5B2N

Crystal structure of the light-driven chloride ion-pumping rhodopsin, ClP, from Nonlabens marinus

Summary for 5B2N

• Entry DOI: 10.2210/pdb5b2n/pdb
• Descriptor: Chloride pumping rhodopsin, RETINAL, CHLORIDE ION, ... (8 entities in total)
• Functional Keywords: retinal, cell-free synthesis, light-driven chloride pump, membrane protein, transport protein
• Biological source: Nonlabens marinus S1-08
• Total number of polymer chains: 1
• Total formula weight: 32597.94

Authors

Hosaka, T.,Kimura-Someya, T.,Shirouzu, M. (deposition date: 2016-01-20, release date: 2016-07-13, Last modification date: 2024-10-23)

Primary citation

Hosaka, T.,Yoshizawa, S.,Nakajima, Y.,Ohsawa, N.,Hato, M.,DeLong, E.F.,Kogure, K.,Yokoyama, S.,Kimura-Someya, T.,Iwasaki, W.,Shirouzu, M.
Structural Mechanism for Light-driven Transport by a New Type of Chloride Ion Pump, Nonlabens marinus Rhodopsin-3
J.Biol.Chem., 291:17488-17495, 2016

PubMed 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.

PubMed: 27365396
DOI: 10.1074/jbc.M116.728220

Experimental method

X-RAY DIFFRACTION (1.581 Å)