8RAG

Crystal structure of class Ie ribonucleotide reductase R2 subunit without Y150 modification from Gardnerella vaginalis

8RAG の概要

• エントリーDOI: 10.2210/pdb8rag/pdb
• 分子名称: ribonucleoside-diphosphate reductase (2 entities in total)
• 機能のキーワード: ribonucleotide reductase r2e, class ie rnr, oxidoreductase, ferritin-like superfamily, nrdf, rnr beta-subunit
• 由来する生物種: Gardnerella vaginalis ATCC 14019
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 167030.30

構造登録者

John, J.,Hogbom, M. (登録日: 2023-12-01, 公開日: 2024-12-11, 最終更新日: 2025-03-05)

主引用文献

John, J.,Lundin, D.,Branca, R.M.,Kumar, R.,Srinivas, V.,Lebrette, H.,Hogbom, M.
Characterization of a second class Ie ribonucleotide reductase.
Commun Biol, 8:281-281, 2025

PubMed Abstract: Class I ribonucleotide reductases (RNRs) convert ribonucleotides into deoxyribonucleotides under oxic conditions. The R2 subunit provides a radical required for catalysis conducted by the R1 subunit. In most R2s the radical is generated on a tyrosine via oxidation by an adjacent metal site. The discovery of a metal-free R2 defined the new RNR subclass Ie. In R2e, three of the otherwise strictly conserved metal-binding glutamates in the active site are substituted. Two variants have been found, VPK and QSK. To date, the VPK version has been the focus of biochemical characterization. Here we characterize a QSK variant of R2e. We analyse the organismal distribution of the two R2e versions and find dozens of organisms relying solely on the QSK RNR for deoxyribonucleotide production. We demonstrate that the R2e of the human pathogen Gardnerella vaginalis (Bifidobacterium vaginale) modifies the active site-adjacent tyrosine to DOPA. The amount of modified protein is shown to be dependent on coexpression with the other proteins encoded in the RNR operon. The DOPA containing R2e can support ribonucleotide reduction in vitro while the unmodified protein cannot. Finally, we determined the first structures of R2e in the unmodified and DOPA states.

PubMed: 39987380
DOI: 10.1038/s42003-025-07565-3

実験手法

X-RAY DIFFRACTION (1.9 Å)