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Crystal structures of the catalytic domain of human protein kinase associated with apoptosis and tumor suppression

Nature Structural Biology volume 8, pages 899–907 (2001)Cite this article

Abstract

We have determined X-ray crystal structures with up to 1.5 Å resolution of the catalytic domain of death-associated protein kinase (DAPK), the first described member of a novel family of pro-apoptotic and tumor-suppressive serine/threonine kinases. The geometry of the active site was studied in the apo form, in a complex with nonhydrolyzable AMPPnP and in a ternary complex consisting of kinase, AMPPnP and either Mg2+ or Mn2+. The structures revealed a previously undescribed water-mediated stabilization of the interaction between the lysine that is conserved in protein kinases and the β- and γ-phosphates of ATP, as well as conformational changes at the active site upon ion binding. Comparison between these structures and nucleotide triphosphate complexes of several other kinases disclosed a number of unique features of the DAPK catalytic domain, among which is a highly ordered basic loop in the N-terminal domain that may participate in enzyme regulation.

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Figure 1
Figure 2: Final electron density and nucleotide binding site geometry.
Figure 3: Structure-based alignment of the DAPK Apo-I structure and five other serine/threonine kinases: twitchin (PDB code 1KOB), titin (1TKI), CaMKI (1A06), PHK (2PHK) and cAPK (1ATP).
Figure 4: Overall views of the DAPK catalytic domain.
Figure 5: Lattice interactions in the orthorhombic and cubic crystal forms of the DAPK catalytic domain.
Figure 6: Active site conformations of kinase–ATP complexes.
Figure 7: Tertiary structure details and main chain hydrogen bond networks in the DAPK catalytic domain.

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Acknowledgements

This work was supported in part by a NIH grant to M.E. and in part by grants from the Alzheimer's Association, the Institute for the Study of Aging and the NIH to D.M.W. We are grateful to W.F. Anderson, T J. Lukas, G. Minasov and A. Velentza for expert assistance during the various stages of the project. Use of the Advanced Photon Source was supported by the U.S. Department of Energy, Basic Energy Sciences, Office of Science. The DuPont-Northwestern-Dow Collaborative Access Team (DND-CAT) Synchrotron Research Center at the Advanced Photon Source (Sector 5) is supported by E. I. DuPont de Nemours & Co., The Dow Chemical Company, the National Science Foundation and the State of Illinois. The Industrial Macromolecular Crystallography Association Collaborative Access Team (IMCA-CAT) at the Advanced Photon Source (Sector 17) is supported by the companies of the Industrial Macromolecular Crystallography Association through a contract with the Illinois Institute of Technology (IIT), executed through the IIT's Center for Synchrotron Radiation Research and Instrumentation.

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  1. Valentina Tereshko & Marianna Teplova

    Present address: Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, New York, 10021, USA

  2. Valentina Tereshko and Marianna Teplova: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Biological Sciences, Vanderbilt University, Nashville, 37235, Tennessee, USA

    Valentina Tereshko, Marianna Teplova & Martin Egli

  2. Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Medical School, Chicago, 60611, Illinois, USA

    Joseph Brunzelle & D. Martin Watterson

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Correspondence to Martin Egli.

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Tereshko, V., Teplova, M., Brunzelle, J. et al. Crystal structures of the catalytic domain of human protein kinase associated with apoptosis and tumor suppression. Nat Struct Mol Biol 8, 899–907 (2001). https://doi.org/10.1038/nsb1001-899

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