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Structure of human dCK suggests strategies to improve anticancer and antiviral therapy

Nature Structural & Molecular Biology volume 10, pages 513–519 (2003)Cite this article

Abstract

Human deoxycytidine kinase (dCK) phosphorylates the natural deoxyribonucleosides deoxycytidine (dC), deoxyguanosine (dG) and deoxyadenosine (dA) and is an essential enzyme for the phosphorylation of numerous nucleoside analog prodrugs routinely used in cancer and antiviral chemotherapy. For many of these compounds, the phosphorylation step catalyzed by dCK is the rate-limiting step in their overall activation pathway. To determine the factors that limit the phosphorylation efficiency of the prodrug, we solved the crystal structure of dCK to a resolution of 1.6 Å in complex with its physiological substrate deoxycytidine and with the prodrugs AraC and gemcitabine. The structures reveal the determinants of dCK substrate specificity. Especially relevant to new prodrug development is the interaction between Arg128 and the hydrogen-bond acceptor at the sugar 2′-arabinosyl position of AraC and gemcitabine. On the basis of the structures, we designed a catalytically superior dCK variant that could be used in suicide gene-therapy applications.

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Figure 1: Overall fold of dCK.
Figure 2: Electron density of the dCK-bound substrates.
Figure 3: Schematic representation of the interactions made by the bound nucleoside with dCK.
Figure 4: Superposition of the dCK (yellow) and dGK (cyan) active-site residues.

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Acknowledgements

We acknowledge the contributions made by K. Storie, L. Shuvalova and A. Arockiasamy in the initial stages of the project, and thank B. Beck and M. Godsey for careful reading of the manuscript. We thank Eli Lilly & Co. for providing gemcitabine as a gift. We thank the staff of BioCars and SerCAT for help in data collection at the Advanced Photon Source. E.S. and A.L. were supported by the US National Institutes of Health (NIH), and S.O., C.M. and M.K. were supported by grants from the Deutsche Forschungsgemeinschaft and the Max Planck Society.

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Authors and Affiliations

  1. Department of Biochemistry and Molecular Biology, University of Illinois at Chicago, 1819 West Polk Street, Chicago, 60612, Illinois, USA

    Elisabetta Sabini & Arnon Lavie

  2. Max Planck Institute for Biophysical Chemistry Department of Molecular Genetics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, D-37077, Germany

    Stephan Ort, Christian Monnerjahn & Manfred Konrad

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Correspondence to Arnon Lavie.

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Sabini, E., Ort, S., Monnerjahn, C. et al. Structure of human dCK suggests strategies to improve anticancer and antiviral therapy. Nat Struct Mol Biol 10, 513–519 (2003). https://doi.org/10.1038/nsb942

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