ArticleNucleic acids research2003
Crystal structure of a wild-type Cre recombinase-loxP synapse reveals a novel spacer conformation suggesting an alternative mechanism for DNA cleavage activation.
Article in Nucleic acids research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed, 82 citations in OpenAlex.
- Development and characterization of a Cre/Synthetic and systems biotechnology · 2027Article
- Advances in large-scale DNA engineering with the CRISPR system.Experimental & molecular medicine · 2025Review
- Protein and DNA Conformational Changes Contribute to Specificity of Cre Recombinase.Biochemistry · 2025Article
- The recombination efficiency of the bacterial integron depends on the mechanical stability of the synaptic complex.Science advances · 2024Article
- Protein and DNA Conformational Changes Contribute to Specificity of Cre Recombinase.bioRxiv : the preprint server for biology · 2024Article
- Activation of recombinases at specific DNA loci by zinc-finger domain insertions.Nature biotechnology · 2024Article
- Engineering spacer specificity of the Cre/loxP system.Nucleic acids research · 2024Article
- Orthogonal LoxPsym sites allow multiplexed site-specific recombination in prokaryotic and eukaryotic hosts.Nature communications · 2024Article
- Structural and functional characterization of MrpR, the master repressor of the Bacillus subtilis prophage SPβ.Nucleic acids research · 2023Article
- Mechanisms of Cre recombinase synaptic complex assembly and activation illuminated by Cryo-EM.Nucleic acids research · 2022Article
- Pairing of single mutations yields obligate Cre-type site-specific recombinases.Nucleic acids research · 2022Article
- Correction of a Factor VIII genomic inversion with designer-recombinases.Nature communications · 2022Article
- Conformational dynamics promotes disordered regions from function-dispensable to essential in evolved site-specific DNA recombinases.Computational and structural biotechnology journal · 2022Article
- Design of time-delayed safety switches for CRISPR gene therapy.Scientific reports · 2021Article
- A single-chain and fast-responding light-inducible Cre recombinase as a novel optogenetic switch.eLife · 2021Article
- Nearest-neighbor amino acids of specificity-determining residues influence the activity of engineered Cre-type recombinases.Scientific reports · 2020Article
- Neural circuit analysis using a novel intersectional split intein-mediated split-Cre recombinase system.Molecular brain · 2020Article
- Loop-closure kinetics reveal a stable, right-handed DNA intermediate in Cre recombination.Nucleic acids research · 2020Article
- High-resolution specificity profiling and off-target prediction for site-specific DNA recombinases.Nature communications · 2019Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Escherichia coli phage P1 Cre recombinase catalyzes the site-specific recombination of DNA containing loxP sites. We report here two crystal structures of a wild-type Cre recombinase-loxP synaptic complex corresponding to two distinct reaction states: an initial pre-cleavage complex, trapped using a phosphorothioate modification at the cleavable scissile bond that prevents the recombination reaction, and a 3'-phosphotyrosine protein-DNA intermediate resulting from the first strand cleavage. In contrast to previously determined Cre complexes, both structures contain a full tetrameric complex in the asymmetric unit, unequivocally showing that the anti-parallel arrangement of the loxP sites is an intrinsic property of the Cre-loxP recombination synapse. The conformation of the spacer is different to the one observed for the symmetrized loxS site: a kink next to the scissile phosphate in the top strand of the pre-cleavage complex leads to unstacking of the TpG step and a widening of the minor groove. This side of the spacer is interacting with a 'cleavage-competent' Cre subunit, suggesting that the first cleavage occurs at the ApT step in the top strand. This is further confirmed by the structure of the 3'-phosphotyrosine intermediate, where the DNA is cleaved in the top strands and covalently linked to the 'cleavage-competent' subunits. The cleavage is followed by a movement of the C-terminal part containing the attacking Y324 and the helix N interacting with the 'non-cleaving' subunit. This rearrangement could be responsible for the interconversion of Cre subunits. Our results also suggest that the Cre-induced kink next to the scissile phosphodiester activates the DNA for cleavage at this position and facilitates strand transfer.
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