacterial metal-dependent protein phosphatase (PPM) family, is a promising candidate for antivirulence targeting. How Stp1 recognizes the phosphorylated peptide remains unclear, however. In order to investigate the recognition mechanism of Stp1 in depth, we have determined a series of crystal structures of S. aureus Stp1 in different states and the structural complex of Stp1 bound with a phosphorylated peptide His12. Different phosphorylated peptides, including MgrA- and GraR-derived phosphopeptides, are substrates of Stp1, which supports the function of Stp1 as a selective Ser/Thr phosphatase. In addition, interestingly, the crystal structures of R161-Stp1 variants combined with the biochemical activity validations have uncovered that R161 residue plays a key role to control the conformation switches of the flap domain in order to facilitate substrate binding and the dephosphorylation process. Our findings provide crucial structural insight into the molecular mechanism of S. aureus Stp1 phosphatase and reveal the phosphorylated peptides for biochemistry study and inhibitor screening of Stp1.

  • Organizational Affiliation

    University of the Chinese Academy of Sciences , 19A Yuquan Road , Beijing 100049 , P. R. China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphorylated protein phosphatase266Staphylococcus aureusMutation(s): 0 
Gene Names: 
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
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
His12B [auth X]3Peptide display vector fth1Mutation(s): 0 
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.57 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.693α = 90
b = 38.609β = 101.89
c = 65.003γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-07
    Type: Initial release
  • Version 1.1: 2019-08-21
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description