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==Crystal Structure of the Cell-Free Synthesized Membrane Protein, Acetabularia Rhodopsin I, at 1.52 angstrom== | ==Crystal Structure of the Cell-Free Synthesized Membrane Protein, Acetabularia Rhodopsin I, at 1.52 angstrom== | ||
<StructureSection load='5ax0' size='340' side='right' caption='[[5ax0]], [[Resolution|resolution]] 1.52Å' scene=''> | <StructureSection load='5ax0' size='340' side='right'caption='[[5ax0]], [[Resolution|resolution]] 1.52Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5ax0]] is a 1 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3wt9 3wt9]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AX0 OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[5ax0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Acetabularia_acetabulum Acetabularia acetabulum]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3wt9 3wt9]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AX0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AX0 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C14:TETRADECANE'>C14</scene>, <scene name='pdbligand=D10:DECANE'>D10</scene>, <scene name='pdbligand=D12:DODECANE'>D12</scene>, <scene name='pdbligand=OLB:(2S)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLB</scene>, <scene name='pdbligand=R16:HEXADECANE'>R16</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.521Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C14:TETRADECANE'>C14</scene>, <scene name='pdbligand=D10:DECANE'>D10</scene>, <scene name='pdbligand=D12:DODECANE'>D12</scene>, <scene name='pdbligand=OLB:(2S)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLB</scene>, <scene name='pdbligand=R16:HEXADECANE'>R16</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5ax0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ax0 OCA], [https://pdbe.org/5ax0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ax0 RCSB], [https://www.ebi.ac.uk/pdbsum/5ax0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ax0 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/G3CEP6_ACEAT G3CEP6_ACEAT] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Although many crystal structures of microbial rhodopsins have been solved, those with sufficient resolution to identify the functional water molecules are very limited. In this study, the Acetabularia rhodopsin I (ARI) protein derived from the marine alga A. acetabulum was synthesized on a large scale by the Escherichia coli cell-free membrane-protein production method, and crystal structures of ARI were determined at the second highest (1.52-1.80 A) resolution for a microbial rhodopsin, following bacteriorhodopsin (BR). Examinations of the photochemical properties of ARI revealed that the photocycle of ARI is slower than that of BR and that its proton-transfer reactions are different from those of BR. In the present structures, a large cavity containing numerous water molecules exists on the extracellular side of ARI, explaining the relatively low pKa of Glu206(ARI), which cannot function as an initial proton-releasing residue at any pH. An interhelical hydrogen bond exists between Leu97(ARI) and Tyr221(ARI) on the cytoplasmic side, which facilitates the slow photocycle and regulates the pKa of Asp100(ARI), a potential proton donor to the Schiff base, in the dark state. | |||
Structural basis for the slow photocycle and late proton release in Acetabularia rhodopsin I from the marine plant Acetabularia acetabulum.,Furuse M, Tamogami J, Hosaka T, Kikukawa T, Shinya N, Hato M, Ohsawa N, Kim SY, Jung KH, Demura M, Miyauchi S, Kamo N, Shimono K, Kimura-Someya T, Yokoyama S, Shirouzu M Acta Crystallogr D Biol Crystallogr. 2015 Nov 1;71(Pt 11):2203-16. doi:, 10.1107/S1399004715015722. Epub 2015 Oct 27. PMID:26527138<ref>PMID:26527138</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 5ax0" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Rhodopsin 3D structures|Rhodopsin 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Acetabularia acetabulum]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Furuse M]] | ||
[[Category: Hosaka T]] | |||
[[Category: | [[Category: Kimura-Someya T]] | ||
[[Category: | [[Category: Shirouzu M]] | ||
[[Category: | [[Category: Yokoyama S]] | ||
[[Category: | |||
Latest revision as of 18:50, 8 November 2023
Crystal Structure of the Cell-Free Synthesized Membrane Protein, Acetabularia Rhodopsin I, at 1.52 angstromCrystal Structure of the Cell-Free Synthesized Membrane Protein, Acetabularia Rhodopsin I, at 1.52 angstrom
Structural highlights
FunctionPublication Abstract from PubMedAlthough many crystal structures of microbial rhodopsins have been solved, those with sufficient resolution to identify the functional water molecules are very limited. In this study, the Acetabularia rhodopsin I (ARI) protein derived from the marine alga A. acetabulum was synthesized on a large scale by the Escherichia coli cell-free membrane-protein production method, and crystal structures of ARI were determined at the second highest (1.52-1.80 A) resolution for a microbial rhodopsin, following bacteriorhodopsin (BR). Examinations of the photochemical properties of ARI revealed that the photocycle of ARI is slower than that of BR and that its proton-transfer reactions are different from those of BR. In the present structures, a large cavity containing numerous water molecules exists on the extracellular side of ARI, explaining the relatively low pKa of Glu206(ARI), which cannot function as an initial proton-releasing residue at any pH. An interhelical hydrogen bond exists between Leu97(ARI) and Tyr221(ARI) on the cytoplasmic side, which facilitates the slow photocycle and regulates the pKa of Asp100(ARI), a potential proton donor to the Schiff base, in the dark state. Structural basis for the slow photocycle and late proton release in Acetabularia rhodopsin I from the marine plant Acetabularia acetabulum.,Furuse M, Tamogami J, Hosaka T, Kikukawa T, Shinya N, Hato M, Ohsawa N, Kim SY, Jung KH, Demura M, Miyauchi S, Kamo N, Shimono K, Kimura-Someya T, Yokoyama S, Shirouzu M Acta Crystallogr D Biol Crystallogr. 2015 Nov 1;71(Pt 11):2203-16. doi:, 10.1107/S1399004715015722. Epub 2015 Oct 27. PMID:26527138[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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