WalKR (YycFG) is the only essential two-component regulator in the human pathogen Staphylococcus aureus. WalKR regulates peptidoglycan synthesis, but this function alone does not explain its essentiality. Here, to further understand WalKR function, we investigate a suppressor mutant that arose when WalKR activity was impaired; a histidine to tyrosine substitution (H271Y) in the cytoplasmic Per-Arnt-Sim (PAS ) domain of the histidine kinase WalK. Introducing the WalK mutation into wild-type S. aureus activates the WalKR regulon. Structural analyses of the WalK PAS domain reveal a metal-binding site, in which a zinc ion (Zn ) is tetrahedrally-coordinated by four amino acids including H271. The WalK mutation abrogates metal binding, increasing WalK kinase activity and WalR phosphorylation. Thus, Zn -binding negatively regulates WalKR. Promoter-reporter experiments using S. aureus confirm Zn sensing by this system. Identification of a metal ligand recognized by the WalKR system broadens our understanding of this critical S. aureus regulon.