9I86

Enterobacteriaphage PRD1 - P12 protein filament in complex with poly(dT) ssDNA

Summary for 9I86

• Entry DOI: 10.2210/pdb9i86/pdb
• Related: 9GFQ
• EMDB information: 52708 52709 52710
• Descriptor: Single-stranded DNA-binding protein, ssDNA poly(dT), 80mer (2 entities in total)
• Functional Keywords: ssb, protein primed replication, protein filament, homooligomer, ssdna-binding, replication
• Biological source: Enterobacteria phage PRD1; More
• Total number of polymer chains: 8
• Total formula weight: 148606.95

Authors

Degen, M.,Traeger, K.L.,Hiller, S. (deposition date: 2025-02-04, release date: 2025-03-19)

Primary citation

Trager, L.K.,Degen, M.,Pereira, J.,Durairaj, J.,Teixeira, R.D.,Hiller, S.,Huguenin-Dezot, N.
Structural basis for cooperative ssDNA binding by bacteriophage protein filament P12.
Nucleic Acids Res., 53:-, 2025

PubMed Abstract: Protein-primed DNA replication is a unique mechanism, bioorthogonal to other known DNA replication modes. It relies on specialised single-stranded DNA (ssDNA)-binding proteins (SSBs) to stabilise ssDNA intermediates by unknown mechanisms. Here, we present the structural and biochemical characterisation of P12, an SSB from bacteriophage PRD1. High-resolution cryo-electron microscopy reveals that P12 forms a unique, cooperative filament along ssDNA. Each protomer binds the phosphate backbone of 6 nucleotides in a sequence-independent manner, protecting ssDNA from nuclease degradation. Filament formation is driven by an intrinsically disordered C-terminal tail, facilitating cooperative binding. We identify residues essential for ssDNA interaction and link the ssDNA-binding ability of P12 to toxicity in host cells. Bioinformatic analyses place the P12 fold as a distinct branch within the OB-like fold family. This work offers new insights into protein-primed DNA replication and lays a foundation for biotechnological applications.

PubMed: 40052821
DOI: 10.1093/nar/gkaf132

Experimental method

ELECTRON MICROSCOPY (2.75 Å)