9PXT
Cryo-EM structure of NapA, the periplasmic nitrate reductase from Campylobacter jejuni
Summary for 9PXT
| Entry DOI | 10.2210/pdb9pxt/pdb |
| Related | 2NYA |
| EMDB information | 71994 |
| Descriptor | Periplasmic nitrate reductase, IRON/SULFUR CLUSTER, MOLYBDENUM ATOM, ... (4 entities in total) |
| Functional Keywords | periplasmic nitrate reductase, molybdenum enzymes, cryo-em, membrane protein, metal binding protein, oxidoreductase |
| Biological source | Campylobacter jejuni |
| Total number of polymer chains | 1 |
| Total formula weight | 107021.52 |
| Authors | |
| Primary citation | Giri, N.C.,Thach, T.,Dhanabalan, K.,Cesiunaite, M.,Radhakrishnan, M.,Wedasingha, L.,Manicke, N.,Wells, M.,Szaleniec, M.,Subramanian, R.,Basu, P. Structure and substrate promiscuity of Campylobacter jejuni periplasmic nitrate reductase (Nap) and phylogenetic analysis of Nap homologs. J.Biol.Chem., 301:110928-110928, 2025 Cited by PubMed Abstract: Periplasmic nitrate reductase NapA is a member of the DMSO reductase (DMSOR) superfamily, which catalyzes the reduction of nitrate to nitrite. Campylobacter jejuni NapA (CjNapA) is notably larger compared to other structurally characterized NapA. Herein, we present the cryo-EM structure of CjNapA, the first of its kind from any ε-proteobacteria, revealing three lysine-rich insertions that could affect the substrate channel, potentially enhancing the affinity towards nitrate and other anionic substrates. Here, we report that wild-type CjNapA and NapA-C176D variants can reduce chlorate, perchlorate, and nitrate. However, the perchlorate and chlorate reductions by the CjNapA C176D variant are considerably slower, even though the perchlorate reductase has an Asp coordination to Mo. Molecular Dynamics (MD) simulations were performed to investigate the impact of the C176D mutation on substrate affinity and protein flexibility. Structural and kinetic comparisons with perchlorate reductase support evolutionary tuning for a desired function. Finally, structural comparisons with other structurally characterized NapAs also suggest the role of proximal pterin in CjNapA in electron transfer to the Mo center. PubMed: 41248713DOI: 10.1016/j.jbc.2025.110928 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3 Å) |
Structure validation
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