Inhibitor binding in a class 2 dihydroorotate dehydrogenase causes variations in the membrane-associated N-terminal domain

Authors

  • Majbritt Hansen,

    1. Centre for Crystallographic Studies, Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
    2. Department of Clinical Microbiology, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark
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  • Jérôme Le Nours,

    1. Centre for Crystallographic Studies, Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
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  • Eva Johansson,

    1. Centre for Crystallographic Studies, Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
    2. European Synchrotron Radiation Facility (ESRF), F-38043 Grenoble Cedex, France
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  • Torben Antal,

    1. Centre for Crystallographic Studies, Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
    2. Department of Clinical Biochemistry, Glostrup Hospital, DK-2600 Glostrup, Denmark
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  • Alexandra Ullrich,

    1. Institute for Physiological Chemistry, Philipps-University, D-35033 Marburg, Germany
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  • Monika Löffler,

    1. Institute for Physiological Chemistry, Philipps-University, D-35033 Marburg, Germany
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  • Sine Larsen

    Corresponding author
    1. Centre for Crystallographic Studies, Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
    2. European Synchrotron Radiation Facility (ESRF), F-38043 Grenoble Cedex, France
    • Centre for Crystallographic Studies, Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark; fax: 45-3532-0299 or 33-4-7688-2160.
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Abstract

The flavin enzyme dihydroorotate dehydrogenase (DHOD; EC 1.3.99.11) catalyzes the oxidation of dihydroorotate to orotate, the fourth step in the de novo pyrimidine biosynthesis of UMP. The enzyme is a promising target for drug design in different biological and clinical applications for cancer and arthritis. The first crystal structure of the class 2 dihydroorotate dehydrogenase from rat has been determined in complex with its two inhibitors brequinar and atovaquone. These inhibitors have shown promising results as anti-proliferative, immunosuppressive, and antiparasitic agents. A unique feature of the class 2 DHODs is their N-terminal extension, which folds into a separate domain comprising two α-helices. This domain serves as the binding site for the two inhibitors and the respiratory quinones acting as the second substrate for the class 2 DHODs. The orientation of the first N-terminal helix is very different in the two complexes of rat DHOD (DHODR). Binding of atovaquone causes a 12 Å movement of the first residue in the first α-helix. Based on the information from the two structures of DHODR, a model for binding of the quinone and the residues important for the interactions could be defined. His 56 and Arg 136, which are fully conserved in all class 2 DHODs, seem to play a key role in the interaction with the electron acceptor. The differences between the membrane-bound rat DHOD and membrane-associated class 2 DHODs exemplified by the Escherichia coli DHOD has been investigated by GRID computations of the hydrophobic probes predicted to interact with the membrane.

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