Crystal structure of heliorhodopsin

Wataru Shihoya, Keiichi Inoue, Manish Singh, Masae Konno, Shoko Hososhima, Keitaro Yamashita, Kento Ikeda, Akimitsu Higuchi, Tamaki Izume, Sae Okazaki, Masanori Hashimoto, Ritsu Mizutori, Sahoko Tomida, Yumeka Yamauchi, Rei Abe-Yoshizumi, Kota Katayama, Satoshi P. Tsunoda, Mikihiro Shibata, Yuji Furutani, Alina Pushkarev, Oded Béjà, Takayuki Uchihashi, Hideki Kandori () and Osamu Nureki ()
Additional contact information
Wataru Shihoya: The University of Tokyo
Keiichi Inoue: Nagoya Institute of Technology
Manish Singh: Nagoya Institute of Technology
Masae Konno: Nagoya Institute of Technology
Shoko Hososhima: Nagoya Institute of Technology
Keitaro Yamashita: The University of Tokyo
Kento Ikeda: Kanazawa University
Akimitsu Higuchi: The University of Tokyo
Tamaki Izume: The University of Tokyo
Sae Okazaki: The University of Tokyo
Masanori Hashimoto: Nagoya Institute of Technology
Ritsu Mizutori: Nagoya Institute of Technology
Sahoko Tomida: Nagoya Institute of Technology
Yumeka Yamauchi: Nagoya Institute of Technology
Rei Abe-Yoshizumi: Nagoya Institute of Technology
Kota Katayama: Nagoya Institute of Technology
Satoshi P. Tsunoda: Nagoya Institute of Technology
Mikihiro Shibata: Kanazawa University
Yuji Furutani: Nagoya Institute of Technology
Alina Pushkarev: Technion–Israel Institute of Technology
Oded Béjà: Technion–Israel Institute of Technology
Takayuki Uchihashi: Nagoya University
Hideki Kandori: Nagoya Institute of Technology
Osamu Nureki: The University of Tokyo

Nature, 2019, vol. 574, issue 7776, 132-136

Abstract: Abstract Heliorhodopsins (HeRs) are a family of rhodopsins that was recently discovered using functional metagenomics1. They are widely present in bacteria, archaea, algae and algal viruses2,3. Although HeRs have seven predicted transmembrane helices and an all-trans retinal chromophore as in the type-1 (microbial) rhodopsin, they display less than 15% sequence identity with type-1 and type-2 (animal) rhodopsins. HeRs also exhibit the reverse orientation in the membrane compared with the other rhodopsins. Owing to the lack of structural information, little is known about the overall fold and the photoactivation mechanism of HeRs. Here we present the 2.4-Å-resolution structure of HeR from an uncultured Thermoplasmatales archaeon SG8-52-1 (GenBank sequence ID LSSD01000000). Structural and biophysical analyses reveal the similarities and differences between HeRs and type-1 microbial rhodopsins. The overall fold of HeR is similar to that of bacteriorhodopsin. A linear hydrophobic pocket in HeR accommodates a retinal configuration and isomerization as in the type-1 rhodopsin, although most of the residues constituting the pocket are divergent. Hydrophobic residues fill the space in the extracellular half of HeR, preventing the permeation of protons and ions. The structure reveals an unexpected lateral fenestration above the β-ionone ring of the retinal chromophore, which has a critical role in capturing retinal from environment sources. Our study increases the understanding of the functions of HeRs, and the structural similarity and diversity among the microbial rhodopsins.

Date: 2019
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DOI: 10.1038/s41586-019-1604-6

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