6V0A
Crystal structure of cytochrome c nitrite reductase from the bacterium Geobacter lovleyi with bound sulfate
Summary for 6V0A
| Entry DOI | 10.2210/pdb6v0a/pdb |
| Descriptor | Nitrite reductase (cytochrome; ammonia-forming), HEME C, SULFATE ION, ... (4 entities in total) |
| Functional Keywords | ammonia-forming, cytochrome c nitrite reductase, oxidoreductase |
| Biological source | Geobacter lovleyi (strain ATCC BAA-1151 / DSM 17278 / SZ) |
| Total number of polymer chains | 6 |
| Total formula weight | 344968.24 |
| Authors | Satyanarayana, L.,Campecino, J.,Hegg, L.H.,Hu, J. (deposition date: 2019-11-18, release date: 2020-06-17, Last modification date: 2024-10-23) |
| Primary citation | Campecino, J.,Lagishetty, S.,Wawrzak, Z.,Sosa Alfaro, V.,Lehnert, N.,Reguera, G.,Hu, J.,Hegg, E.L. Cytochromecnitrite reductase from the bacteriumGeobacter lovleyirepresents a new NrfA subclass. J.Biol.Chem., 295:11455-11465, 2020 Cited by PubMed Abstract: Cytochrome 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 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 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 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-independent, Arg-containing NrfA from represents a new subclass of cytochrome nitrite reductase. Most genera from the exclusive clades of Arg-containing NrfA proteins are also represented in clades containing Ca-dependent enzymes, suggesting convergent evolution. PubMed: 32518164DOI: 10.1074/jbc.RA120.013981 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.55 Å) |
Structure validation
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