1Q3V image
Deposition Date 2003-08-01
Release Date 2003-09-16
Last Version Date 2024-11-13
Entry Detail
PDB ID:
1Q3V
Keywords:
Title:
Crystal structure of a wild-type Cre recombinase-loxP synapse: phosphotyrosine covalent intermediate
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.91 Å
R-Value Free:
0.27
R-Value Work:
0.24
R-Value Observed:
0.24
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Cre recombinase
Gene (Uniprot):cre
Chain IDs:G (auth: A), H (auth: B), I (auth: E), J (auth: F)
Chain Length:347
Number of Molecules:4
Biological Source:Enterobacteria phage P1
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
A3P A A ADENOSINE-3'-5'-DIPHOSPHATE
UMP A U 2'-DEOXYURIDINE 5'-MONOPHOSPHATE
Primary Citation
Crystal structure of a wild-type Cre recombinase-loxP synapse reveals a novel spacer conformation suggesting an alternative mechanism for DNA cleavage activation
Nucleic Acids Res. 31 5449 5460 (2003)
PMID: 12954782 DOI: 10.1093/nar/gkg732

Abstact

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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Primary Citation of related structures