Crystal structures of archaerhodopsin-1 and-2: Common structural motif in archaeal light-driven proton pumps

Archaerhodopsin-1 and -2 (aR-1 and aR-2) are light-driven proton pumps found in Halorubrum sp. aus-1 and -2, which share 55-58% sequence identity with bacteriorhodopsin (bR), a proton pump found in Halobacterium salinarum. In this study, aR-1 and aR-2 were crytallized into 3D crystals belonging. to P4(3)2(1)2 (a = b = 128.1 angstrom, c = 117.6 angstrom) and C222(1) (a = 122.9 angstrom, b = 139.5 angstrom, c = 108.1 angstrom), respectively In both the crystals, the asymmetric unit contains two protein molecules with slightly different conformations. Each subunit is composed of seven helical segments as seen in bR but, unlike bR, aR-1 as well as aR-2 has a unique omega loop near the N terminus. 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 pK(a) of the acid purple-to-blue transition among the three proton pumps. AN 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 sidechain of Leu93 at the early stage of the photocycle, which has been shown to accompany water translocation across the Schiff base. (c) 2006 Elsevier Ltd. All rights reserved.