HDX and Native Mass Spectrometry Reveals the Different Structural Basis for Interaction of the Staphylococcal Pathogenicity Island Repressor Stl with Dimeric and Trimeric Phage dUTPases

Biomolecules. 2019 Sep 14;9(9):488. doi: 10.3390/biom9090488.


The dUTPase enzyme family plays an essential role in maintaining the genome integrity and are represented by two distinct classes of proteins; the β-pleated homotrimeric and the all-α homodimeric dUTPases. Representatives of both trimeric and dimeric dUTPases are encoded by Staphylococcus aureus phage genomes and have been shown to interact with the Stl repressor protein of S. aureus pathogenicity island SaPIbov1. In the present work we set out to characterize the interactions between these proteins based on a range of biochemical and biophysical methods and shed light on the binding mechanism of the dimeric φNM1 phage dUTPase and Stl. Using hydrogen deuterium exchange mass spectrometry, we also characterize the protein regions involved in the dUTPase:Stl interactions. Based on these results we provide reasonable explanation for the enzyme inhibitory effect of Stl observed in both types of complexes. Our experiments reveal that Stl employs different peptide segments and stoichiometry for the two different phage dUTPases which allows us to propose a functional plasticity of Stl. The malleable character of Stl serves as a basis for the inhibition of both dimeric and trimeric dUTPases.

Keywords: Stl staphylococcal repressor; dUTPase; inhibition; interaction surface.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / chemistry
  • Bacterial Proteins / metabolism*
  • Genomic Islands
  • Hydrogen Deuterium Exchange-Mass Spectrometry
  • Models, Molecular
  • Protein Binding
  • Protein Conformation
  • Protein Multimerization
  • Pyrophosphatases / chemistry
  • Pyrophosphatases / genetics
  • Pyrophosphatases / metabolism*
  • Staphylococcus Phages / chemistry
  • Staphylococcus Phages / enzymology*
  • Staphylococcus Phages / genetics
  • Staphylococcus aureus / metabolism
  • Staphylococcus aureus / pathogenicity*
  • Staphylococcus aureus / virology
  • Viral Proteins / chemistry
  • Viral Proteins / metabolism


  • Bacterial Proteins
  • Viral Proteins
  • Pyrophosphatases
  • dUTP pyrophosphatase