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Structural basis for the slow photocycle and late proton release in Acetabularia rhodopsin I from the marine plant Acetabularia acetabulum.

Furuse M, Tamogami J, Hosaka T, Kikukawa T, Shinya N, Hato M, Ohsawa N, Kim SY, Jung KH, Demura M, Miyauchi S, Kamo N, Shimono K, Kimura-Someya T, Yokoyama S, Shirouzu M
Acta Crystallogr D Biol Crystallogr 71 2203-16 (2015)
Related entries: 5ax0, 5ax1

Cited: 11 times
EuropePMC logo PMID: 26527138

Abstract

Although many crystal structures of microbial rhodopsins have been solved, those with sufficient resolution to identify the functional water molecules are very limited. In this study, the Acetabularia rhodopsin I (ARI) protein derived from the marine alga A. acetabulum was synthesized on a large scale by the Escherichia coli cell-free membrane-protein production method, and crystal structures of ARI were determined at the second highest (1.52-1.80 Å) resolution for a microbial rhodopsin, following bacteriorhodopsin (BR). Examinations of the photochemical properties of ARI revealed that the photocycle of ARI is slower than that of BR and that its proton-transfer reactions are different from those of BR. In the present structures, a large cavity containing numerous water molecules exists on the extracellular side of ARI, explaining the relatively low pKa of Glu206(ARI), which cannot function as an initial proton-releasing residue at any pH. An interhelical hydrogen bond exists between Leu97(ARI) and Tyr221(ARI) on the cytoplasmic side, which facilitates the slow photocycle and regulates the pKa of Asp100(ARI), a potential proton donor to the Schiff base, in the dark state.

Articles - 5awz mentioned but not cited (5)

  1. Structural Mechanism for Light-driven Transport by a New Type of Chloride Ion Pump, Nonlabens marinus Rhodopsin-3. Hosaka T, Yoshizawa S, Nakajima Y, Ohsawa N, Hato M, DeLong EF, Kogure K, Yokoyama S, Kimura-Someya T, Iwasaki W, Shirouzu M. J Biol Chem 291 17488-17495 (2016)
  2. Opsin 1 and Opsin 2 of the Corn Smut Fungus Ustilago maydis Are Green Light-Driven Proton Pumps. Panzer S, Brych A, Batschauer A, Terpitz U. Front Microbiol 10 735 (2019)
  3. Structure-based insights into evolution of rhodopsins. Zabelskii D, Dmitrieva N, Volkov O, Shevchenko V, Kovalev K, Balandin T, Soloviov D, Astashkin R, Zinovev E, Alekseev A, Round E, Polovinkin V, Chizhov I, Rogachev A, Okhrimenko I, Borshchevskiy V, Chupin V, Büldt G, Yutin N, Bamberg E, Koonin E, Gordeliy V. Commun Biol 4 821 (2021)
  4. Structural Foundations of Potassium Selectivity in Channelrhodopsins. Govorunova EG, Sineshchekov OA, Brown LS, Bondar AN, Spudich JL. mBio 13 e0303922 (2022)
  5. The Photoreaction of the Proton-Pumping Rhodopsin 1 From the Maize Pathogenic Basidiomycete Ustilago maydis. La Greca M, Chen JL, Schubert L, Kozuch J, Berneiser T, Terpitz U, Heberle J, Schlesinger R. Front Mol Biosci 9 826990 (2022)


Reviews citing this publication (2)

  1. Diversity, Mechanism, and Optogenetic Application of Light-Driven Ion Pump Rhodopsins. Inoue K. Adv Exp Med Biol 1293 89-126 (2021)
  2. Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering. de Grip WJ, Ganapathy S. Front Chem 10 879609 (2022)

Articles citing this publication (4)

  1. Cell-free methods to produce structurally intact mammalian membrane proteins. Shinoda T, Shinya N, Ito K, Ishizuka-Katsura Y, Ohsawa N, Terada T, Hirata K, Kawano Y, Yamamoto M, Tomita T, Ishibashi Y, Hirabayashi Y, Kimura-Someya T, Shirouzu M, Yokoyama S. Sci Rep 6 30442 (2016)
  2. NeoR, a near-infrared absorbing rhodopsin. Broser M, Spreen A, Konold PE, Schiewer E, Adam S, Borin V, Schapiro I, Seifert R, Kennis JTM, Bernal Sierra YA, Hegemann P. Nat Commun 11 5682 (2020)
  3. Lokiarchaeota archaeon schizorhodopsin-2 (LaSzR2) is an inward proton pump displaying a characteristic feature of acid-induced spectral blue-shift. Kojima K, Yoshizawa S, Hasegawa M, Nakama M, Kurihara M, Kikukawa T, Sudo Y. Sci Rep 10 20857 (2020)
  4. Graphs of protein-water hydrogen bond networks to dissect structural movies of ion-transfer microbial rhodopsins. Bertalan É, Bondar AN. Front Chem 10 1075648 (2022)


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