1. Cytochrome c nitrite reductase from the bacterium Geobacter lovleyi represents a new NrfA subclass.
- Author
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Campeciño J, Lagishetty S, Wawrzak Z, Sosa Alfaro V, Lehnert N, Reguera G, Hu J, and Hegg EL
- Subjects
- Ammonium Compounds metabolism, Bacterial Proteins chemistry, Bacterial Proteins genetics, Crystallography, X-Ray, Cytochromes a1 chemistry, Cytochromes a1 genetics, Cytochromes c1 chemistry, Cytochromes c1 genetics, Geobacter chemistry, Geobacter genetics, Kinetics, Models, Molecular, Nitrate Reductases chemistry, Nitrate Reductases genetics, Nitrates metabolism, Phylogeny, Protein Conformation, Bacterial Proteins metabolism, Cytochromes a1 metabolism, Cytochromes c1 metabolism, Geobacter metabolism, Nitrate Reductases metabolism
- Abstract
Cytochrome c nitrite reductase (NrfA) catalyzes the reduction of nitrite to ammonium in the dissimilatory nitrate reduction to ammonium (DNRA) pathway, a process that competes with denitrification, conserves nitrogen, and minimizes nutrient loss in soils. The environmental bacterium Geobacter lovleyi has recently been recognized as a key driver of DNRA in nature, but its enzymatic pathway is still uncharacterized. To address this limitation, here we overexpressed, purified, and characterized G. lovleyi NrfA. We observed that the enzyme crystallizes as a dimer but remains monomeric in solution. Importantly, its crystal structure at 2.55-Å resolution revealed the presence of an arginine residue in the region otherwise occupied by calcium in canonical NrfA enzymes. The presence of EDTA did not affect the activity of G. lovleyi NrfA, and site-directed mutagenesis of this arginine reduced enzymatic activity to <3% of the WT levels. Phylogenetic analysis revealed four separate emergences of Arg-containing NrfA enzymes. Thus, the Ca
2+ -independent, Arg-containing NrfA from G. lovleyi represents a new subclass of cytochrome c nitrite reductase. Most genera from the exclusive clades of Arg-containing NrfA proteins are also represented in clades containing Ca2+ -dependent enzymes, suggesting convergent evolution., Competing Interests: Conflict of interest—The authors declare no conflicts of interest in regards to this work., (© 2020 Campeciño et al.)- Published
- 2020
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