Article | Published:

Structural basis for recognition of 5′-phosphotyrosine adducts by Tdp2

Nature Structural & Molecular Biology volume 19, pages 13721377 (2012) | Download Citation

Abstract

The DNA-repair enzyme Tdp2 resolves 5′-phosphotyrosyl DNA adducts and mediates resistance to anticancer drugs that target covalent topoisomerase–DNA complexes. Tdp2 also participates in key signaling pathways during development and tumorigenesis and cleaves a protein-RNA linkage during picornavirus replication. The crystal structure of zebrafish Tdp2 bound to DNA reveals a deep, narrow basic groove that selectively accommodates the 5′ end of single-stranded DNA in a stretched conformation. The crystal structure of the full-length Caenorhabditis elegans Tdp2 shows that this groove can also accommodate an acidic peptide stretch in vitro, with glutamate and aspartate side chains occupying the DNA backbone phosphate–binding sites. This extensive molecular mimicry suggests a potential mechanism for autoregulation and interaction of Tdp2 with phosphorylated proteins in signaling. Our study provides a framework to interrogate functions of Tdp2 and develop inhibitors for chemotherapeutic and antiviral applications.

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Acknowledgements

We thank the beamline staff at Sector-24 of the Advanced Photon Source (APS) and J. Nix of the Molecular Biology Consortium at the Advanced Light Source (ALS) for help in data collection and H. Hiasa, D. Grandgenett and J. Lee for comments on the manuscript. Computer resources were provided by the Basic Sciences Computing Laboratory of the University of Minnesota Supercomputing Institute. The work conducted at the APS NE-CAT beamlines was supported by award RR15301 from the National Center for Research Resources at the US National Institutes of Health (NIH). Use of the APS, an Office of Science User Facility operated for the US Department of Energy (DOE) Office of Science by Argonne National Laboratory, was supported by the US DOE under contract no. DE-AC02-06CH11357. This work was supported by NIH grants GM095558 and AI087098 (H.A.), the Center for Cancer Research (Z01 BC 006150-19), the Intramural Program of the US National Cancer Institute (R.G. and Y.P.) and NCI P01 CA092584 and GM046312 (J.A.T.). SAXS data were collected at the ALS SIBYLS beamline 12.3.1 supported by the IDAT DOE program DE-AC02-05CH11231 and by NIH R01GM105404.

Author information

Author notes

    • Ke Shi
    •  & Kayo Kurahashi

    These authors contributed equally to this work.

Affiliations

  1. Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA.

    • Ke Shi
    • , Kayo Kurahashi
    •  & Hideki Aihara
  2. Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA.

    • Rui Gao
    •  & Yves Pommier
  3. Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.

    • Susan E Tsutakawa
    •  & John A Tainer
  4. Department of Molecular Biology, Scripps Research Institute, Skaggs Institute for Chemical Biology, La Jolla, California, USA.

    • John A Tainer

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Contributions

K.K. purified the proteins and performed the activity assay on a substrate mimic. K.K., K.S. and H.A. crystallized the proteins. K.S. collected X-ray diffraction data and determined all crystal structures. R.G. and Y.P. examined enzyme activities on the 5′-phosphotyrosyl DNA substrate. S.E.T. and J.A.T. collected and analyzed the SAXS data. H.A. wrote the manuscript. All authors contributed in editing and figure preparation.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Hideki Aihara.

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DOI

https://doi.org/10.1038/nsmb.2423

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