title: Crystal structure and functional characterization of a light-driven chloride pump having an NTQ motif.
abstract: A novel light-driven chloride-pumping rhodopsin (ClR) containing an 'NTQ motif' in its putative ion conduction pathway has been discovered and functionally characterized in a genomic analysis study of a marine bacterium. Here we report the crystal structure of ClR from the flavobacterium Nonlabens marinus S1-08(T) determined under two conditions at 2.0 and 1.56 Å resolutions. The structures reveal two chloride-binding sites, one around the protonated Schiff base and the other on a cytoplasmic loop. We identify a '3 omega motif' formed by three non-consecutive aromatic amino acids that is correlated with the B-C loop orientation. Detailed ClR structural analyses with functional studies in E. coli reveal the chloride ion transduction pathway. Our results help understand the molecular mechanism and physiological role of ClR and provide a structural basis for optogenetic applications.
authors.affiliation: Department of Systems Biology and Division of Life Sciences, Yonsei University, 50 Yonsei-ro, Seoul 03722, Republic of Korea.
authors.forename: Kuglae
authors.initials: K
authors.lastname: Kim
authors.affiliation: Department of Systems Biology and Division of Life Sciences, Yonsei University, 50 Yonsei-ro, Seoul 03722, Republic of Korea.
authors.forename: Soon-Kyeong
authors.initials: SK
authors.lastname: Kwon
authors.affiliation: Department of Systems Biology and Division of Life Sciences, Yonsei University, 50 Yonsei-ro, Seoul 03722, Republic of Korea.
authors.forename: Sung-Hoon
authors.initials: SH
authors.lastname: Jun
authors.affiliation: Department of Systems Biology and Division of Life Sciences, Yonsei University, 50 Yonsei-ro, Seoul 03722, Republic of Korea.
authors.forename: Jeong Seok
authors.initials: JS
authors.lastname: Cha
authors.affiliation: Department of Systems Biology and Division of Life Sciences, Yonsei University, 50 Yonsei-ro, Seoul 03722, Republic of Korea.
authors.forename: Hoyoung
authors.initials: H
authors.lastname: Kim
authors.affiliation: Department of Biochemistry and Division of Life Sciences, Yonsei University, 50 Yonsei-ro, Seoul 03722, Republic of Korea.
authors.forename: Weontae
authors.initials: W
authors.lastname: Lee
authors.affiliation: Department of Systems Biology and Division of Life Sciences, Yonsei University, 50 Yonsei-ro, Seoul 03722, Republic of Korea.|Strategic Initiative for Microbiomes in Agriculture and Food, Yonsei University, 50 Yonsei-ro, Seoul 03722, Republic of Korea.
authors.forename: Jihyun F
authors.initials: JF
authors.lastname: Kim
authors.affiliation: Department of Systems Biology and Division of Life Sciences, Yonsei University, 50 Yonsei-ro, Seoul 03722, Republic of Korea.
authors.forename: Hyun-Soo
authors.initials: HS
authors.lastname: Cho
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D001665:Binding Sites / Q000235:genetics; D002712:Chlorides / Q000378:metabolism*; D018360:Crystallography, X-Ray; D041965:Flavobacteriaceae / Q000235:genetics / Q000378:metabolism*; D016623:Ion Pumps / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D017136:Ion Transport / Q000528:radiation effects; D008027:Light; D008958:Models, Molecular; D062308:Optogenetics; D011487:Protein Conformation; D012243:Rhodopsin / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D017386:Sequence Homology, Amino Acid
chemical_list: D001426:Bacterial Proteins; D002712:Chlorides; D016623:Ion Pumps; D012243:Rhodopsin