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Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse

Nature volume 389, pages 40–46 (1997)Cite this article

Abstract

During site-specific DNA recombination, which brings about genetic rearrangement in processes such as viral integration and excision and chromosomal segregation, recombinase enzymes recognize specific DNA sequences and catalyse the reciprocal exchange of DNA strands between these sites. The bacteriophage recombinase Cre catalyses site-specific recombination between two 34-base-pair loxP sites. The crystal structure at 2.4 Å resolution of Cre bound to a loxP substrate reveals an intermediate in the recombination reaction, in which a Cre molecule has cleaved the substrate to form a covalent 3′-phosphotyrosine linkage with the DNA. Four recombinases and two loxP sites form a synapsed structure in which the DNA resembles models of four-way Holliday-junction intermediates. The Cre–loxP complex challenges models of site-specific recombination that require large changes in quaternary structure. Subtle allosteric changes at the carboxy termini of the Cre subunits may instead coordinate the cleavage and strand-exchange reactions.

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Figure 1: a, The Cre–loxP site-specific recombination reaction, based on studies in the lambda integrase family1 and on the work described here.
Figure 2: Stereo ribbon model49 of the Cre–loxA complex.
Figure 5: Ribbon and space-filling models50 of the Cre–loxA synapse.
Figure 3: a, Ribbon model49 of Cre recombinase.
Figure 4: The Cre–loxA active sites.

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Acknowledgements

We thank L. Berman and Z. Yin for access to and help with the NSLS X25 beamline, W. Hendrickson and C. Ogata for access to and help with the NSLS X4A beamline, J. Ni for assistance with data collection, Y.-M. Zheng for technical support, R. Hoess for valuable discussions, and M. Lemmon, H. Nelson, M. Lewis, H. Lu and K. Ferguson for helpful comments. This work was partly supported by ACS IRG and NCI core support grants through the V. Penn Cancer Center.

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  1. Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, 19104, Pennsylvania, USA

    Feng Guo, Deshmukh N. Gopaul & Gregory D. Van Duyne

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Guo, F., Gopaul, D. & Van Duyne, G. Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse. Nature 389, 40–46 (1997). https://doi.org/10.1038/37925

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