6lm1: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 6lm1 is ON HOLD  until Paper Publication
+==The crystal structure of cyanorhodopsin (CyR) N4075R from cyanobacteria Tolypothrix sp. NIES-4075==
+<StructureSection load='6lm1' size='340' side='right'caption='[[6lm1]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LM1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LM1 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]] 1.9&#8491;</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=HEX:HEXANE'>HEX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=OCT:N-OCTANE'>OCT</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'>[https://proteopedia.org/fgij/fg.htm?mol=6lm1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lm1 OCA], [https://pdbe.org/6lm1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lm1 RCSB], [https://www.ebi.ac.uk/pdbsum/6lm1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lm1 ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Microbial rhodopsin is a photoreceptor protein found in various bacteria and archaea, and it is considered to be a light-utilization device unique to heterotrophs. Recent studies have shown that several cyanobacterial genomes also include genes that encode rhodopsins, indicating that these auxiliary light-utilizing proteins may have evolved within photoautotroph lineages. To explore this possibility, we performed a large-scale genomic survey to clarify the distribution of rhodopsin and its phylogeny. Our surveys revealed a novel rhodopsin clade, cyanorhodopsin (CyR), that is unique to cyanobacteria. Genomic analysis revealed that rhodopsin genes show a habitat-biased distribution in cyanobacterial taxa, and that the CyR clade is composed exclusively of non-marine cyanobacterial strains. Functional analysis using a heterologous expression system revealed that CyRs function as light-driven outward H(+) pumps. Examination of the photochemical properties and crystal structure (2.65 A resolution) of a representative CyR protein, N2098R from Calothrix sp. NIES-2098, revealed that the structure of the protein is very similar to that of other rhodopsins such as bacteriorhodopsin, but that its retinal configuration and spectroscopic characteristics (absorption maximum and photocycle) are distinct from those of bacteriorhodopsin. These results suggest that the CyR clade proteins evolved together with chlorophyll-based photosynthesis systems and may have been optimized for the cyanobacterial environment.
-Authors:
+A unique clade of light-driven proton-pumping rhodopsins evolved in the cyanobacterial lineage.,Hasegawa M, Hosaka T, Kojima K, Nishimura Y, Nakajima Y, Kimura-Someya T, Shirouzu M, Sudo Y, Yoshizawa S Sci Rep. 2020 Oct 7;10(1):16752. doi: 10.1038/s41598-020-73606-y. PMID:33028840<ref>PMID:33028840</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 6lm1" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Rhodopsin 3D structures|Rhodopsin 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Hosaka T]]
+[[Category: Kimura-Someya T]]
+[[Category: Shirouzu M]]