title: Structural Mechanism for Light-driven Transport by a New Type of Chloride Ion Pump, Nonlabens marinus Rhodopsin-3.
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.
authors.affiliation: From the Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, and.
authors.forename: Toshiaki
authors.initials: T
authors.lastname: Hosaka
authors.affiliation: the Atmosphere and Ocean Research Institute, University of Tokyo, Chiba 277-8564, Japan.
authors.forename: Susumu
authors.initials: S
authors.lastname: Yoshizawa
authors.affiliation: the Atmosphere and Ocean Research Institute, University of Tokyo, Chiba 277-8564, Japan.
authors.forename: Yu
authors.initials: Y
authors.lastname: Nakajima
authors.affiliation: From the Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, and.
authors.forename: Noboru
authors.initials: N
authors.lastname: Ohsawa
authors.affiliation: From the Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, and.
authors.forename: Masakatsu
authors.initials: M
authors.lastname: Hato
authors.affiliation: the Center for Microbial Oceanography, Research and Education, University of Hawaii, Honolulu, Hawaii 96822, and.
authors.forename: Edward F
authors.initials: EF
authors.lastname: DeLong
authors.affiliation: the Atmosphere and Ocean Research Institute, University of Tokyo, Chiba 277-8564, Japan.
authors.forename: Kazuhiro
authors.initials: K
authors.lastname: Kogure
authors.affiliation: RIKEN Structural Biology Laboratory, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Shigeyuki
authors.initials: S
authors.lastname: Yokoyama
authors.affiliation: From the Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, and.
authors.forename: Tomomi
authors.initials: T
authors.lastname: Kimura-Someya
authors.affiliation: the Atmosphere and Ocean Research Institute, University of Tokyo, Chiba 277-8564, Japan, iwasaki@bs.s.u-tokyo.ac.jp.|the Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-0032, Japan.
authors.forename: Wataru
authors.initials: W
authors.lastname: Iwasaki
authors.affiliation: From the Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, and mikako.shirouzu@riken.jp.
authors.forename: Mikako
authors.initials: M
authors.lastname: Shirouzu
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D018118:Chloride Channels / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D018360:Crystallography, X-Ray; D041965:Flavobacteriaceae / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D025602:Halorhodopsins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D008027:Light; D000072417:Protein Domains; D013329:Structure-Activity Relationship
chemical_list: D001426:Bacterial Proteins; D018118:Chloride Channels; D025602:Halorhodopsins
keywords: cell-free protein synthesis; chloride ion pump; chloride ion-releasing residues; crystal structure; membrane protein; microbial rhodopsin; protein crystallization; structure-function; tertiary structure