6IHT

Crystal structure of bacterial serine phosphatase bound with phosphorylated peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.569 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1021/acsinfecdis.8b00316
  • Primary Citation of Related Structures:  

  • 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 in ...

    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.,School of Life Sciences , Fudan University , 2005 Songhu Road , Shanghai 200433 , P. R. China.,State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , P. R. China.,State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals , Guizhou University , 2708 South Huaxi Road , Guiyang , Guizhou 550025 , P. R. China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphorylated protein phosphatase
A
266Staphylococcus aureusMutation(s): 0 
Gene Names: prpC_1 (prpC)
EC: 3.1.3.16
Find proteins for Q9RL81 (Staphylococcus aureus)
Go to UniProtKB:  Q9RL81
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
His12
X
3N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
X
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.569 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.159 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 46.693α = 90.00
b = 38.609β = 101.89
c = 65.003γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data reduction
PHASERphasing
HKL-3000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-10-02 
  • Released Date: 2019-08-07 
  • Deposition Author(s): Yang, C.-G., yang, T.

Revision History 

  • Version 1.0: 2019-08-07
    Type: Initial release
  • Version 1.1: 2019-08-21
    Type: Data collection, Database references