1vgo: Difference between revisions

==Crystal Structure of Archaerhodopsin-2==

<StructureSection load='1vgo' size='340' side='right'caption='[[1vgo]], [[Resolution|resolution]] 2.50&Aring;' scene=''>

<table><tr><td colspan='2'>[[1vgo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Halobacterium_sp._AUS-2 Halobacterium sp. AUS-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VGO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VGO FirstGlance]. <br>

</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BNG:B-NONYLGLUCOSIDE'>BNG</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>

<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1vgo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vgo OCA], [https://pdbe.org/1vgo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vgo RCSB], [https://www.ebi.ac.uk/pdbsum/1vgo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vgo ProSAT]</span></td></tr>

[https://www.uniprot.org/uniprot/BACR2_HALS2 BACR2_HALS2]  

[[Image:Consurf_key_small.gif|200px|right]]

</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1vgo ConSurf].

<div style="background-color:#fffaf0;">

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.

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<ref>PMID:16540121</ref>

 

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>

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[[Category: Large Structures]]

[[Category: Enami N]]

[[Category: Ihara K]]