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Open AccessArticle

Crystal Structure of the N112A Mutant of the Light-Driven Sodium Pump KR2

1
Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
2
Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 38000 Grenoble, France
3
Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
4
JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
5
Institute of Crystallography, University of Aachen (RWTH), 52062 Aachen, Germany
6
European Synchrotron Radiation Facility (ESRF), 38000 Grenoble, France
7
Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, 141980 Dubna, Russia
8
M. M. Shemyakin–Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
9
Biological Faculty, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
*
Authors to whom correspondence should be addressed.
These authors contributed equally to the work.
Crystals 2020, 10(6), 496; https://doi.org/10.3390/cryst10060496
Received: 8 May 2020 / Revised: 3 June 2020 / Accepted: 5 June 2020 / Published: 8 June 2020
The light-driven sodium pump KR2, found in 2013 in the marine bacteria Krokinobacter eikastus, serves as a model protein for the studies of the sodium-pumping microbial rhodopsins (NaRs). KR2 possesses a unique NDQ (N112, D116, and Q123) set of the amino acid residues in the functionally relevant positions, named the NDQ motif. The N112 was shown to determine the Na+/H+ selectivity and pumping efficiency of the protein. Thus, N112A mutation converts KR2 into an outward proton pump. However, no structural data on the functional conversions of the light-driven sodium pumps are available at the moment. Here we present the crystal structure of the N112A mutant of KR2 in the ground state at the resolution of 2.4 Å. The structure revealed a minor deflection in the central part of the helix C and a double conformation of the L74 residue in the mutant. The organization of the retinal Schiff base and neighboring water molecules is preserved in the ground state of KR2-N112A. The presented data provide structural insights into the effects of the alterations of the characteristic NDQ motif of NaRs. Our findings also demonstrate that for the rational design of the KR2 variants with modified ion selectivity for optogenetic applications, the structures of the intermediate states of both the protein and its functional variants are required. View Full-Text
Keywords: microbial rhodopsin; retinal; ion transport; mutation; NDQ motif; sodium pump; X-ray crystallography microbial rhodopsin; retinal; ion transport; mutation; NDQ motif; sodium pump; X-ray crystallography
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Maliar, N.; Kovalev, K.; Baeken, C.; Balandin, T.; Astashkin, R.; Rulev, M.; Alekseev, A.; Ilyinsky, N.; Rogachev, A.; Chupin, V.; Dolgikh, D.; Kirpichnikov, M.; Gordeliy, V. Crystal Structure of the N112A Mutant of the Light-Driven Sodium Pump KR2. Crystals 2020, 10, 496.

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