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Discovery of a Ni2+-dependent guanidine hydrolase in bacteria

Author

Listed:
  • D. Funck

    (University of Konstanz)

  • M. Sinn

    (University of Konstanz)

  • J. R. Fleming

    (University of Konstanz)

  • M. Stanoppi

    (University of Konstanz)

  • J. Dietrich

    (University of Konstanz)

  • R. López-Igual

    (Universidad de Sevilla and C.S.I.C)

  • O. Mayans

    (University of Konstanz
    University of Konstanz)

  • J. S. Hartig

    (University of Konstanz
    University of Konstanz)

Abstract

Nitrogen availability is a growth-limiting factor in many habitats1, and the global nitrogen cycle involves prokaryotes and eukaryotes competing for this precious resource. Only some bacteria and archaea can fix elementary nitrogen; all other organisms depend on the assimilation of mineral or organic nitrogen. The nitrogen-rich compound guanidine occurs widely in nature2–4, but its utilization is impeded by pronounced resonance stabilization5, and enzymes catalysing hydrolysis of free guanidine have not been identified. Here we describe the arginase family protein GdmH (Sll1077) from Synechocystis sp. PCC 6803 as a Ni2+-dependent guanidine hydrolase. GdmH is highly specific for free guanidine. Its activity depends on two accessory proteins that load Ni2+ instead of the typical Mn2+ ions into the active site. Crystal structures of GdmH show coordination of the dinuclear metal cluster in a geometry typical for arginase family enzymes and allow modelling of the bound substrate. A unique amino-terminal extension and a tryptophan residue narrow the substrate-binding pocket and identify homologous proteins in further cyanobacteria, several other bacterial taxa and heterokont algae as probable guanidine hydrolases. This broad distribution suggests notable ecological relevance of guanidine hydrolysis in aquatic habitats.

Suggested Citation

  • D. Funck & M. Sinn & J. R. Fleming & M. Stanoppi & J. Dietrich & R. López-Igual & O. Mayans & J. S. Hartig, 2022. "Discovery of a Ni2+-dependent guanidine hydrolase in bacteria," Nature, Nature, vol. 603(7901), pages 515-521, March.
  • Handle: RePEc:nat:nature:v:603:y:2022:i:7901:d:10.1038_s41586-022-04490-x
    DOI: 10.1038/s41586-022-04490-x
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    Cited by:

    1. David Sychantha & Xuefei Chen & Kalinka Koteva & Gerd Prehna & Gerard D. Wright, 2024. "Targeting bacterial nickel transport with aspergillomarasmine A suppresses virulence-associated Ni-dependent enzymes," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    2. M. Sinn & L. Riede & J. R. Fleming & D. Funck & H. Lutz & A. Bachmann & O. Mayans & J. S. Hartig, 2024. "Metformin hydrolase is a recently evolved nickel-dependent heteromeric ureohydrolase," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    3. Tao Li & Zhi-Jing Xu & Shu-Ting Zhang & Jia Xu & Piaopiao Pan & Ning-Yi Zhou, 2024. "Discovery of a Ni2+-dependent heterohexameric metformin hydrolase," Nature Communications, Nature, vol. 15(1), pages 1-10, December.

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