8CNK

Cryo-EM structure of retinal-free proteoopsin bound to decanoate

8CNK の概要

• エントリーDOI: 10.2210/pdb8cnk/pdb
• 関連するPDBエントリー: 7B03
• EMDBエントリー: 16759
• 分子名称: Green-light absorbing proteorhodopsin, DECANOIC ACID (2 entities in total)
• 機能のキーワード: membrane protein, light-driven proton pump, proteorhodopsin, proteoopsin, proton transport
• 由来する生物種: uncultured Gammaproteobacteria bacterium
• タンパク質・核酸の鎖数: 5
• 化学式量合計: 132659.46

構造登録者

Hirschi, S.,Lemmin, T.,Fotiadis, D. (登録日: 2023-02-23, 公開日: 2024-07-03, 最終更新日: 2024-09-04)

主引用文献

Hirschi, S.,Lemmin, T.,Ayoub, N.,Kalbermatter, D.,Pellegata, D.,Ucurum, Z.,Gertsch, J.,Fotiadis, D.
Structural insights into the mechanism and dynamics of proteorhodopsin biogenesis and retinal scavenging.
Nat Commun, 15:6950-6950, 2024

PubMed Abstract: Microbial ion-pumping rhodopsins (MRs) are extensively studied retinal-binding membrane proteins. However, their biogenesis, including oligomerisation and retinal incorporation, remains poorly understood. The bacterial green-light absorbing proton pump proteorhodopsin (GPR) has emerged as a model protein for MRs and is used here to address these open questions using cryo-electron microscopy (cryo-EM) and molecular dynamics (MD) simulations. Specifically, conflicting studies regarding GPR stoichiometry reported pentamer and hexamer mixtures without providing possible assembly mechanisms. We report the pentameric and hexameric cryo-EM structures of a GPR mutant, uncovering the role of the unprocessed N-terminal signal peptide in the assembly of hexameric GPR. Furthermore, certain proteorhodopsin-expressing bacteria lack retinal biosynthesis pathways, suggesting that they scavenge the cofactor from their environment. We shed light on this hypothesis by solving the cryo-EM structure of retinal-free proteoopsin, which together with mass spectrometry and MD simulations suggests that decanoate serves as a temporary placeholder for retinal in the chromophore binding pocket. Further MD simulations elucidate possible pathways for the exchange of decanoate and retinal, offering a mechanism for retinal scavenging. Collectively, our findings provide insights into the biogenesis of MRs, including their oligomeric assembly, variations in protomer stoichiometry and retinal incorporation through a potential cofactor scavenging mechanism.

PubMed: 39138159
DOI: 10.1038/s41467-024-50960-3

実験手法

ELECTRON MICROSCOPY (2.97 Å)