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	How ATP and dATP reposition class III ribonucleotide reductase cone domains to regulate enzyme activity.
ジャーナル・号・ページ	Sci Adv, Vol. 11, Issue 48, Page eady9156, Year 2025
掲載日	2025年11月28日
著者	Gisele A Andree / Kelsey R Miller-Brown / Zhuangyu Zhao / Ally K Smith / Christopher D Dawson / Daniel J Deredge / Catherine L Drennan /
PubMed 要旨	Ribonucleotide reductases (RNRs) catalyze the conversion of ribonucleotides to deoxyribonucleotides. In the majority of cases, RNR activity is allosterically regulated by the cellular 2'- ...Ribonucleotide reductases (RNRs) catalyze the conversion of ribonucleotides to deoxyribonucleotides. In the majority of cases, RNR activity is allosterically regulated by the cellular 2'-deoxyadenosine 5'-triphosphate (dATP)/adenosine 5'-triphosphate (ATP) ratio. To investigate allosteric activity regulation in anaerobic or class III (glycyl radical containing) RNRs, we determine cryo-electron microscopy structures of the class III RNR from (StNrdD). We find that StNrdD's regulatory "cone" domains adopt markedly different conformations depending on whether the activator ATP or the inhibitor dATP is bound and that these different conformations alternatively position an "active site flap" toward the active site (ATP-bound) or away (dATP-bound). In contrast, the position of the glycyl radical domain is unaffected by the cone domain conformations, suggesting that StNrdD activity is regulated through control of substrate binding rather than control of radical transfer. Hydrogen-deuterium exchange mass spectrometry and mutagenesis support the structural findings. In addition, our structural data provide insight into the molecular basis by which ATP and dATP binding lead to the observed differential cone domain conformations.
リンク	Sci Adv / PubMed:41313771 / PubMed Central
手法	EM (単粒子) / X線回折
解像度	2.6 - 4.5 Å
構造データ	EMDB-46692: S. thermophilus class III ribonucleotide reductase signal subtracted cone domains and core 手法: EM (単粒子) / 解像度: 3.7 Å EMDB-46693: S. thermophilus class III ribonucleotide reductase focused refined core 手法: EM (単粒子) / 解像度: 3.1 Å EMDB-46696: S. thermophilus class III ribonucleotide reductase consensus 手法: EM (単粒子) / 解像度: 3.6 Å 46698 9dau EMDB-46698, PDB-9dau: S. thermophilus class III ribonucleotide reductase with dATP and TTP 手法: EM (単粒子) / 解像度: 3.6 Å EMDB-46712: S. thermophilus class III ribonucleotide reductase signal subtracted cone domains and core 手法: EM (単粒子) / 解像度: 4.1 Å EMDB-46713: S. thermophilus class III ribonucleotide reductase focused refined core 手法: EM (単粒子) / 解像度: 3.8 Å EMDB-46746: S. thermophilus class III ribonucleotide reductase consensus 手法: EM (単粒子) / 解像度: 4.5 Å 46747 9dca EMDB-46747, PDB-9dca: S. thermophilus class III ribonucleotide reductase with ATP and TTP 手法: EM (単粒子) / 解像度: 3.6 Å PDB-9d3x: Crystal structure of S. thermophilus class III ribonucleotide reductase bound to dATP 手法: X-RAY DIFFRACTION / 解像度: 2.6 Å
化合物	ChemComp-MG: Unknown entry ChemComp-DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE ChemComp-ZN: Unknown entry ChemComp-SO4: SULFATE ION ChemComp-HOH: WATER ChemComp-TTP: THYMIDINE-5'-TRIPHOSPHATE ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, エネルギー貯蔵分子*YM
由来	streptococcus thermophilus (ストレプトコッカス・サリバリウス亜種サーモフィラス)
キーワード	OXIDOREDUCTASE / Ribonucleotide reductase / allosteric regulation / cone domain / glycyl radical enzyme