Department of Physics, Graduate School of Science, Nagoya University
○Tsutomu Kouyama Keiko YOSHIMURA Nobuo ENAMI
Since bacteriorhodopsin (bR) was discovered in Halobacterium salinarum, the number of archaeal retinal proteins for which amino-acid sequences are available have increased to >25. They are classified into three types of rhodopsin according to their physiological functions; i.e., light-driven proton pumps, chloride ion pumps and phototaxis receptors. To elucidate a common structural motif utilized for light-driven proton pumps, we have recently investigated the crystal structures of archaerhodopsin-1 and -2 (aR-1 and aR-2), light-driven proton pumps found in Halorubrum sp. aus-1 and -2, which share 55% - 58 % sequence identity with bR . It is found that the proton pathway in the extracellular half (i.e., the proton release channel) is more opened in aR-2 than in aR-1 or bR. This structural difference accounts for a large variation in the pKa of the acid purple-to-blue transition among the three proton pumps. All the aromatic residues surrounding the retinal polyene chain are conserved among the three proton pumps, confirming a previous argument that these residues are required for the stereo-specificity of the retinal isomerization. In the cytoplasmic half, the region surrounded by helices B, C and G is highly conserved, while the structural conservation is very low for residues extruded from helices E and F. Structural conservation of the hydrophobic residues located on the proton uptake pathway suggests that their precise arrangement is necessary to prevent a backward flow of proton in the presence of a large pH gradient and membrane potential. An empty cavity is commonly seen in the vicinity of Leu93 contacting the retinal C13 methyl. Existence of such a cavity is required to allow a large rotation of the side chain of Leu93 at the early stage of photocycle, which has been shown to accompany water relocation near the active site.
 N. Enami, K. Yoshimura, M Murakami, H. Okumura, K. Ihara and T. Kouyama., J. Mol. Biol., 358, 675-685 (2006).