1vgo
From Proteopedia
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'''Crystal Structure of Archaerhodopsin-2''' | '''Crystal Structure of Archaerhodopsin-2''' | ||
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| + | ==Overview== | ||
| + | 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. | ||
==About this Structure== | ==About this Structure== | ||
1VGO is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Halobacterium_sp. Halobacterium sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VGO OCA]. | 1VGO is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Halobacterium_sp. Halobacterium sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VGO OCA]. | ||
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| + | ==Reference== | ||
| + | Crystal structures of archaerhodopsin-1 and -2: Common structural motif in archaeal light-driven proton pumps., Enami N, Yoshimura K, Murakami M, Okumura H, Ihara K, Kouyama T, J Mol Biol. 2006 May 5;358(3):675-85. Epub 2006 Mar 3. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16540121 16540121] | ||
[[Category: Halobacterium sp.]] | [[Category: Halobacterium sp.]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
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[[Category: Okumura, H.]] | [[Category: Okumura, H.]] | ||
[[Category: Yoshimura, K.]] | [[Category: Yoshimura, K.]] | ||
| + | [[Category: Proton transport]] | ||
[[Category: Retinal-binding protein]] | [[Category: Retinal-binding protein]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 11 10:53:33 2008'' |
Revision as of 07:53, 11 June 2008
Crystal Structure of Archaerhodopsin-2
Overview
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.
About this Structure
1VGO is a Single protein structure of sequence from Halobacterium sp.. Full crystallographic information is available from OCA.
Reference
Crystal structures of archaerhodopsin-1 and -2: Common structural motif in archaeal light-driven proton pumps., Enami N, Yoshimura K, Murakami M, Okumura H, Ihara K, Kouyama T, J Mol Biol. 2006 May 5;358(3):675-85. Epub 2006 Mar 3. PMID:16540121 Page seeded by OCA on Wed Jun 11 10:53:33 2008
