As their name indicates, microbial rhodopsins are found in Archaea and Bacteria, and also in Eukaryota (such as algae) and viruses; although they are rare in complex multicellular organisms.

In a broad non-genetic sense, rhodopsin refers to any molecule, whether related by genetic descent or not (mostly not), consisting of an opsin and a chromophore (generally a variant of retinal).

The retinal chromophore is found solely in the opsin branch of this large gene family, meaning its occurrence elsewhere represents convergent evolution, not homology.

Members of the MR family catalyze light-driven ion translocation across microbial cytoplasmic membranes or serve as light receptors.

Most proteins of the MR family are all of about the same size (250-350 amino acyl residues) and possess seven transmembrane helical spanners with their N-termini on the outside and their C-termini on the inside.

Association of a sensory rhodopsin receptor with its transducer occurs via the transmembrane helical domains of the two interacting proteins.

[29] Homologues include putative fungal chaperone proteins, a retinal-containing rhodopsin from Neurospora crassa,[30] a H+-pumping rhodopsin from Leptosphaeria maculans,[20] retinal-containing proton pumps isolated from marine bacteria,[31] a green light-activated photoreceptor in cyanobacteria that does not pump ions and interacts with a small (14 kDa) soluble transducer protein [27][32] and light-gated H+ channels from the green alga, Chlamydomonas reinhardtii.

[33] The N. crassa NOP-1 protein exhibits a photocycle and conserved H+ translocation residues that suggest that this putative photoreceptor is a slow H+ pump.

They have been suggested to function as pmf-driven chaperones that fold extracellular proteins, but only indirect evidence supports this postulate.

[26][36][37] The mechanism involves: Six structural models describe the transformations of the retinal and its interaction with water 402, Asp85, and Asp212 in atomic detail, as well as the displacements of functional residues farther from the Schiff base.

The changes provide rationales for how relaxation of the distorted retinal causes movements of water and protein atoms that result in vectorial proton transfers to and from the Schiff base.

Despite a large alteration in the amino acid sequence, the shape of the intratrimer hydrophobic space filled by lipids is highly conserved between archaerhodopsin-2 and bacteriorhodopsin.

Since a transmembrane helix facing this space undergoes a large conformational change during the proton pumping cycle, it is feasible that trimerization is an important strategy to capture special lipid components that are relevant to the protein activity.

The polyene chain of the second chromophore is inclined from the membrane normal by an angle of about 20 degrees and, on the cytoplasmic side, it is surrounded by helices AB and DE of neighboring subunits.

The internal proton acceptor and donor groups, corresponding to D212 and D115 in bacteriorhodopsin, are clearly different from other microbial rhodopsins, indicating that their spatial positions in the protein were relocated during evolution.

Although the ions move in the opposite direction, the current generated (as defined by the movement of positive charge) is the same as for bacteriorhodopsin and the archaerhodopsins.