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Disordered regions in proteusin peptides guide post-translational modification by a flavin-dependent RiPP brominase

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  • Nguyet A. Nguyen

    (Georgia Institute of Technology)

  • F. N. U. Vidya

    (Georgia Institute of Technology)

  • Neela H. Yennawar

    (Pennsylvania State University)

  • Hongwei Wu

    (Georgia Institute of Technology)

  • Andrew C. McShan

    (Georgia Institute of Technology)

  • Vinayak Agarwal

    (Georgia Institute of Technology
    Georgia Institute of Technology)

Abstract

To biosynthesize ribosomally synthesized and post-translationally modified peptides (RiPPs), enzymes recognize and bind to the N-terminal leader region of substrate peptides which enables catalytic modification of the C-terminal core. Our current understanding of RiPP leaders is that they are short and largely unstructured. Proteusins are RiPP precursor peptides that defy this characterization as they possess unusually long leaders. Proteusin peptides have not been structurally characterized, and we possess scant understanding of how these atypical leaders engage with modifying enzymes. Here, we determine the structure of a proteusin peptide which shows that unlike other RiPP leaders, proteusin leaders are preorganized into a rigidly structured region and a smaller intrinsically disordered region. With residue level resolution gained from NMR titration experiments, the intermolecular peptide-protein interactions between proteusin leaders and a flavin-dependent brominase are mapped onto the disordered region, leaving the rigidly structured region of the proteusin leader to be functionally dispensable. Spectroscopic observations are biochemically validated to identify a binding motif in proteusin peptides that is conserved among other RiPP leaders as well. This study provides a structural characterization of the proteusin peptides and extends the paradigm of RiPP modification enzymes using not only unstructured peptides, but also structured proteins as substrates.

Suggested Citation

  • Nguyet A. Nguyen & F. N. U. Vidya & Neela H. Yennawar & Hongwei Wu & Andrew C. McShan & Vinayak Agarwal, 2024. "Disordered regions in proteusin peptides guide post-translational modification by a flavin-dependent RiPP brominase," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-45593-5
    DOI: 10.1038/s41467-024-45593-5
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    References listed on IDEAS

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    1. Manuel A. Ortega & Yue Hao & Qi Zhang & Mark C. Walker & Wilfred A. van der Donk & Satish K. Nair, 2015. "Structure and mechanism of the tRNA-dependent lantibiotic dehydratase NisB," Nature, Nature, vol. 517(7535), pages 509-512, January.
    2. John Jumper & Richard Evans & Alexander Pritzel & Tim Green & Michael Figurnov & Olaf Ronneberger & Kathryn Tunyasuvunakool & Russ Bates & Augustin Žídek & Anna Potapenko & Alex Bridgland & Clemens Me, 2021. "Highly accurate protein structure prediction with AlphaFold," Nature, Nature, vol. 596(7873), pages 583-589, August.
    3. Fredarla S. Miller & Kathryn K. Crone & Matthew R. Jensen & Sudipta Shaw & William R. Harcombe & Mikael H. Elias & Michael F. Freeman, 2021. "Conformational rearrangements enable iterative backbone N-methylation in RiPP biosynthesis," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
    4. Sunil V. Sharma & Xiaoxue Tong & Cristina Pubill-Ulldemolins & Christopher Cartmell & Emma J. A. Bogosyan & Emma J. Rackham & Enrico Marelli & Refaat B. Hamed & Rebecca J. M. Goss, 2017. "Living GenoChemetics by hyphenating synthetic biology and synthetic chemistry in vivo," Nature Communications, Nature, vol. 8(1), pages 1-10, December.
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