Krokinobacter eikastus rhodopsin 2 (KR2) is a light-driven sodium ion pump that was discovered in marine bacteria. Although KR2 is able to pump lithium ions similarly, it is converted into a proton pump in potassium chloride or salts of larger cations. In this paper, we applied light-induced difference Fourier-transform infrared (FTIR) spectroscopy to KR2, a compatible sodium ion-proton pump, at 77 K. The first structural study of the functional cycle showed that the structure and structural changes in the primary processes of KR2 are common to all microbial rhodopsins. The red shifted K formation (KR2(K)) was accompanied by retinal photo-isomerization from an all-trans to a 13-cis form, resulting in a distorted retinal chromophore. The observed hydrogen out-of-plane vibrations were H/D exchangeable, indicating that the chromophore distortion by retinal isomerization is located near the Schiff base region in KR2. This tendency was also the case for bacteriorhodopsin and halorhodopsin but not the case for sensory rhodopsin I and II. Therefore, ion pumps such as proton, chloride, and sodium pumps exhibit local structural perturbations of retinal at the Schiff base moiety, while photosensors show more extended structural perturbations of retinal. The retinal Schiff base of KR2 forms a hydrogen bond that is stronger than in BR KR2 possesses more protein-bound water molecules than other microbial rhodopsins and contains strongly hydrogen-bonded water (O-D stretch at 2333 cm(-1) in D2O). The light-induced difference FTIR spectra at 77 K were identical between the two states functioning as light-driven sodium ion and proton pumps, indicating that the structural changes in the primary processes are identical between different ion pump functions in KR2. In other words, it is unknown which ions are transported by molecules when they absorb photons and photoisomerize. It is likely that the relaxation processes from the K state lead to an alternative function, namely a sodium ion pump or proton pump, depending on the environment.