Archaearhodopsin (formerly Bacteriorhodopsin) is a protein used by Archaea, the most notable one being Haloarchaea. It acts as a proton pump; that is, it captures light energy and uses it to move protons across the membrane out of the cell. The resulting proton gradient is subsequently converted into chemical energy.
Archaearhodopsin is an integral membrane protein usually found in two-dimensional crystalline patches known as "purple membrane", which can occupy up to nearly 50% of the surface area of the archaeal cell. The repeating element of the hexagonal lattice is composed of three identical protein chains, each rotated by 120 degrees relative to the others. Each chain has seven transmembrane alpha helices and contains one molecule of retinal buried deep within, the typical structure for retinylidene proteins.
Archaearhodopsin is a light-driven proton pump
It is the retinal molecule that changes its conformation when absorbing a photon, resulting in a conformational change of the surrounding protein and the proton pumping action. It is covalently linked to Lys216 in the chromophore by Schiff base action. After photoisomerization of the retinal molecule, Asp85 becomes a proton acceptor of the donor proton from the retinal molecule. This releases a proton from a "holding site" into the extracellular side (EC) of the membrane. Reprotonation of the retinal molecule by Asp96 restores its original isomerized form. This results in a second proton being released to the EC side. Asp85 releases its proton into the "holding site," where a new cycle may begin.
The archaearhodopsin molecule is purple and is most efficient at absorbing green light (wavelength 500-650 nm, with the absorption maximum at 568 nm).
Archaearhodopsin belongs to a family of archeaial proteins related to vertebrate rhodopsins, the pigments that sense light in the retina. Rhodopsins also contain retinal; however, the functions of rhodopsin and archaearhodopsin are different, and there is limited similarity in their amino acid sequences. Both rhodopsin and archaearhodopsin belong to the 7TM receptor family of proteins, but rhodopsin is a G protein-coupled receptor and archaearhodopsin is not. In the first use of electron crystallography to obtain an atomic-level protein structure, the structure of archaearhodopsin was resolved in 1990. It was then used as a template to build models of G protein-coupled receptors before crystallographic structures were also available for these proteins.
Many molecules have homology to archaearhodopsin, including the light-driven chloride pump halorhodopsin (for which the crystal structure is also known), and some directly light-activated channels like channelrhodopsin.
All other phototrophic systems in bacteria, algae, and plants use chlorophylls or bacteriochlorophylls rather than archaearhodopsin. These also produce a proton gradient, but in a quite different and more indirect way involving an electron transfer chain consisting of several other proteins. Furthermore, chlorophylls are aided in capturing light energy by other pigments known as "antennas"; these are not present in bacteriorhodopsin-based systems. It is possible that phototrophy independently evolved at least twice, once in bacteria and once in archaea.
Archaearhodopsin is a trimer. Red line indicates extracellular side (EC) of the membrane
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