Spectroscopic glimpses of the transition state of ATP hydrolysis trapped in a bacterial DnaB helicase

Nature Communications, vol. 12, pp. 5293

Abstract

Abstract The ATP hydrolysis transition state of motor proteins is a weakly populated protein state that can be stabilized and investigated by replacing ATP with chemical mimics. We present atomic-level structural and dynamic insights on a state created by ADP aluminum fluoride binding to the bacterial DnaB helicase from Helicobacter pylori . We determined the positioning of the metal ion cofactor within the active site using electron paramagnetic resonance, and identified the protein protons coordinating to the phosphate groups of ADP and DNA using proton-detected 31 P, 1 H solid-state nuclear magnetic resonance spectroscopy at fast magic-angle spinning > 100 kHz, as well as temperature-dependent proton chemical-shift values to prove their engagements in hydrogen bonds. 19 F and 27 Al MAS NMR spectra reveal a highly mobile, fast-rotating aluminum fluoride unit pointing to the capture of a late ATP hydrolysis transition state in which the phosphoryl unit is already detached from the arginine and lysine fingers.

Authors 15

1. Alexander A. Malär

   ETH Zurich

   Affiliation as printed

   Physical Chemistry, ETH Zürich, Zürich, Switzerland

2. Nino Wili

   ETH Zurich

   Affiliation as printed

   Physical Chemistry, ETH Zürich, Zürich, Switzerland

3. Laura A. Vӧlker

   ETH Zurich

   Affiliation as printed

   Physical Chemistry, ETH Zürich, Zürich, Switzerland

4. Maria I. Kozlova

   Osnabrück University

   Affiliation as printed

   Department of Physics, Osnabrück University, Osnabrück, Germany

5. Riccardo Cadalbert

   ETH Zurich

   Affiliation as printed

   Physical Chemistry, ETH Zürich, Zürich, Switzerland

6. Alexander Däpp

   ETH Zurich

   Affiliation as printed

   Physical Chemistry, ETH Zürich, Zürich, Switzerland

7. Marco E. Weber

   ETH Zurich

   Affiliation as printed

   Physical Chemistry, ETH Zürich, Zürich, Switzerland

8. Johannes Zehnder

   ETH Zurich

   Affiliation as printed

   Physical Chemistry, ETH Zürich, Zürich, Switzerland

9. Gunnar Jeschke

   ETH Zurich

   Affiliation as printed

   Physical Chemistry, ETH Zürich, Zürich, Switzerland

10. Hellmut Eckert

    University of Münster · Universidade de São Paulo · Instituto de Física de São Carlos

    Affiliation as printed

    Institut für Physikalische Chemie, WWU Münster, Münster, Germany

    Instituto de Física de Sao Carlos, Universidade de Sao Paulo, Sao Carlos, SP, Brazil

    Instituto de Física de Sao Carlos, Universidade de Sao Paulo, Sao Carlos, Brazil

11. Anja Böckmann

    Centre National de la Recherche Scientifique · Microbiologie moléculaire et biochimie structurale

    Affiliation as printed

    Molecular Microbiology and Structural Biochemistry UMR 5086 CNRS/Université de Lyon, Lyon, France

12. Daniel Klose corresponding

    ETH Zurich · Laboratory of Physical Chemistry

    Affiliation as printed

    Physical Chemistry, ETH Zürich, Zürich, Switzerland. daniel.klose@phys.chem.ethz.ch

    Physical Chemistry, ETH Zürich, Zürich, Switzerland

13. Armen Y. Mulkidjanian corresponding

    Osnabrück University · Lomonosov Moscow State University

    Affiliation as printed

    Department of Physics, Osnabrück University, Osnabrück, Germany. armen.mulkidjanian@uni-osnabrueck.de

    School of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia. armen.mulkidjanian@uni-osnabrueck.de

    Department of Physics, Osnabrück University, Osnabrück, Germany

    School of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia

14. Beat H. Meier corresponding

    ETH Zurich

    Affiliation as printed

    Physical Chemistry, ETH Zürich, Zürich, Switzerland. beme@ethz.ch

    Physical Chemistry, ETH Zürich, Zürich, Switzerland

15. Thomas Wiegand corresponding Aachen Institute of Technical and Macromolecular Chemistry

    RWTH Aachen University · ETH Zurich · Max Planck Institute for Chemical Energy Conversion · Laboratory of Physical Chemistry

    Affiliation as printed

    Institute of Technical and Macromolecular Chemistry, RWTH Aachen, Aachen, Germany. thomas.wiegand@phys.chem.ethz.ch

    Max-Planck-Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany. thomas.wiegand@phys.chem.ethz.ch

    Physical Chemistry, ETH Zürich, Zürich, Switzerland. thomas.wiegand@phys.chem.ethz.ch

    Institute of Technical and Macromolecular Chemistry, RWTH Aachen, Aachen, Germany

    Max-Planck-Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany

    Physical Chemistry, ETH Zürich, Zürich, Switzerland