Haloarcula sp. arg-2, a natural bacterial isolate from Andes heights, has a light-driven proton pump but not a light-driven anion pump. We have cloned and sequenced the gene encoding for the proton pump which has been named cruxrhodopsin-2. The gene consists of 768 bp encoding 255 amino acids with a molecular mass of 27 544 Da. The deduced amino acid sequence of cruxrhodopsin-2 is 77%, 50%, 48% and 48% identical to those of cruxrhodopsin-1, bacteriorhodopsin, archaerhodopsin-1 and archaerhodopsin-2, respectively. The charged amino acids important for the proton pump function were conserved among all these molecules. Cruxrhodopsin-2 accounted for 0.05 nmol/mg protein in arg-2, which was 20-30-fold less than the proportion of bacteriorhodopsin in Halobacterium salinarium R(1)M(1). In contrast to R(1)M(1), under anaerobic conditions, arg-2 showed light-induced proton extrusion concomitant with an increase in ATP level without transient proton uptake. Dicyclohexylcarbodiimide enhanced the rate and extent of proton extrusion and inhibited ATP formation in the light. The apparent stoichiometry of H+/ATP was estimated to be more than three in this natural bR(+)hR(-) strain.