1VGO

Crystal Structure of Archaerhodopsin-2

Summary for 1VGO

• Entry DOI: 10.2210/pdb1vgo/pdb
• Related: 1uaz
• Descriptor: Archaerhodopsin 2, nonyl beta-D-glucopyranoside, SULFATE ION, ... (5 entities in total)
• Functional Keywords: retinal-binding protein, proton transport
• Biological source: Halobacterium sp.
• Cellular location: Cell membrane; Multi-pass membrane protein: P29563
• Total number of polymer chains: 2
• Total formula weight: 59159.31

Authors

Yoshimura, K.,Enami, N.,Murakami, M.,Okumura, H.,Ihara, K.,Kouyama, T. (deposition date: 2004-04-28, release date: 2005-10-04, Last modification date: 2024-11-06)

Primary citation

Enami, N.,Yoshimura, K.,Murakami, M.,Okumura, H.,Ihara, K.,Kouyama, T.
Crystal structures of archaerhodopsin-1 and -2: Common structural motif in archaeal light-driven proton pumps
J.Mol.Biol., 358:675-685, 2006

PubMed Abstract: 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 crystallized into 3D crystals belonging to P4(3)2(1)2 (a = b = 128.1 A, c = 117.6 A) and C222(1) (a = 122.9 A, b = 139.5 A, c = 108.1 A), 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 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 the photocycle, which has been shown to accompany water translocation across the Schiff base.

PubMed: 16540121
DOI: 10.1016/j.jmb.2006.02.032

Experimental method

X-RAY DIFFRACTION (2.5 Å)