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Structures of Pup ligase PafA and depupylase Dop from the prokaryotic ubiquitin-like modification pathway

Author

Listed:
  • Dennis Özcelik

    (ETH Zurich, Institute of Molecular Biology & Biophysics, CH-8093, Switzerland.)

  • Jonas Barandun

    (ETH Zurich, Institute of Molecular Biology & Biophysics, CH-8093, Switzerland.)

  • Nikolaus Schmitz

    (ETH Zurich, Institute of Molecular Biology & Biophysics, CH-8093, Switzerland.)

  • Markus Sutter

    (ETH Zurich, Institute of Molecular Biology & Biophysics, CH-8093, Switzerland.)

  • Ethan Guth

    (ETH Zurich, Institute of Molecular Biology & Biophysics, CH-8093, Switzerland.)

  • Fred F. Damberger

    (ETH Zurich, Institute of Molecular Biology & Biophysics, CH-8093, Switzerland.)

  • Frédéric H.-T. Allain

    (ETH Zurich, Institute of Molecular Biology & Biophysics, CH-8093, Switzerland.)

  • Nenad Ban

    (ETH Zurich, Institute of Molecular Biology & Biophysics, CH-8093, Switzerland.)

  • Eilika Weber-Ban

    (ETH Zurich, Institute of Molecular Biology & Biophysics, CH-8093, Switzerland.)

Abstract

Pupylation is a posttranslational protein modification occurring in mycobacteria and other actinobacteria that is functionally analogous to ubiquitination. Here we report the crystal structures of the modification enzymes involved in this pathway, the prokaryotic ubiquitin-like protein (Pup) ligase PafA and the depupylase/deamidase Dop. Both feature a larger amino-terminal domain consisting of a central β-sheet packed against a cluster of helices, a fold characteristic for carboxylate-amine ligases, and a smaller C-terminal domain unique to PafA/Dop members. The active site is located on the concave surface of the β-sheet with the nucleotide bound in a deep pocket. A conserved groove leading into the active site could have a role in Pup-binding. Nuclear magnetic resonance and biochemical experiments determine the region of Pup that interacts with PafA and Dop. Structural data and mutational studies identify crucial residues for the catalysis of both enzymes.

Suggested Citation

  • 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.
    • Handle: RePEc:nat:natcom:v:3:y:2012:i:1:d:10.1038_ncomms2009
    DOI: 10.1038/ncomms2009
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    Cited by:

    1. 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.

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