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A structural basis for allosteric control of DNA recombination by λ integrase

Abstract

Site-specific DNA recombination is important for basic cellular functions including viral integration, control of gene expression, production of genetic diversity and segregation of newly replicated chromosomes, and is used by bacteriophage λ to integrate or excise its genome into and out of the host chromosome. λ recombination is carried out by the bacteriophage-encoded integrase protein (λ-int) together with accessory DNA sites and associated bending proteins that allow regulation in response to cell physiology. Here we report the crystal structures of λ-int in higher-order complexes with substrates and regulatory DNAs representing different intermediates along the reaction pathway. The structures show how the simultaneous binding of two separate domains of λ-int to DNA facilitates synapsis and can specify the order of DNA strand cleavage and exchange. An intertwined layer of amino-terminal domains bound to accessory (arm) DNAs shapes the recombination complex in a way that suggests how arm binding shifts the reaction equilibrium in favour of recombinant products.

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Figure 1: Pathways for integrative and excisive recombination.
Figure 2: Structure of the λ-int tetramer bound to a Holliday junction and arm DNAs.
Figure 3: Three different conformations of λ-int tetramers representing distinct steps of the recombination reaction.
Figure 4: Control of catalytic activity by trans cyclic interactions of the C-terminal tail.
Figure 5: Models showing the topology of DNA during λ integration and excision.

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Acknowledgements

X-ray data were measured at beamlines X-26C and X-25 of the National Synchrotron Light Source, station A1 of the Cornell High Energy Synchrotron Source, and beamline 19ID at the Advanced Photon Source, facilities that are supported by the US Department of Energy and the National Institutes of Health. This work was supported by research grants from the National Institutes of Health (to T.E. and A.L.) and fellowships from Jeane B. Kempner Fund (to T.B.) and the Human Frontier Science Program (to H.A.). T.E. is the Hsien Wu and Daisy Yen Wu Professor at Harvard Medical School.

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Correspondence to Tom Ellenberger.

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Coordinates and structure factors are deposited in the Protein Data Bank under accession codes 1Z19, 1Z1B and 1Z1G. Reprints and permissions information is available at npg.nature.com/reprintsandpermissions. The authors declare no competing financial interests.

Supplementary information

Supplementary Figure S1

Secondary structure assignments of for γ integrase along with the sequence alignment of its N- and CB/catalytic domains with Tn916 and Cre recombinases, respectively. (PDF 67 kb)

Supplementary Table S1

Summary of crystallographic data analyses for γ int Holliday junction, int post- exchange, and for γ int(75-356) synaptic complexes. (DOC 36 kb)

Supplementary Methods

Purification offor γ int, formation of for γ int recombinogenic complexes, and the structural modeling of P and P' arms. (DOC 67 kb)

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Biswas, T., Aihara, H., Radman-Livaja, M. et al. A structural basis for allosteric control of DNA recombination by λ integrase. Nature 435, 1059–1066 (2005). https://doi.org/10.1038/nature03657

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