Structure-based modeling and dynamics of MurM, a Streptococcus pneumoniae penicillin resistance determinant present at the cytoplasmic membrane

Summary Branched Lipid II, required for the formation of indirectly crosslinked peptidoglycan, is generated by MurM, a protein essential for high-level penicillin resistance in the human pathogen Streptococcus pneumoniae. We have solved the X-ray crystal structure of Staphylococcus aureus FemX, an isofunctional homolog, and have used this as a template to generate a MurM homology model. Using this model, we perform molecular docking and molecular dynamics to examine the interaction of MurM with the phospholipid bilayer and the membrane-embedded Lipid II substrate. Our model suggests that MurM is associated with the major membrane phospholipid cardiolipin, and experimental evidence confirms that the activity of MurM is enhanced by this phospholipid and inhibited by its direct precursor phosphatidylglycerol. The spatial association of pneumococcal membrane phospholipids and their impact on MurM activity may therefore be critical to the final architecture of peptidoglycan and the expression of clinically relevant penicillin resistance in this pathogen.
Graphical abstract
Highlights • S. aureus FemX structure generated an improved homology model of S. pneumoniae MurM • A Lipid II binding site in MurM was identified by docking and molecular dynamics • Modeling indicates cardiolipin is enriched at the MurM protein:membrane interface • Enzyme assays show that phospholipids influence MurM activity
With an improved homology model of MurM, York et al., use docking and molecular dynamics studies to identify a potential Lipid II binding site and simulate how MurM interacts with this membrane-embedded substrate. Cardiolipin, a membrane phospholipid, was also found to associate with MurM and upregulate its enzymatic activity.