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3.E.3.  The HelioRhodopsin (HelioR) Family 

Many organisms capture or sense sunlight using rhodopsin pigments, integral 7 TMS membrane proteins that bind retinal chromophores. Rhodopsin, both from animals and microorganims, are members of the TOG superfamily (Yee et al. 2013). The 7 helices form a pocket in which retinal is linked covalently as a protonated Schiff base to a lysine in the seventh TMS (Pushkarev et al. 2018). Heliorhodopsins are distantly related to microbial rhodopsins (MR, TC# 3.E.1), and animal rhodopsins (TC# 9.A. 14.1) but they are embedded in the membrane with their N termini facing the cell cytoplasm, an orientation that is opposite to that of MRs and animal rhodopsins. Heliorhodopsins show photocycles that last about 5 seconds, suggesting that they have light-sensory activity. The photocycles accompany retinal isomerization and proton transfer, as in other rhodopsins, but protons are never released from the protein, even transiently. Thus, they are not believed to transport protons across the membrane. Heliorhodopsins are abundant and distributed globally in Archaea, Bacteria, Eukarya and their viruses. They are widespread in the microbial world (Pushkarev et al. 2018).

The conserved E107 in TMS3 of heliorhodopsin 48C12 (TC# 3.E.3.1.1) may be the counterion of the protonated Schiff base, as in microbial rhodopsins. From pH titration studies, the pKa was determined to be 11.5 for the Schiff base. Light converts the all trans Schiff base retinal in heliorhodopsin to 13-cis. The Schiff base proton is transferred to the proton-accepting group in the M intermediate, which involves H23 and H80 but not E107. Thus, this accepting group is probably located within the N-terminal region of heliorhodopsins that faces the cytoplasmic side, assuming that the membrane topology of heliorhodopsins is opposite to that of microbial rhodopsins as proposed (Pushkarev et al. 2018).

Heliorhodopsins (HeRs) are present in bacteria, archaea, algae and algal viruses (Shihoya et al. 2019) and less than 15% sequence identity with type-1 and type-2 (animal) rhodopsins. HeRs exhibit a reverse orientation in the membrane compared with the other rhodopsins.  Shihoya et al. 2019 presented the 2.4 Å-resolution structure of HeR from an uncultured Thermoplasmatales archaeon SG8-52-1 (GenBank sequence ID LSSD01000000). Structural and biophysical analyses revealed 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 beta-ionone ring of the retinal chromophore, which plays a role in capturing retinal from environment sources (Shihoya et al. 2019). The X-ray crystal structure of heliiorhodopsin (HeR) 48C12 was elucidated after the first report on a HeR variant from Thermoplasmatales archaeon SG8-52-1, which revealed the water-mediated hydrogen-bonding network connected to the Schiff base region in the cytoplasmic side (Tomida et al. 2021). An inverse hydrogen-bonding change between the protonated retinal schiff base and water molecules upon photoisomerization in heliorhodopsin 48C12 (Tomida et al. 2021).

References associated with 3.E.3 family:

Pushkarev, A., K. Inoue, S. Larom, J. Flores-Uribe, M. Singh, M. Konno, S. Tomida, S. Ito, R. Nakamura, S.P. Tsunoda, A. Philosof, I. Sharon, N. Yutin, E.V. Koonin, H. Kandori, and O. Béjà. (2018). A distinct abundant group of microbial rhodopsins discovered using functional metagenomics. Nature. [Epub: Ahead of Print] 29925949
Shihoya, W., K. Inoue, M. Singh, M. Konno, S. Hososhima, K. Yamashita, K. Ikeda, A. Higuchi, T. Izume, S. Okazaki, M. Hashimoto, R. Mizutori, S. Tomida, Y. Yamauchi, R. Abe-Yoshizumi, K. Katayama, S.P. Tsunoda, M. Shibata, Y. Furutani, A. Pushkarev, O. Béjà, T. Uchihashi, H. Kandori, and O. Nureki. (2019). Crystal structure of heliorhodopsin. Nature 574: 132-136. 31554965
Tomida, S., S. Kitagawa, H. Kandori, and Y. Furutani. (2021). Inverse Hydrogen-Bonding Change Between the Protonated Retinal Schiff Base and Water Molecules upon Photoisomerization in Heliorhodopsin 48C12. J Phys Chem B 125: 8331-8341. 34292728
Yee, D.C., M.A. Shlykov, A. Västermark, V.S. Reddy, S. Arora, E.I. Sun, and M.H. Saier, Jr. (2013). The transporter-opsin-G protein-coupled receptor (TOG) superfamily. FEBS J. 280: 5780-5800. 23981446