Figure 9.

Typical photocycle of microbial rhodopsins showing isomeric and protonation state of retinal. X⁻ represents the Schiff base counterion, and D85 in BR also acts as the H⁺ acceptor from the Schiff base. In a Cl⁻ pump such as HR and FR, X⁻ is a Cl⁻, so that the M intermediate is not formed because the Schiff base is not deprotonated. Instead, the Cl⁻ is transported upwards (in this figure). In KR2, a Na⁺ pump, X⁻ is a D116 acting as the Schiff base counterion and H⁺ acceptor from the Schiff base. CP and EC indicate cytoplasmic and extracellular domains, respectively. In the unphotolyzed state of microbial rhodopsins, the EC side is generally open through a hydrogen-bonding network but the CP side is closed. While this is persistent in the K and M states, the CP side is open in the N state. When the EC side is closed (black), the CP side is open, as is the case for an ion pump, as occurs in the N intermediate of BR. Such alternative access must work for all H⁺, Cl⁻, and Na⁺ pumps.