Proteorhodopsin was first discovered in 2000. It was found in the genomes of several species of uncultivated marine γ-proteobacteria present in the Eastern Pacific Ocean, Central North Pacific Ocean and Southern Ocean, Antarctica . Subsequently, genes of proteorhodopsin variants have been identified in samples from the Mediterranean and Red Seas and the Sargasso Sea and the Sea of Japan. These variants are not spread randomly, but have different distributions of absorption maxima along depth gradients and across locations .
On comparison to its better-known archaeal homolog bacteriorhodopsin, most of the active site residues of known importance to the bacteriorhodopsin mechanism are conserved in proteorhodopsin. Homologues of the active site residues Arg82, Asp85 (the primary proton acceptor), Asp212 and Lys216 (the retinal Schiff base binding site) in bacteriorhodopsin are conserved as Arg94, Asp97, Asp227 and Lys231 in proteorhodopsin. However, in proteorhodopsin, there are no carboxylic acid residues directly homologous to Glu194 or Glu204 of bacteriorhodopsin, which are thought to be involved in the proton release pathway at the extracellular surface.
It seems likely that proteorhodopsin functions throughout the Earth's oceans as a light-driven H+ pump, by a mechanism similar to that of bacteriorhodopsin. As in bacteriorhodopsin, the retinal chromophore of bacteriorhodopsin is covalently bound to the apoprotein via a protonated Schiff base at Lys231. The configuration of the retinal chromophore in unphotolyzed proteorhodopsin is predominantly all-trans, and changes to 13-cis upon illumination with light. Several models of the complete proteorhodopsin photocycle have been proposed, based on FTIR and UV–visible spectroscopy; they resemble established photocycle models for bacteriorhodopsin.