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Structure paper

タイトル	2.6-Å resolution cryo-EM structure of a class Ia ribonucleotide reductase trapped with mechanism-based inhibitor NCDP.
ジャーナル・号・ページ	Proc Natl Acad Sci U S A, Vol. 121, Issue 45, Page e2417157121, Year 2024
掲載日	2024年11月5日
著者	Dana E Westmoreland / Patricia R Feliciano / Gyunghoon Kang / Chang Cui / Albert Kim / JoAnne Stubbe / Daniel G Nocera / Catherine L Drennan /
PubMed 要旨	Ribonucleotide reductases (RNRs) reduce ribonucleotides to deoxyribonucleotides using radical-based chemistry. For class Ia RNRs, the radical species is stored in a separate subunit (β2) from the ...Ribonucleotide reductases (RNRs) reduce ribonucleotides to deoxyribonucleotides using radical-based chemistry. For class Ia RNRs, the radical species is stored in a separate subunit (β2) from the subunit housing the active site (α2), requiring the formation of a short-lived α2β2 complex and long-range radical transfer (RT). RT occurs via proton-coupled electron transfer (PCET) over a long distance (~32-Å) and involves the formation and decay of multiple amino acid radical species. Here, we use cryogenic electron microscopy and a mechanism-based inhibitor 2'-azido-2'-deoxycytidine-5'-diphosphate (NCDP) to trap a wild-type α2β2 complex of class Ia RNR. We find that one α subunit has turned over and that the other is trapped, bound to β in a midturnover state. Instead of NCDP in the active site, forward RT has resulted in N loss, migration of the third nitrogen from the ribose C2' to C3' positions, and attachment of this nitrogen to the sulfur of cysteine-225. In this study, an inhibitor has been visualized as an adduct to an RNR. Additionally, this structure reveals the positions of PCET residues following forward RT, complementing the previous structure that depicted a preturnover PCET pathway and suggesting how PCET is gated at the α-β interface. This NCDP-trapped structure is also of sufficient resolution (2.6 Å) to visualize water molecules, allowing us to evaluate the proposal that water molecules are proton acceptors and donors as part of the PCET process.
リンク	Proc Natl Acad Sci U S A / PubMed:39475643
手法	EM (単粒子)
解像度	2.6 Å
構造データ	46711 9db2 EMDB-46711, PDB-9db2: Class Ia ribonucleotide reductase with mechanism-based inhibitor N3CDP 手法: EM (単粒子) / 解像度: 2.6 Å
化合物	ChemComp-DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / dATP ChemComp-MG: Unknown entry / マグネシウムジカチオン ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP / ATP, エネルギー貯蔵分子YM 化合物画像なし ChemComp-UNL: Unknown ligand PDB-1a3l: CATALYSIS OF A DISFAVORED REACTION: AN ANTIBODY EXO DIELS-ALDERASE-TSA-INHIBITOR COMPLEX AT 1.95 A RESOLUTION ChemComp-FEO: MU-OXO-DIIRON ChemComp-HOH*: WATER
由来	escherichia coli (大腸菌)
キーワード	OXIDOREDUCTASE / ribonucleotide reductase / class Ia / mechanistic inhibition