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 S1-08T 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.
Highlights
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
The ClR crystal structure presented in this work together with the recently reported NaR structures[13,14] reveals the molecular architectures of novel light-driven ion pumps in marine bacteria
The HR and BR crystal structures showed that the chloride ion-binding site at protonated Schiff base (PSB) of HR corresponds to the position of the negatively charged side chain of Asp[85] of BR7,26, suggesting that BR and HR use a common mechanism for ion conductance and that the chloride ion at PSB of HR compensates for the negative charge from Asp[85] of BR27,28
Summary
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. In 2000, a BR-like protonpumping rhodopsin from a proteobacterium was identified and named proteorhodopsin[8] This showed that light-driven energy accumulation via ion-pumping rhodopsins is widely used among marine bacteria. In 2013, a novel class of microbial rhodopsins was found in Nonlabens (Donghaeana) dokdonensis DSW-6T and other marine flavobacteria[9] These rhodopsins were dubbed NQ rhodopsins because they have Asn (N) and Gln (Q) at the positions of the proton acceptor and donor residues of BR9. Our results demonstrate the unique structural features of ClR and provide a basis to understand the mechanism of chloride ion transport through this new light-driven chloride pump in marine bacteria
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