Structural insights into the mechanism of rhodopsin phosphodiesterase

Ikuta, Tatsuya; Shihoya, Wataru; Sugiura, Masahiro; Yoshida, Kazuho; Watari, Masahito; Tokano, Takaya; Yamashita, Keitaro; Katayama, Kota; Tsunoda, Satoshi P.; Uchihashi, Takayuki; Kandori, Hideki; Nureki, Osamu

doi:10.1038/s41467-020-19376-7

Cited by 33 publications

(21 citation statements)

References 68 publications

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“…As previously described ( 40 ), the protein was crystallized in lipidic cubic phase (LCP). The protein was reconstituted into monoolein at a weight ratio of 1:1.5 (protein:lipid).…”

Section: Methodsmentioning

confidence: 99%

Crystal structure of schizorhodopsin reveals mechanism of inward proton pumping

Higuchi

Shihoya

Konno

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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Schizorhodopsins (SzRs), a new rhodopsin family identified in Asgard archaea, are phylogenetically located at an intermediate position between type-1 microbial rhodopsins and heliorhodopsins. SzRs work as light-driven inward H+ pumps as xenorhodopsins in bacteria. Although E81 plays an essential role in inward H+ release, the H+ is not metastably trapped in such a putative H+ acceptor, unlike the other H+ pumps. It remains elusive why SzR exhibits different kinetic behaviors in H+ release. Here, we report the crystal structure of SzR AM_5_00977 at 2.1 Å resolution. The SzR structure superimposes well on that of bacteriorhodopsin rather than heliorhodopsin, suggesting that SzRs are classified with type-1 rhodopsins. The structure-based mutagenesis study demonstrated that the residues N100 and V103 around the β-ionone ring are essential for color tuning in SzRs. The cytoplasmic parts of transmembrane helices 2, 6, and 7 are shorter than those in the other microbial rhodopsins, and thus E81 is located near the cytosol and easily exposed to the solvent by light-induced structural change. We propose a model of untrapped inward H+ release; H+ is released through the water-mediated transport network from the retinal Schiff base to the cytosol by the side of E81. Moreover, most residues on the H+ transport pathway are not conserved between SzRs and xenorhodopsins, suggesting that they have entirely different inward H+ release mechanisms.

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“…As previously described ( 40 ), the protein was crystallized in lipidic cubic phase (LCP). The protein was reconstituted into monoolein at a weight ratio of 1:1.5 (protein:lipid).…”

Section: Methodsmentioning

confidence: 99%

Crystal structure of schizorhodopsin reveals mechanism of inward proton pumping

Higuchi

Shihoya

Konno

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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“…The rhodopsin proteorhodopsin and related proteins have aroused continuous and extensive interest both experimentally and theoretically among researchers, especially during the past 20 years [ 1 , 2 , 3 , 4 , 5 ]. Rhodopsin is a seven transmembrane α-helices (TM) protein which uses retinal as a chromophore.…”

Section: Introductionmentioning

confidence: 99%

Accurate Prediction of Absorption Spectral Shifts of Proteorhodopsin Using a Fragment-Based Quantum Mechanical Method

et al. 2021

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Many experiments have been carried out to display different colors of Proteorhodopsin (PR) and its mutants, but the mechanism of color tuning of PR was not fully elucidated. In this study, we applied the Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Caps (EE-GMFCC) method to the prediction of excitation energies of PRs. Excitation energies of 10 variants of Blue Proteorhodopsin (BPR-PR105Q) in residue 105GLN were calculated with the EE-GMFCC method at the TD-B3LYP/6-31G* level. The calculated results show good correlation with the experimental values of absorption wavelengths, although the experimental wavelength range among these systems is less than 50 nm. The ensemble-averaged electric fields along the polyene chain of retinal correlated well with EE-GMFCC calculated excitation energies for these 10 PRs, suggesting that electrostatic interactions from nearby residues are responsible for the color tuning. We also utilized the GMFCC method to decompose the excitation energy contribution per residue surrounding the chromophore. Our results show that residues ASP97 and ASP227 have the largest contribution to the absorption spectral shift of PR among the nearby residues of retinal. This work demonstrates that the EE-GMFCC method can be applied to accurately predict the absorption spectral shifts for biomacromolecules.

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“…The results achieved by ZOO have successfully proven the effectiveness of SWSX in the structural analysis of various samples at SPring-8 (Taniguchi et al, 2017;Kato et al, 2018;Shihoya et al, 2018;Liu et al, 2019;Ikuta et al, 2020;Jiang et al, 2020;Shiimura et al, 2020;Umeda et al, 2020;Yu et al, 2020). In these studies, hierarchical clustering was shown to be essential to select homogeneous sub-datasets to be merged.…”

Section: Introductionmentioning

confidence: 87%

Guidelines for de novo phasing using multiple small-wedge data collection

Baba¹,

Matsuura²,

Kawamura³

et al. 2021

J Synchrotron Rad

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Intense micro-focus X-ray beamlines available at synchrotron facilities have achieved high-quality data collection even from the microcrystals of membrane proteins. The automatic data collection system developed at SPring-8, named ZOO, has contributed to many structure determinations of membrane proteins using small-wedge synchrotron crystallography (SWSX) datasets. The `small-wedge' (5–20°) datasets are collected from multiple crystals and then merged to obtain the final structure factors. To our knowledge, no systematic investigation on the dose dependence of data accuracy has so far been reported for SWSX, which is between `serial crystallography' and `rotation crystallography'. Thus, herein, we investigated the optimal dose conditions for experimental phasing with SWSX. Phase determination using anomalous scattering signals was found to be more difficult at higher doses. Furthermore, merging more homogeneous datasets grouped by hierarchical clustering with controlled doses mildly reduced the negative factors in data collection, such as `lack of signal' and `radiation damage'. In turn, as more datasets were merged, more probable phases could be obtained across a wider range of doses. Therefore, our findings show that it is essential to choose a lower dose than 10 MGy for de novo structure determination by SWSX. In particular, data collection using a dose of 5 MGy proved to be optimal in balancing the amount of signal available while reducing the amount of damage as much as possible.

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Structural insights into the mechanism of rhodopsin phosphodiesterase

Cited by 33 publications

References 68 publications

Crystal structure of schizorhodopsin reveals mechanism of inward proton pumping

Crystal structure of schizorhodopsin reveals mechanism of inward proton pumping

Accurate Prediction of Absorption Spectral Shifts of Proteorhodopsin Using a Fragment-Based Quantum Mechanical Method

Guidelines for de novo phasing using multiple small-wedge data collection

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