9db2

Publication Abstract from PubMed

Ribonucleotide reductases (RNRs) reduce ribonucleotides to deoxyribonucleotides using radical-based chemistry. For class Ia RNRs, the radical species is stored in a separate subunit (beta2) from the subunit housing the active site (alpha2), requiring the formation of a short-lived alpha2beta2 complex and long-range radical transfer (RT). RT occurs via proton-coupled electron transfer (PCET) over a long distance (~32-A) 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 (N(3)CDP) to trap a wild-type alpha2beta2 complex of Escherichia coli class Ia RNR. We find that one alpha subunit has turned over and that the other is trapped, bound to beta in a midturnover state. Instead of N(3)CDP in the active site, forward RT has resulted in N(2) 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 alpha-beta interface. This N(3)CDP-trapped structure is also of sufficient resolution (2.6 A) to visualize water molecules, allowing us to evaluate the proposal that water molecules are proton acceptors and donors as part of the PCET process.

2.6-A resolution cryo-EM structure of a class Ia ribonucleotide reductase trapped with mechanism-based inhibitor N(3)CDP.,Westmoreland DE, Feliciano PR, Kang G, Cui C, Kim A, Stubbe J, Nocera DG, Drennan CL Proc Natl Acad Sci U S A. 2024 Nov 5;121(45):e2417157121. doi: , 10.1073/pnas.2417157121. Epub 2024 Oct 30. PMID:39475643^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.