V-ATPase from Enterococcus hirae forms a large supramolecular protein complex (total molecular weight similar to 700 000) and physiologically transports Na+ and Li+ across a hydrophobic lipid bilayer. Stabilization of these cations in the binding site has been discussed on the basis of X-ray crystal structures of a membrane-embedded domain, the K-ring (Na+- and Li+-bound forms). Here, sodium or lithium ion-binding-induced difference IR spectra of the intact V-ATPase have for the first time been measured at physiological temperature under a sufficient amount of hydration. The results suggest that sodium or lithium ion binding induces the deprotonation of Glu139, a hydrogen-bonding change in the tyrosine residue, and a small conformational change in the K-ring. These structural changes, especially the deprotonation of Glu139, are considered to be important for reducing energetic barriers to the transport of cations through the membrane.