Structural insights into the mechanism of rhodopsin phosphodiesterase

Ikuta, T.; Shihoya, W.; Sugiura, M.; Yoshida, K.; Watari, M.; Tokano, T.; Yamashita, K.; Katayama, K.; Tsunoda, S. P.; Uchihashi, T.; Kandori, H.; Nureki, O.

doi:10.1101/2020.04.14.040642

bioRxiv · 10.1101/2020.04.14.040642

Structural insights into the mechanism of rhodopsin phosphodiesterase

Ikuta, T.·Shihoya, W.·Sugiura, M.·Yoshida, K.·Watari, M.·Tokano, T.·Yamashita, K.·Katayama, K.·Tsunoda, S. P.·Uchihashi, T.·Kandori, H.·Nureki, O.

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Abstract

Rhodopsin phosphodiesterase (Rh-PDE) is an enzyme rhodopsin belonging to a recently discovered class of microbial rhodopsins with light-dependent enzymatic activity. Rh-PDE consists of the N-terminal rhodopsin domain and C-terminal phosphodiesterase (PDE) domain, connected by 76-residue linker, and hydrolyzes both cAMP and cGMP in a light-dependent manner. Thus, Rh-PDE has potential for the optogenetic manipulation of cyclic nucleotide concentrations, as a complementary tool to rhodopsin guanylyl cyclase (Rh-GC) and photosensitive adenylyl cyclase (PAC). Here we present structural and functional analyses of the Rh-PDE derived from Salpingoeca rosetta. The 2.6 [A] resolution crystal structure of the transmembrane domain revealed a new topology of rhodopsin, with 8 TMs including the N-terminal extra TM, TM0. Mutational analyses demonstrated that TM0 plays a crucial role in the enzymatic photoactivity. We further solved the crystal structures of the transmembrane and PDE domain (2.1 [A]) with their connecting linkers. Integrating these structures, we proposed a model of full-length Rh-PDE, based on the HS-AFM observations and computational modeling of the linker region. These findings provide insight into the photoactivation mechanisms of other 8-TM enzyme rhodopsins and expand the definition of rhodopsins.

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Ikuta, T., Shihoya, W., Sugiura, M., Yoshida, K., Watari, M., Tokano, T., Yamashita, K., Katayama, K., Tsunoda, S. P., Uchihashi, T., Kandori, H., Nureki, O.. 2020-04-15. Structural insights into the mechanism of rhodopsin phosphodiesterase. https://doi.org/10.1101/2020.04.14.040642

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