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An iron (II) dependent oxygenase performs the last missing step of plant lysine catabolism

Author

Listed:
  • Mitchell G. Thompson

    (Joint BioEnergy Institute
    Lawrence Berkeley National Laboratory
    University of California-Berkeley)

  • Jacquelyn M. Blake-Hedges

    (Joint BioEnergy Institute
    Lawrence Berkeley National Laboratory
    University of California-Berkeley)

  • Jose Henrique Pereira

    (Joint BioEnergy Institute
    Lawrence Berkeley National Laboratory)

  • John A. Hangasky

    (University of California-Berkeley)

  • Michael S. Belcher

    (Joint BioEnergy Institute
    Lawrence Berkeley National Laboratory
    University of California-Berkeley)

  • William M. Moore

    (Joint BioEnergy Institute
    Lawrence Berkeley National Laboratory
    University of California-Berkeley)

  • Jesus F. Barajas

    (Joint BioEnergy Institute
    Lawrence Berkeley National Laboratory
    Department of Energy Agile BioFoundry)

  • Pablo Cruz-Morales

    (Joint BioEnergy Institute
    Lawrence Berkeley National Laboratory)

  • Lorenzo J. Washington

    (Joint BioEnergy Institute
    Lawrence Berkeley National Laboratory
    University of California-Berkeley)

  • Robert W. Haushalter

    (Joint BioEnergy Institute
    Lawrence Berkeley National Laboratory)

  • Christopher B. Eiben

    (Joint BioEnergy Institute
    Lawrence Berkeley National Laboratory
    University of California-Berkeley)

  • Yuzhong Liu

    (Joint BioEnergy Institute
    Lawrence Berkeley National Laboratory)

  • Will Skyrud

    (University of California-Berkeley)

  • Veronica T. Benites

    (Joint BioEnergy Institute
    Lawrence Berkeley National Laboratory)

  • Tyler P. Barnum

    (University of California-Berkeley)

  • Edward E. K. Baidoo

    (Joint BioEnergy Institute
    Lawrence Berkeley National Laboratory)

  • Henrik V. Scheller

    (Joint BioEnergy Institute
    Lawrence Berkeley National Laboratory
    University of California-Berkeley)

  • Michael A. Marletta

    (University of California-Berkeley
    University of California-Berkeley)

  • Patrick M. Shih

    (Joint BioEnergy Institute
    Lawrence Berkeley National Laboratory
    University of California-Davis
    University of California-Davis)

  • Paul D. Adams

    (Joint BioEnergy Institute
    Lawrence Berkeley National Laboratory
    University of California-Berkeley)

  • Jay D. Keasling

    (Joint BioEnergy Institute
    Lawrence Berkeley National Laboratory
    University of California-Berkeley
    University of California-Berkeley)

Abstract

Despite intensive study, plant lysine catabolism beyond the 2-oxoadipate (2OA) intermediate remains unvalidated. Recently we described a missing step in the D-lysine catabolism of Pseudomonas putida in which 2OA is converted to D-2-hydroxyglutarate (2HG) via hydroxyglutarate synthase (HglS), a DUF1338 family protein. Here we solve the structure of HglS to 1.1 Å resolution in substrate-free form and in complex with 2OA. We propose a successive decarboxylation and intramolecular hydroxylation mechanism forming 2HG in a Fe(II)- and O2-dependent manner. Specificity is mediated by a single arginine, highly conserved across most DUF1338 proteins. An Arabidopsis thaliana HglS homolog coexpresses with known lysine catabolism enzymes, and mutants show phenotypes consistent with disrupted lysine catabolism. Structural and biochemical analysis of Oryza sativa homolog FLO7 reveals identical activity to HglS despite low sequence identity. Our results suggest DUF1338-containing enzymes catalyze the same biochemical reaction, exerting the same physiological function across bacteria and eukaryotes.

Suggested Citation

  • Mitchell G. Thompson & Jacquelyn M. Blake-Hedges & Jose Henrique Pereira & John A. Hangasky & Michael S. Belcher & William M. Moore & Jesus F. Barajas & Pablo Cruz-Morales & Lorenzo J. Washington & Ro, 2020. "An iron (II) dependent oxygenase performs the last missing step of plant lysine catabolism," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-16815-3
    DOI: 10.1038/s41467-020-16815-3
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