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TitleStructure and substrate promiscuity of Campylobacter jejuni periplasmic nitrate reductase (Nap) and phylogenetic analysis of Nap homologs.
Journal, issue, pagesJ Biol Chem, Vol. 301, Issue 12, Page 110928, Year 2025
Publish dateNov 15, 2025
AuthorsNitai C Giri / Trung Thach / KanagaVijayan Dhanabalan / Mintare Cesiunaite / Manohar Radhakrishnan / Lahiru Wedasingha / Nicholas Manicke / Michael Wells / Maciej Szaleniec / Ramaswamy Subramanian / Partha Basu /
PubMed AbstractPeriplasmic 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 ...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.
External linksJ Biol Chem / PubMed:41248713 / PubMed Central
MethodsEM (single particle)
Resolution3.0 Å
Structure data

71994

9pxt

EMDB-71994, PDB-9pxt:
Cryo-EM structure of NapA, the periplasmic nitrate reductase from Campylobacter jejuni
Method: EM (single particle) / Resolution: 3.0 Å

Chemicals

ChemComp-SF4:
IRON/SULFUR CLUSTER

ChemComp-MO:
MOLYBDENUM ATOM

ChemComp-MGD:
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE

Source
  • campylobacter jejuni (Campylobacter)
KeywordsOXIDOREDUCTASE / Periplasmic nitrate reductase / molybdenum enzymes / cryo-EM / MEMBRANE PROTEIN / METAL BINDING PROTEIN

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