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J Biol Chem. 2016 Aug 19;291(34):17488-17495. doi: 10.1074/jbc.M116.728220. Epub 2016 Jun 30.

Structural Mechanism for Light-driven Transport by a New Type of Chloride Ion Pump, Nonlabens marinus Rhodopsin-3.

Author information

1
From the Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, and.
2
the Atmosphere and Ocean Research Institute, University of Tokyo, Chiba 277-8564, Japan.
3
the Center for Microbial Oceanography, Research and Education, University of Hawaii, Honolulu, Hawaii 96822, and.
4
RIKEN Structural Biology Laboratory, Yokohama, Kanagawa 230-0045, Japan.
5
the Atmosphere and Ocean Research Institute, University of Tokyo, Chiba 277-8564, Japan, iwasaki@bs.s.u-tokyo.ac.jp.
6
the Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-0032, Japan.
7
From the Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, and mikako.shirouzu@riken.jp.

Abstract

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 Å 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.

KEYWORDS:

cell-free protein synthesis; chloride ion pump; chloride ion-releasing residues; crystal structure; membrane protein; microbial rhodopsin; protein crystallization; structure-function; tertiary structure

PMID:
27365396
PMCID:
PMC5016146
DOI:
10.1074/jbc.M116.728220
[Indexed for MEDLINE]
Free PMC Article

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