8B6E

crystal structure of the DNA-binding short chromatophore-targeted protein sCTP-23166 from Paulinella chromatophora

Summary for 8B6E

• Entry DOI: 10.2210/pdb8b6e/pdb
• Descriptor: sCTP-23166, 1,2-ETHANEDIOL, SODIUM ION, ... (4 entities in total)
• Functional Keywords: endosymbiosis, effector proteins, antimicrobial peptides, host control, dna binding protein
• Biological source: Paulinella chromatophora
• Total number of polymer chains: 2
• Total formula weight: 15735.83

Authors

Macorano, L.,Applegate, V.,Hoeppner, A.,Smits, S.H.J.,Nowack, E.C.M. (deposition date: 2022-09-27, release date: 2023-07-12, Last modification date: 2024-05-01)

Primary citation

Macorano, L.,Binny, T.M.,Spiegl, T.,Klimenko, V.,Singer, A.,Oberleitner, L.,Applegate, V.,Seyffert, S.,Stefanski, A.,Gremer, L.,Gertzen, C.G.W.,Hoppner, A.,Smits, S.H.J.,Nowack, E.C.M.
DNA-binding and protein structure of nuclear factors likely acting in genetic information processing in the Paulinella chromatophore.
Proc.Natl.Acad.Sci.USA, 120:e2221595120-e2221595120, 2023

PubMed Abstract: The chromatophores in are evolutionary-early-stage photosynthetic organelles. Biological processes in chromatophores depend on a combination of chromatophore and nucleus-encoded proteins. Interestingly, besides proteins carrying chromatophore-targeting signals, a large arsenal of short chromatophore-targeted proteins (sCTPs; <90 amino acids) without recognizable targeting signals were found in chromatophores. This situation resembles endosymbionts in plants and insects that are manipulated by host-derived antimicrobial peptides. Previously, we identified an expanded family of sCTPs of unknown function, named here "DNA-binding (DB)-sCTPs". DB-sCTPs contain a ~45 amino acid motif that is conserved in some bacterial proteins with predicted functions in DNA processing. Here, we explored antimicrobial activity, DNA-binding capacity, and structures of three purified recombinant DB-sCTPs. All three proteins exhibited antimicrobial activity against bacteria involving membrane permeabilization, and bound to bacterial lipids in vitro. A combination of in vitro assays demonstrated binding of recombinant DB-sCTPs to chromatophore-derived genomic DNA sequences with an affinity in the low nM range. Additionally, we report the 1.2 Å crystal structure of one DB-sCTP. In silico docking studies suggest that helix α2 inserts into the DNA major grove and the exposed residues, that are highly variable between different DB-sCTPs, confer interaction with the DNA bases. Identification of photosystem II subunit CP43 as a potential interaction partner of one DB-sCTP, suggests DB-sCTPs to be involved in more complex regulatory mechanisms. We hypothesize that membrane binding of DB-sCTPs is related to their import into chromatophores. Once inside, they interact with the chromatophore genome potentially providing nuclear control over genetic information processing.

PubMed: 37364116
DOI: 10.1073/pnas.2221595120

Experimental method

X-RAY DIFFRACTION (1.2 Å)