9PXT

Cryo-EM structure of NapA, the periplasmic nitrate reductase from Campylobacter jejuni

9PXT の概要

• エントリーDOI: 10.2210/pdb9pxt/pdb
• 関連するPDBエントリー: 2NYA
• EMDBエントリー: 71994
• 分子名称: Periplasmic nitrate reductase, IRON/SULFUR CLUSTER, MOLYBDENUM ATOM, ... (4 entities in total)
• 機能のキーワード: periplasmic nitrate reductase, molybdenum enzymes, cryo-em, membrane protein, metal binding protein, oxidoreductase
• 由来する生物種: Campylobacter jejuni
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 107021.52

構造登録者

Thach, T.,Subramanian, R. (登録日: 2025-08-06, 公開日: 2026-06-17)

主引用文献

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

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: 41248713
DOI: 10.1016/j.jbc.2025.110928

実験手法

ELECTRON MICROSCOPY (3 Å)