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TitleStructural insights into the mechanism and dynamics of proteorhodopsin biogenesis and retinal scavenging.
Journal, issue, pagesNat Commun, Vol. 15, Issue 1, Page 6950, Year 2024
Publish dateAug 13, 2024
AuthorsStephan Hirschi / Thomas Lemmin / Nooraldeen Ayoub / David Kalbermatter / Daniele Pellegata / Zöhre Ucurum / Jürg Gertsch / Dimitrios Fotiadis /
PubMed AbstractMicrobial ion-pumping rhodopsins (MRs) are extensively studied retinal-binding membrane proteins. However, their biogenesis, including oligomerisation and retinal incorporation, remains poorly ...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.
External linksNat Commun / PubMed:39138159 / PubMed Central
MethodsEM (single particle)
Resolution2.82 - 3.54 Å
Structure data

16759

8cnk

EMDB-16759, PDB-8cnk:
Cryo-EM structure of retinal-free proteoopsin bound to decanoate
Method: EM (single particle) / Resolution: 2.97 Å

16795

8cqc

EMDB-16795, PDB-8cqc:
Cryo-EM structure of pentameric proteorhodopsin A18L mutant
Method: EM (single particle) / Resolution: 2.82 Å

16796

8cqd

EMDB-16796, PDB-8cqd:
Cryo-EM structure of hexameric proteorhodopsin A18L mutant
Method: EM (single particle) / Resolution: 3.54 Å

Chemicals

ChemComp-DKA:
DECANOIC ACID

ChemComp-RET:
RETINAL

ChemComp-HOH:
WATER

Source
  • uncultured gammaproteobacteria bacterium (environmental samples)
KeywordsPROTON TRANSPORT / Membrane protein / Light-driven proton pump / Proteorhodopsin / Proteoopsin

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