Department of Physics, Graduate School of Science, Nagoya University
â—‹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 [1]. 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.
[1] N. Enami, K. Yoshimura, M Murakami, H. Okumura, K. Ihara and T. Kouyama., J. Mol. Biol., 358, 675-685 (2006).