ArticleThe Journal of biological chemistry2011
Creating directed double-strand breaks with the Ref protein: a novel RecA-dependent nuclease from bacteriophage P1.
Article in The Journal of biological chemistry, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 18 citations in OpenAlex.
- Bacteriophage deploys a RecA-dependent nuclease to inhibit Staphylococcus aureus replication and promote phage propagation.Nucleic acids research · 2026Article
- Molecular basis of the phosphorothioation-sensing antiphage defense system IscS-DndBCDE-DndI.Nucleic acids research · 2024Article
- Article
- Characterization and genomic analysis of the first Oceanospirillum phage, vB_OliS_GJ44, representing a novel siphoviral cluster.BMC genomics · 2021Article
- The Order-Disorder Continuum: Linking Predictions of Protein Structure and Disorder through Molecular Simulation.Scientific reports · 2020Review
- The Transcriptomic and Phenotypic Response of the Melanized YeastFrontiers in microbiology · 2020Article
- Systematic classification of the His-Me finger superfamily.Nucleic acids research · 2017Article
- P1 Ref Endonuclease: A Molecular Mechanism for Phage-Enhanced Antibiotic Lethality.PLoS genetics · 2016Article
- Function of the N-terminal segment of the RecA-dependent nuclease Ref.Nucleic acids research · 2015Article
- RecA-dependent programmable endonuclease Ref cleaves DNA in two distinct steps.Nucleic acids research · 2014Article
- The protein gp74 from the bacteriophage HK97 functions as a HNH endonuclease.Protein science : a publication of the Protein Society · 2012Article
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
The bacteriophage P1-encoded Ref protein enhances RecA-dependent recombination in vivo by an unknown mechanism. We demonstrate that Ref is a new type of enzyme; that is, a RecA-dependent nuclease. Ref binds to ss- and dsDNA but does not cleave any DNA substrate until RecA protein and ATP are added to form RecA nucleoprotein filaments. Ref cleaves only where RecA protein is bound. RecA functions as a co-nuclease in the Ref/RecA system. Ref nuclease activity can be limited to the targeted strands of short RecA-containing D-loops. The result is a uniquely programmable endonuclease activity, producing targeted double-strand breaks at any chosen DNA sequence in an oligonucleotide-directed fashion. We present evidence indicating that cleavage occurs in the RecA filament groove. The structure of the Ref protein has been determined to 1.4 Å resolution. The core structure, consisting of residues 77-186, consists of a central 2-stranded β-hairpin that is sandwiched between several α-helical and extended loop elements. The N-terminal 76 amino acid residues are disordered; this flexible region is required for optimal activity. The overall structure of Ref, including several putative active site histidine residues, defines a new subclass of HNH-family nucleases. We propose that enhancement of recombination by Ref reflects the introduction of directed, recombinogenic double-strand breaks.
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