Proteorhodopsin (pR), a retinal protein that functions as a light-driven proton pump, is the first archaeal rhodopsin homolog identified in the domain Bacteria. Recently, pR was discovered 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 pR variants have been identified in samples from the Mediterranean and Red Seas and the Sargasso Sea and the Japanese Sea.
On comparison to its better-known archaeal homolog bacteriorhodopsin (bR), most of the active site residues of known importance to the bR mechanism are conserved in pR. Homologues of the active-site residues Arg82, Asp85 (the primary proton acceptor), Asp212 and Lys216 (the retinal Schiff base binding site) in bR are conserved as Arg94, Asp97, Asp227 and Lys231 in pR. However, in pR, there are no carboxylic acid residues directly homologous to Glu194 or Glu204 of bR, which are thought to be involved in the proton release pathway at the extracellular surface.
It seems likely that pR functions throughout the Earth's oceans as a light-driven H+ pump, by a mechanism similar to that of bR. As in bR, the retinal chromophore of pR is covalently bound to the apoprotein via a protonated Schiff's base at Lys231. The configuration of the retinal chromophore in unphotolyzed pR is predominantly all-trans, and changes to 13-cis upon illumination with light. Several models of the complete pR photocycle have been proposed, based on FTIR and UV–visible spectroscopy; they resemble established photocycle models for bR.