7D7Q

Crystal structure of the transmembrane domain and linker region of Salpingoeca rosetta rhodopsin phosphodiesterase

Summary for 7D7Q

• Entry DOI: 10.2210/pdb7d7q/pdb
• Related: 7CJ3 7D7P
• Descriptor: Phosphodiesterase, RETINAL, (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (3 entities in total)
• Functional Keywords: microbial rhodopsin, eight-transmembrane, light-dependent phosphodiesterase, membrane protein
• Biological source: Salpingoeca rosetta (strain ATCC 50818 / BSB-021)
• Total number of polymer chains: 2
• Total formula weight: 80522.16

Authors

Ikuta, T.,Shihoya, W.,Yamashita, K.,Nureki, O. (deposition date: 2020-10-05, release date: 2020-11-18, Last modification date: 2024-10-16)

Primary citation

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.
Structural insights into the mechanism of rhodopsin phosphodiesterase.
Nat Commun, 11:5605-5605, 2020

PubMed 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 and photosensitive adenylyl cyclase. Here we present structural and functional analyses of the Rh-PDE derived from Salpingoeca rosetta. The crystal structure of the rhodopsin domain at 2.6 Å resolution revealed a new topology of rhodopsins, 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 rhodopsin domain (3.5 Å) and PDE domain (2.1 Å) with their connecting linkers, which showed a rough sketch of the full-length Rh-PDE. 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.

PubMed: 33154353
DOI: 10.1038/s41467-020-19376-7

Experimental method

X-RAY DIFFRACTION (3.5 Å)