9BZ9

Class 15 model for combined refinement of Bacillus subtilis ribonucleotide reductase complex

9BZ9 の概要

• エントリーDOI: 10.2210/pdb9bz9/pdb
• EMDBエントリー: 45057
• 分子名称: Ribonucleoside-diphosphate reductase subunit alpha, Ribonucleoside-diphosphate reductase subunit beta, ADENOSINE-5'-TRIPHOSPHATE, ... (7 entities in total)
• 機能のキーワード: ribonucleotide reductase, oxidoreductase
• 由来する生物種: Bacillus subtilis; 詳細
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 246158.38

構造登録者

Xu, D.,Thomas, W.C.,Burnim, A.A.,Ando, N. (登録日: 2024-05-24, 公開日: 2025-03-19, 最終更新日: 2025-03-26)

主引用文献

Xu, D.,Thomas, W.C.,Burnim, A.A.,Ando, N.
Conformational landscapes of a class I ribonucleotide reductase complex during turnover reveal intrinsic dynamics and asymmetry.
Nat Commun, 16:2458-2458, 2025

PubMed Abstract: Understanding the structural dynamics associated with enzymatic catalysis has been a long-standing goal of biochemistry. With the advent of modern cryo-electron microscopy (cryo-EM), it has become conceivable to redefine a protein's structure as the continuum of all conformations and their distributions. However, capturing and interpreting this information remains challenging. Here, we use classification and deep-learning-based analyses to characterize the conformational heterogeneity of a class I ribonucleotide reductase (RNR) during turnover. By converting the resulting information into physically interpretable 2D conformational landscapes, we demonstrate that RNR continuously samples a wide range of motions while maintaining surprising asymmetry to regulate the two halves of its turnover cycle. Remarkably, we directly observe the appearance of highly transient conformations needed for catalysis, as well as the interaction of RNR with its endogenous reductant thioredoxin also contributing to the asymmetry and dynamics of the enzyme complex. Overall, this work highlights the role of conformational dynamics in regulating key steps in enzyme mechanisms.

PubMed: 40075098
DOI: 10.1038/s41467-025-57735-4

実験手法

ELECTRON MICROSCOPY (4.64 Å)