7D7P

Crystal structure of the phosphodiesterase domain of Salpingoeca rosetta rhodopsin phosphodiesterase

7D7P の概要

• エントリーDOI: 10.2210/pdb7d7p/pdb
• 関連するPDBエントリー: 7CJ3
• 分子名称: Phosphodiesterase, NONAETHYLENE GLYCOL, DI(HYDROXYETHYL)ETHER, ... (7 entities in total)
• 機能のキーワード: microbial rhodopsin, eight-transmembrane, light-dependent phosphodiesterase, membrane protein
• 由来する生物種: Salpingoeca rosetta (strain ATCC 50818 / BSB-021)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 42815.02

構造登録者

Ikuta, T.,Shihoya, W.,Yamashita, K.,Nureki, O. (登録日: 2020-10-05, 公開日: 2020-11-18, 最終更新日: 2023-11-29)

主引用文献

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

実験手法

X-RAY DIFFRACTION (2.1 Å)