Journal
JOURNAL OF BIOLOGICAL CHEMISTRY
Volume 291, Issue 34, Pages 17488-17495Publisher
AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC
DOI: 10.1074/jbc.M116.728220
Keywords
crystal structure; membrane protein; protein crystallization; structure-function; tertiary structure; cell-free protein synthesis; chloride ion pump; chloride ion-releasing residues; microbial rhodopsin
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Funding
- Canon Foundation
- Ministry of Education, Culture, Sports, Science and Technology
- Japan Agency for Medical Research and Development
- CREST, Japan Science and Technology Agency
- Japan Society for the Promotion of Science KAKENHI [15H02800, 15K14601, 221S0002, 15K18523]
- Grants-in-Aid for Scientific Research [15J07201, 15K18523, 15H02800, 16H06279, 15K14601] Funding Source: KAKEN
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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 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.
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