6QO7

Crystal structure of ribonucleotide reductase NrdF from Bacillus anthracis aerobically soaked with ferrous ions (photo-reduced)

6QO7 の概要

• エントリーDOI: 10.2210/pdb6qo7/pdb
• 分子名称: Ribonucleoside-diphosphate reductase subunit beta, FE (II) ION, CHLORIDE ION, ... (4 entities in total)
• 機能のキーワード: metal binding; oxidation reduction process; 2'-deoxyribonucleotide metabolism; dna replication, oxidoreductase
• 由来する生物種: Bacillus anthracis str. Sterne
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 74370.80

構造登録者

Grave, K.,Hogbom, M. (登録日: 2019-02-12, 公開日: 2019-08-21, 最終更新日: 2024-05-15)

主引用文献

Grave, K.,Lambert, W.,Berggren, G.,Griese, J.J.,Bennett, M.D.,Logan, D.T.,Hogbom, M.
Redox-induced structural changes in the di-iron and di-manganese forms of Bacillus anthracis ribonucleotide reductase subunit NrdF suggest a mechanism for gating of radical access.
J.Biol.Inorg.Chem., 24:849-861, 2019

PubMed Abstract: Class Ib ribonucleotide reductases (RNR) utilize a di-nuclear manganese or iron cofactor for reduction of superoxide or molecular oxygen, respectively. This generates a stable tyrosyl radical (Y·) in the R2 subunit (NrdF), which is further used for ribonucleotide reduction in the R1 subunit of RNR. Here, we report high-resolution crystal structures of Bacillus anthracis NrdF in the metal-free form (1.51 Å) and in complex with manganese (Mn/Mn, 1.30 Å). We also report three structures of the protein in complex with iron, either prepared anaerobically (Fe/Fe form, 1.32 Å), or prepared aerobically in the photo-reduced Fe/Fe form (1.63 Å) and with the partially oxidized metallo-cofactor (1.46 Å). The structures reveal significant conformational dynamics, likely to be associated with the generation, stabilization, and transfer of the radical to the R1 subunit. Based on observed redox-dependent structural changes, we propose that the passage for the superoxide, linking the FMN cofactor of NrdI and the metal site in NrdF, is closed upon metal oxidation, blocking access to the metal and radical sites. In addition, we describe the structural mechanics likely to be involved in this process.

PubMed: 31410573
DOI: 10.1007/s00775-019-01703-z

実験手法

X-RAY DIFFRACTION (1.628 Å)