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An excess of catalytically required motions inhibits the scavenger decapping enzyme

Nature Chemical Biology volume 11, pages 697704 (2015) | Download Citation

Abstract

The scavenger decapping enzyme hydrolyzes the protective 5′ cap structure on short mRNA fragments that are generated from the exosomal degradation of mRNAs. From static crystal structures and NMR data, it is apparent that the dimeric enzyme has to undergo large structural changes to bind its substrate in a catalytically competent conformation. Here we studied the yeast enzyme and showed that the associated opening and closing motions can be orders of magnitude faster than the catalytic turnover rate. This excess of motion is induced by the binding of a second ligand to the enzyme, which occurs at high substrate concentrations. We designed a mutant that disrupted the allosteric pathway that links the second binding event to the dynamics and showed that this mutant enzyme is hyperactive. Our data reveal a unique mechanism of substrate inhibition in which motions that are required for catalytic activity also inhibit efficient turnover when they are present in excess.

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Acknowledgements

We acknowledge J. Peters for excellent technical support, S. Wiesner for discussions, G. Zocher for assistance in recording diffraction data, T. Stehle for support and L. Kay for valuable comments on the manuscript. This work has received funding from the Max Planck Society and the European Research Council under the EU's Seventh Framework Programme (FP7/2007–2013), ERC grant agreement no. 616052.

Author information

Author notes

    • Ursula Neu
    •  & Benjamin Schlager

    Present addresses: Max Planck Institute for Colloids and Interfaces, Potsdam, Germany (U.N.); FluidSolids AG, Zürich, Switzerland (B.S.).

Affiliations

  1. Max Planck Institute for Developmental Biology, Tübingen, Germany.

    • Ancilla Neu
    • , Anna-Lisa Fuchs
    • , Benjamin Schlager
    •  & Remco Sprangers
  2. Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany.

    • Ursula Neu

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Contributions

R.S. conceived the project. A.N. and R.S. designed the experiments. All authors performed experiments. R.S., A.N., U.N. and A.-L.F. analyzed and interpreted the data. R.S. wrote the manuscript and all authors commented on the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Remco Sprangers.

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    Supplementary Results, Supplementary Figures 1–7 and Supplementary Table 1.

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https://doi.org/10.1038/nchembio.1866

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