EMDB/PDB/SASBDBから引用されている文献のデータベース

キーワード
構造解析手法	All X線回折 NMR 電子顕微鏡小角散乱中性子線回折線維回折粉末回折赤外分光 EPR FRET 理論モデルハイブリッド
著者・登録者
ジャーナル
IF	>30 >20 >10 >5 all

タイトル	The Na-pumping mechanism driven by redox reactions in the NADH-quinone oxidoreductase from relies on dynamic conformational changes.
ジャーナル・号・ページ	bioRxiv, Year 2025
掲載日	2025年6月8日
著者	Moe Ishikawa-Fukuda / Takehito Seki / Jun-Ichi Kishikawa / Takahiro Masuya / Kei-Ichi Okazaki / Takayuki Kato / Blanca Barquera / Hideto Miyoshi / Masatoshi Murai /
PubMed 要旨	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 ...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.
リンク	bioRxiv / PubMed:40501732 / PubMed Central
手法	EM (単粒子)
解像度	2.59 - 3.8 Å
構造データ	63872 9u5g EMDB-63872, PDB-9u5g: Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase NqrC-T225Y mutant from Vibrio cholerae 手法: EM (単粒子) / 解像度: 2.66 Å 64059 9ud2 EMDB-64059, PDB-9ud2: Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase NqrC-T225Y mutant from Vibrio cholerae reduced by NADH 手法: EM (単粒子) / 解像度: 2.59 Å 64060 9ud3 EMDB-64060, PDB-9ud3: Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase NqrB-T236Y mutant from Vibrio cholerae 手法: EM (単粒子) / 解像度: 3.8 Å 64061 9ud4 EMDB-64061, PDB-9ud4: Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase NqrB-T236Y mutant from Vibrio cholerae reduced by NADH 手法: EM (単粒子) / 解像度: 3.31 Å 64062 9ud5 EMDB-64062, PDB-9ud5: Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase from Vibrio cholerae reduced by NADH, with bound korormicin A 手法: EM (単粒子) / 解像度: 2.9 Å 64063 9ud6 EMDB-64063, PDB-9ud6: Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase from Vibrio cholerae reduced by NADH, in the absence of Na+, upper state 手法: EM (単粒子) / 解像度: 2.65 Å 64064 9ud8 EMDB-64064, PDB-9ud8: Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase from Vibrio cholerae reduced by NADH, in the absence of Na+, middle state 手法: EM (単粒子) / 解像度: 3.75 Å 64065 9ud9 EMDB-64065, PDB-9ud9: Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase from Vibrio cholerae reduced by NADH, in the absence of Na+, down state 手法: EM (単粒子) / 解像度: 3.11 Å 64066 9uda EMDB-64066, PDB-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 手法: EM (単粒子) / 解像度: 2.61 Å 64068 9udf EMDB-64068, PDB-9udf: Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase NqrB-G141A mutant from Vibrio cholerae reduced by NADH, with bound korormicin A, shifted state 手法: EM (単粒子) / 解像度: 2.93 Å 64069 9udg EMDB-64069, PDB-9udg: Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase from Vibrio cholerae reduced by NADH, with bound aurachin D-42 手法: EM (単粒子) / 解像度: 3.18 Å 64518 9uuu EMDB-64518, PDB-9uuu: Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase from Vibrio cholerae reduced by NADH 手法: EM (単粒子) / 解像度: 3.17 Å
化合物	ChemComp-FMN: FLAVIN MONONUCLEOTIDE / FMN ChemComp-RBF: RIBOFLAVIN / リボフラビン ChemComp-LMT: DODECYL-BETA-D-MALTOSIDE / ドデシルβ-D-マルトシド / 可溶化剤YM ChemComp-CA: Unknown entry / カルシウムジカチオン ChemComp-FES: FE2/S2 (INORGANIC) CLUSTER ChemComp-FAD: FLAVIN-ADENINE DINUCLEOTIDE / FAD / FADYM ChemComp-HOH: WATER ChemComp-IQT: Korormicin ChemComp-PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE, リン脂質YM ChemComp-0NI: Aurachin D ChemComp-NAI*: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH
由来	vibrio cholerae o395 (コレラ菌)
キーワード	MEMBRANE PROTEIN / Na+-NQR / Na+ pump / oxidoreductase / inhibitor