5b2n: Difference between revisions
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==Crystal structure of the light-driven chloride ion-pumping rhodopsin, ClP, from Nonlabens marinus== | |||
<StructureSection load='5b2n' size='340' side='right'caption='[[5b2n]], [[Resolution|resolution]] 1.58Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5b2n]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Nonlabens_marinus_S1-08 Nonlabens marinus S1-08]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B2N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B2N 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]] 1.581Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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=OCT:N-OCTANE'>OCT</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=5b2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b2n OCA], [https://pdbe.org/5b2n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b2n RCSB], [https://www.ebi.ac.uk/pdbsum/5b2n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b2n ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/W8VZW3_9FLAO W8VZW3_9FLAO] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The light-driven inward chloride ion-pumping rhodopsin Nonlabens marinus rhodopsin-3 (NM-R3), from a marine flavobacterium, belongs to a phylogenetic lineage distinct from the halorhodopsins known as archaeal inward chloride ion-pumping rhodopsins. NM-R3 and halorhodopsin have distinct motif sequences that are important for chloride ion binding and transport. In this study, we present the crystal structure of a new type of light-driven chloride ion pump, NM-R3, at 1.58 A resolution. The structure revealed the chloride ion translocation pathway and showed that a single chloride ion resides near the Schiff base. The overall structure, chloride ion-binding site, and translocation pathway of NM-R3 are different from those of halorhodopsin. Unexpectedly, this NM-R3 structure is similar to the crystal structure of the light-driven outward sodium ion pump, Krokinobacter eikastus rhodopsin 2. Structural and mutational analyses of NM-R3 revealed that most of the important amino acid residues for chloride ion pumping exist in the ion influx region, located on the extracellular side of NM-R3. In contrast, on the opposite side, the cytoplasmic regions of K. eikastus rhodopsin 2 were reportedly important for sodium ion pumping. These results provide new insight into ion selection mechanisms in ion pumping rhodopsins, in which the ion influx regions of both the inward and outward pumps are important for their ion selectivities. | |||
Structural Mechanism for Light-driven Transport by a New Type of Chloride Ion Pump, Nonlabens marinus Rhodopsin-3.,Hosaka T, Yoshizawa S, Nakajima Y, Ohsawa N, Hato M, DeLong EF, Kogure K, Yokoyama S, Kimura-Someya T, Iwasaki W, Shirouzu M J Biol Chem. 2016 Aug 19;291(34):17488-95. doi: 10.1074/jbc.M116.728220. Epub, 2016 Jun 30. PMID:27365396<ref>PMID:27365396</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 5b2n" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
[[Category: | ==See Also== | ||
*[[Rhodopsin 3D structures|Rhodopsin 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Nonlabens marinus S1-08]] | |||
[[Category: Hosaka T]] | |||
[[Category: Kimura-Someya T]] | |||
[[Category: Shirouzu M]] | |||
Latest revision as of 18:57, 8 November 2023
Crystal structure of the light-driven chloride ion-pumping rhodopsin, ClP, from Nonlabens marinusCrystal structure of the light-driven chloride ion-pumping rhodopsin, ClP, from Nonlabens marinus
Structural highlights
FunctionPublication Abstract from PubMedThe light-driven inward chloride ion-pumping rhodopsin Nonlabens marinus rhodopsin-3 (NM-R3), from a marine flavobacterium, belongs to a phylogenetic lineage distinct from the halorhodopsins known as archaeal inward chloride ion-pumping rhodopsins. NM-R3 and halorhodopsin have distinct motif sequences that are important for chloride ion binding and transport. In this study, we present the crystal structure of a new type of light-driven chloride ion pump, NM-R3, at 1.58 A resolution. The structure revealed the chloride ion translocation pathway and showed that a single chloride ion resides near the Schiff base. The overall structure, chloride ion-binding site, and translocation pathway of NM-R3 are different from those of halorhodopsin. Unexpectedly, this NM-R3 structure is similar to the crystal structure of the light-driven outward sodium ion pump, Krokinobacter eikastus rhodopsin 2. Structural and mutational analyses of NM-R3 revealed that most of the important amino acid residues for chloride ion pumping exist in the ion influx region, located on the extracellular side of NM-R3. In contrast, on the opposite side, the cytoplasmic regions of K. eikastus rhodopsin 2 were reportedly important for sodium ion pumping. These results provide new insight into ion selection mechanisms in ion pumping rhodopsins, in which the ion influx regions of both the inward and outward pumps are important for their ion selectivities. Structural Mechanism for Light-driven Transport by a New Type of Chloride Ion Pump, Nonlabens marinus Rhodopsin-3.,Hosaka T, Yoshizawa S, Nakajima Y, Ohsawa N, Hato M, DeLong EF, Kogure K, Yokoyama S, Kimura-Someya T, Iwasaki W, Shirouzu M J Biol Chem. 2016 Aug 19;291(34):17488-95. doi: 10.1074/jbc.M116.728220. Epub, 2016 Jun 30. PMID:27365396[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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