Structural insights into the proton pumping by unusual proteorhodopsin from nonmarine bacteria

Light-driven proton pumps are present in many organisms. Here, we present a high-resolution structure of a proteorhodopsin from a permafrost bacterium, Exiguobacterium sibiricum rhodopsin (ESR). Contrary to the proton pumps of known structure, ESR possesses three unique features. First, ESR's p...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 2013-07, Vol.110 (31), p.12631-12636
Main Authors: Gushchin, Ivan, Chervakov, Pavel, Kuzmichev, Pavel, Popov, Alexander N., Round, Ekaterina, Borshchevskiy, Valentin, Ishchenko, Andrii, Petrovskaya, Lada, Chupin, Vladimir, Dolgikh, Dmitry A., Arseniev, Alexander A., Kirpichnikov, Mikhail, Gordeliy, Valentin
Format: Article
Language:English
Subjects:
Amino acids
Bacillaceae
Bacillaceae - chemistry
Bacteria
Bacterial Proteins
Bacterial Proteins - chemistry
Bacteriorhodopsins
Biochemistry, Molecular Biology
Biological Sciences
Crystallography, X-Ray
Crystals
Electron paramagnetic resonance
Hydrogen bonds
Life Sciences
Molecules
Protein Structure, Secondary
Protein Structure, Tertiary
Proteins
Proton pumps
Protons
Rhodopsin
Rhodopsin - chemistry
Rhodopsins, Microbial
Schiff bases
Solvents
Structural Biology
Structure-Activity Relationship
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Summary:Light-driven proton pumps are present in many organisms. Here, we present a high-resolution structure of a proteorhodopsin from a permafrost bacterium, Exiguobacterium sibiricum rhodopsin (ESR). Contrary to the proton pumps of known structure, ESR possesses three unique features. First, ESR's proton donor is a lysine side chain that is situated very close to the bulk solvent. Second, the α-helical structure in the middle of the helix F is replaced by 3 ₁₀- and π-helix–like elements that are stabilized by the Trp-154 and Asn-224 side chains. This feature is characteristic for the proteorhodopsin family of proteins. Third, the proton release region is connected to the bulk solvent by a chain of water molecules already in the ground state. Despite these peculiarities, the positions of water molecule and amino acid side chains in the immediate Schiff base vicinity are very well conserved. These features make ESR a very unusual proton pump. The presented structure sheds light on the large family of proteorhodopsins, for which structural information was not available previously.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.1221629110