To gain a better insight of how Copper (Cu) ions toxify cells, metabolomic analyses were performed inS.aureusstrains that lacks the described Cu ion detoxification systems (ΔcopBLΔcopAZ;cop-). Exposure of thecop-strain to Cu(II) resulted in an increase in the concentrations of metabolites utilized to synthesize phosphoribosyl diphosphate (PRPP). PRPP is created using the enzyme phosphoribosylpyrophosphate synthetase (Prs) which catalyzes the interconversion of ATP and ribose 5-phosphate to PRPP and AMP. Supplementing growth medium with metabolites requiring PRPP for synthesis improved growth in the presence of Cu(II). A suppressor screen revealed that a strain with a lesion in the gene coding adenine phosphoribosyltransferase (apt) was more resistant to Cu. Apt catalyzes the conversion of adenine with PRPP to AMP. Theaptmutant had an increased pool of adenine suggesting that the PRPP pool was being redirected. Over-production ofapt, or alternate enzymes that utilize PRPP, increased sensitivity to Cu(II). Increasing or decreasing expression ofprsresulted in decreased and increased sensitivity to growth in the presence of Cu(II), respectively. We demonstrate that Prs is inhibited by Cu ionsin vivoandin vitroand that treatment of cells with Cu(II) results in decreased PRPP levels. Lastly, we establish thatS.aureusthat lacks the ability to remove Cu ions from the cytosol is defective in colonizing the airway in a murine model of acute pneumonia, as well as the skin. The data presented are consistent with a model wherein Cu ions inhibits pentose phosphate pathway function and are used by the immune system to preventS.aureusinfections.