A newly identified microbial rhodopsin, NM-R3, from the marine flavobacterium Nonlabens marinus, was recently shown to drive chloride ion uptake, extending our understanding of the diversity of mechanisms for biological energy conversion. To clarify the mechanism underlying its function, we characterized the crystal structures of NM-R3 in both the dark state and early intermediate photoexcited states produced by laser pulses of different intensities and temperatures. The displacement of chloride ions at five different locations in the model reflected the detailed anion-conduction pathway, and the activity-related key residues—Cys105, Ser60, Gln224, and Phe90—were identified by mutation assays and spectroscopy. Comparisons with other proteins, including a closely related outward sodium ion pump, revealed key motifs and provided structural insights into light-driven ion transport across membranes by the NQ subfamily of rhodopsins. Unexpectedly, the response of the retinal in NM-R3 to photostimulation appears to be substantially different from that seen in bacteriorhodopsin.
Bibliographical noteFunding Information:
We thank all staff members at the NW12A beamline station at the Photon Factory for assistance with data collection. Funding: This work was supported by the Research Program (NRF-20171A2B2008483, 2019M3A9F6021810 to W.L. and NRF-20161A6A3A04010213 to J.-H.Y.) through the National Research Foundation of Korea and the Platform Project for Supporting Drug Discovery and Life Science Research (BINDS) from AMED under grant number JP18am0101076 (to S.-Y.P.), JSPS KAKENHI grant number JP19H05779 (to S.-Y.P.), and Takeda Science Foundation (to S.-Y.P.). The work was supported in part by Brain Korea 21 (BK21) PLUS program. J.-H.P. and Wonbin Lee are fellowship awardees of the BK21 PLUS program.
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