Crystal structure of the staphylococcal serine protease SplA in complex with a specific phosphonate inhibitor

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

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Development and binding characteristics of phosphonate inhibitors of SplA protease from Staphylococcus aureus.

Burchacka, E.Zdzalik, M.Niemczyk, J.S.Pustelny, K.Popowicz, G.Wladyka, B.Dubin, A.Potempa, J.Sienczyk, M.Dubin, G.Oleksyszyn, J.

(2014) Protein Sci 23: 179-189

  • DOI: https://doi.org/10.1002/pro.2403
  • Primary Citation of Related Structures:  
    3UFA, 4MVN

  • PubMed Abstract: 

    Staphylococcus aureus is responsible for a variety of human infections, including life-threatening, systemic conditions. Secreted proteome, including a range of proteases, constitutes the major virulence factor of the bacterium. However, the functions of individual enzymes, in particular SplA protease, remain poorly characterized. Here, we report development of specific inhibitors of SplA protease. The design, synthesis, and activity of a series of α-aminoalkylphosphonate diaryl esters and their peptidyl derivatives are described. Potent inhibitors of SplA are reported, which may facilitate future investigation of physiological function of the protease. The binding modes of the high-affinity compounds Cbz-Phe(P) -(OC6 H4 -4-SO2 CH3 )2 and Suc-Val-Pro-Phe(P) -(OC6 H5 )2 are revealed by high-resolution crystal structures of complexes with the protease. Surprisingly, the binding mode of both compounds deviates from previously characterized canonical interaction of α-aminoalkylphosphonate peptidyl derivatives and family S1 serine proteases.

  • Organizational Affiliation

    Division of Medicinal Chemistry and Microbiology, Faculty of Chemistry, Wroclaw University of Technology, Wroclaw, Poland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine protease splA
A, B, C, D
200Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: SPLASAOUHSC_01942
EC: 3.4.21
Find proteins for Q2FXC2 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FXC2 
Go to UniProtKB:  Q2FXC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FXC2
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.131α = 90
b = 81.626β = 90
c = 133.787γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-22
    Type: Initial release
  • Version 1.1: 2014-03-05
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description