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Structures of prokaryotic ubiquitin-like protein Pup in complex with depupylase Dop reveal the mechanism of catalytic phosphate formation

Author

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  • Hengjun Cui

    (ETH Zurich, Institute of Molecular Biology & Biophysics)

  • Andreas U. Müller

    (ETH Zurich, Institute of Molecular Biology & Biophysics)

  • Marc Leibundgut

    (ETH Zurich, Institute of Molecular Biology & Biophysics)

  • Jiawen Tian

    (ETH Zurich, Institute of Molecular Biology & Biophysics)

  • Nenad Ban

    (ETH Zurich, Institute of Molecular Biology & Biophysics)

  • Eilika Weber-Ban

    (ETH Zurich, Institute of Molecular Biology & Biophysics)

Abstract

Pupylation is the post-translational modification of lysine side chains with prokaryotic ubiquitin-like protein (Pup) that targets proteins for proteasomal degradation in mycobacteria and other members of Actinobacteria. Pup ligase PafA and depupylase Dop are the two enzymes acting in this pathway. Although they share close structural and sequence homology indicative of a common evolutionary origin, they catalyze opposing reactions. Here, we report a series of high-resolution crystal structures of Dop in different functional states along the reaction pathway, including Pup-bound states in distinct conformations. In combination with biochemical analysis, the structures explain the role of the C-terminal residue of Pup in ATP hydrolysis, the process that generates the catalytic phosphate in the active site, and suggest a role for the Dop-loop as an allosteric sensor for Pup-binding and ATP cleavage.

Suggested Citation

  • Hengjun Cui & Andreas U. Müller & Marc Leibundgut & Jiawen Tian & Nenad Ban & Eilika Weber-Ban, 2021. "Structures of prokaryotic ubiquitin-like protein Pup in complex with depupylase Dop reveal the mechanism of catalytic phosphate formation," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-26848-x
    DOI: 10.1038/s41467-021-26848-x
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    References listed on IDEAS

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    1. Dennis Özcelik & Jonas Barandun & Nikolaus Schmitz & Markus Sutter & Ethan Guth & Fred F. Damberger & Frédéric H.-T. Allain & Nenad Ban & Eilika Weber-Ban, 2012. "Structures of Pup ligase PafA and depupylase Dop from the prokaryotic ubiquitin-like modification pathway," Nature Communications, Nature, vol. 3(1), pages 1-10, January.
    2. Haruo Ogawa & Flemming Cornelius & Ayami Hirata & Chikashi Toyoshima, 2015. "Sequential substitution of K+ bound to Na+,K+-ATPase visualized by X-ray crystallography," Nature Communications, Nature, vol. 6(1), pages 1-9, November.
    3. Chikashi Toyoshima & Hiromi Nomura & Takeo Tsuda, 2004. "Lumenal gating mechanism revealed in calcium pump crystal structures with phosphate analogues," Nature, Nature, vol. 432(7015), pages 361-368, November.
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    Cited by:

    1. Matthias F. Block & Cyrille L. Delley & Lena M. L. Keller & Timo T. Stuehlinger & Eilika Weber-Ban, 2023. "Electrostatic interactions guide substrate recognition of the prokaryotic ubiquitin-like protein ligase PafA," Nature Communications, Nature, vol. 14(1), pages 1-13, December.

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