9BYH

Consensus model for turnover condition of Bacillus subtilis ribonucleotide reductase complex

Summary for 9BYH

• Entry DOI: 10.2210/pdb9byh/pdb
• EMDB information: 45031
• Descriptor: Ribonucleoside-diphosphate reductase subunit alpha, Ribonucleoside-diphosphate reductase subunit beta, ADENOSINE-5'-TRIPHOSPHATE, ... (6 entities in total)
• Functional Keywords: ribonucleotide reductase, oxidoreductase
• Biological source: Bacillus subtilis; More
• Total number of polymer chains: 4
• Total formula weight: 245938.63

Authors

Xu, D.,Thomas, W.C.,Burnim, A.A.,Ando, N. (deposition date: 2024-05-23, release date: 2025-03-19, Last modification date: 2025-03-26)

Primary citation

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

Experimental method

ELECTRON MICROSCOPY (2.53 Å)