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Human DNA ligase I completely encircles and partially unwinds nicked DNA

Nature volume 432, pages 473–478 (2004)Cite this article

Abstract

The end-joining reaction catalysed by DNA ligases is required by all organisms and serves as the ultimate step of DNA replication, repair and recombination processes. One of three well characterized mammalian DNA ligases, DNA ligase I, joins Okazaki fragments during DNA replication. Here we report the crystal structure of human DNA ligase I (residues 233 to 919) in complex with a nicked, 5′ adenylated DNA intermediate. The structure shows that the enzyme redirects the path of the double helix to expose the nick termini for the strand-joining reaction. It also reveals a unique feature of mammalian ligases: a DNA-binding domain that allows ligase I to encircle its DNA substrate, stabilizes the DNA in a distorted structure, and positions the catalytic core on the nick. Similarities in the toroidal shape and dimensions of DNA ligase I and the proliferating cell nuclear antigen sliding clamp are suggestive of an extensive protein–protein interface that may coordinate the joining of Okazaki fragments.

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Figure 1: Function and organization of Lig1.
Figure 2: Lig1 intimately engages its DNA substrate.
Figure 3: Lig1 engages the minor groove of DNA.
Figure 4: Ligation fidelity.
Figure 5: Two active conformations of the OBD.

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Acknowledgements

X-ray data were measured at beamlines X-12C and X-25 of the National Synchrotron Light Source (Upton, New York), and the SIBYLS beamline 12.3.1 of the Advanced Light Source (Berkeley, California), which are supported by the Offices of Biological and Environmental Research and of Basic Energy Sciences of the US Department of Energy, and the National Center for Research Resources of the National Institutes of Health. This work was supported by the Structural Cell Biology of DNA Repair Program Grant from the National Cancer Institute, and research grants from the National Institute of General Medical Sciences awarded to T.E. and A.E.T. J.M.P. and P.J.O. are supported by NRSA postdoctoral fellowships from the National Institutes of Health. T.E. is the Hsien Wu and Daisy Yen Wu Professor at Harvard Medical School.

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  1. Patrick J. O'Brien

    Present address: Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA

Authors and Affiliations

  1. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, 02115, USA

    John M. Pascal, Patrick J. O'Brien & Tom Ellenberger

  2. Radiation Oncology Research Laboratory and Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland, 21201, USA

    Alan E. Tomkinson

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Correspondence to Tom Ellenberger.

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Pascal, J., O'Brien, P., Tomkinson, A. et al. Human DNA ligase I completely encircles and partially unwinds nicked DNA. Nature 432, 473–478 (2004). https://doi.org/10.1038/nature03082

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