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

• Published in: Nature communications Vol. 11; no. 1; p. 2931
• Main Authors: Thompson, Mitchell G., Blake-Hedges, Jacquelyn M., Pereira, Jose Henrique, Hangasky, John A., Belcher, Michael S., Moore, William M., Barajas, Jesus F., Cruz-Morales, Pablo, Washington, Lorenzo J., Haushalter, Robert W., Eiben, Christopher B., Liu, Yuzhong, Skyrud, Will, Benites, Veronica T., Barnum, Tyler P., Baidoo, Edward E. K., Scheller, Henrik V., Marletta, Michael A., Shih, Patrick M., Adams, Paul D., Keasling, Jay D.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 10.06.2020; Nature Publishing Group; Nature Portfolio
• Subjects: 631/449; 631/45; 631/45/173; 631/535; Arabidopsis - metabolism; Arginine; Bacteria; BASIC BIOLOGICAL SCIENCES; Biochemical analysis; Biochemistry; Catabolism; Decarboxylation; enzyme mechanisms; Enzymes; Eukaryotes; Free form; Homology; Humanities and Social Sciences; Hydroxylation; Iron; Iron - metabolism; Lysine; Lysine - metabolism; multidisciplinary; Oryza - metabolism; Oxygenase; Oxygenases - metabolism; Phenotypes; plant sciences; Proteins; Pseudomonas putida; Pseudomonas putida - metabolism; Science; Science (multidisciplinary); structural biology; Substrates
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-020-16815-3

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 O 2 -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. Hydroxyglutarate synthase (HglS) converts 2-oxoadipate to D-2- hydroxyglutarate during lysine catabolism in bacteria. Here the authors use structural and biochemical approaches to show that HglS acts via successive decarboxylation and intramolecular hydroxylation and that homologous enzymes catalyze the final step of lysine catabolism in plants.