Molecular mechanism of light-driven sodium pumping

• Published in: Nature communications 2020-05, Vol.11 (1), p.2137-11, Article 2137
• Main Authors: Kovalev, Kirill, Astashkin, Roman, Gushchin, Ivan, Orekhov, Philipp, Volkov, Dmytro, Zinovev, Egor, Marin, Egor, Rulev, Maksim, Alekseev, Alexey, Royant, Antoine, Carpentier, Philippe, Vaganova, Svetlana, Zabelskii, Dmitrii, Baeken, Christian, Sergeev, Ilya, Balandin, Taras, Bourenkov, Gleb, Carpena, Xavier, Boer, Roeland, Maliar, Nina, Borshchevskiy, Valentin, Büldt, Georg, Bamberg, Ernst, Gordeliy, Valentin
• Format: Article
• Language: English
• Subjects: 631/337/470; 631/535/1266; 631/57/2270/1140; 82/16; 82/80; 82/83; Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; Binding sites; Biochemistry, Molecular Biology; Cations; Crystal structure; Crystallography; Crystallography, X-Ray; Escherichia coli - metabolism; Flavobacteriaceae - metabolism; Genetics; Humanities and Social Sciences; Imines; Information processing; Lasers; Life Sciences; Light; Lipids; Molecular Dynamics Simulation; multidisciplinary; Mutants; Na+/K+-exchanging ATPase; Optics; Physiology; Protein Folding; Proteins; Protons; Pumping; Retina; Rhodopsin; Rhodopsin - chemistry; Rhodopsin - metabolism; Science; Science (multidisciplinary); Sodium; Sodium - metabolism; Sodium-Potassium-Exchanging ATPase - chemistry; Sodium-Potassium-Exchanging ATPase - metabolism; Structural Biology; X-Ray Diffraction
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-020-16032-y

The light-driven sodium-pumping rhodopsin KR2 from Krokinobacter eikastus is the only non-proton cation active transporter with demonstrated potential for optogenetics. However, the existing structural data on KR2 correspond exclusively to its ground state, and show no sodium inside the protein, which hampers the understanding of sodium-pumping mechanism. Here we present crystal structure of the O-intermediate of the physiologically relevant pentameric form of KR2 at the resolution of 2.1 Å, revealing a sodium ion near the retinal Schiff base, coordinated by N112 and D116 of the characteristic NDQ triad. We also obtained crystal structures of D116N and H30A variants, conducted metadynamics simulations and measured pumping activities of putative pathway mutants to demonstrate that sodium release likely proceeds alongside Q78 towards the structural sodium ion bound between KR2 protomers. Our findings highlight the importance of pentameric assembly for sodium pump function, and may be used for rational engineering of enhanced optogenetic tools. The Na + -pumping KR2 rhodopsin from Krokinobacter eikastus is a light-driven non-proton cation pump whose mechanism of pumping remains to be understood. Here authors solved crystal structures of the O-intermediate state of the pentameric form of KR2 and its D116N and H30A mutants, which sheds light on the mechanism of non-proton cation light-driven pumping.