9UDA

Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase NqrB-G141A mutant from Vibrio cholerae reduced by NADH, with bound korormicin A, stable state

9UDA の概要

• エントリーDOI: 10.2210/pdb9uda/pdb
• EMDBエントリー: 64066
• 分子名称: Na(+)-translocating NADH-quinone reductase subunit A, CALCIUM ION, FE2/S2 (INORGANIC) CLUSTER, ... (13 entities in total)
• 機能のキーワード: na+-nqr, na+ pump, oxidoreductase, inhibitor, membrane protein
• 由来する生物種: Vibrio cholerae O395; 詳細
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 214915.07

構造登録者

Ishikawa-Fukuda, M.,Kishikawa, J.,Kato, T.,Murai, M. (登録日: 2025-04-06, 公開日: 2025-06-25)

主引用文献

Ishikawa-Fukuda, M.,Seki, T.,Kishikawa, J.I.,Takahiro, M.,Okazaki, K.I.,Kato, T.,Barquera, B.,Miyoshi, H.,Murai, M.
The Na + -pumping mechanism driven by redox reactions in the NADH-quinone oxidoreductase from Vibrio cholerae relies on dynamic conformational changes.
Biorxiv, 2025

PubMed Abstract: The Na-pumping NADH-quinone oxidoreductase (Na-NQR) is a key respiratory enzyme in many marine and pathogenic bacteria that couples electron transfer to Na-pumping across the membrane. Earlier X-ray and cryo-EM structures of Na-NQR from suggested that the subunits harboring redox cofactors undergo conformational changes during catalytic turnover. However, these proposed rearrangements have not yet been confirmed. Here, we have identified at least five distinct conformational states of Na-NQR using: mutants that lack specific cofactors, specific inhibitors or low-sodium conditions. Molecular dynamics simulations based on these structural insights indicate that 2Fe-2S reduction in NqrD/E plays a crucial role in triggering Na translocation by driving structural rearrangements in the NqrD/E subunits, which subsequently influence NqrC and NqrF positioning. This study provides the first structural insights into the mechanism of Na translocation coupled to electron transfer in Na-NQR.

PubMed: 40501732
DOI: 10.1101/2025.06.01.656757

実験手法

ELECTRON MICROSCOPY (2.61 Å)