Conformational Landscapes of a Class I Ribonucleotide Reductase Complex during Turnover Reveal Intrinsic Dynamics and Asymmetry

Understanding the structural dynamics associated with enzymatic catalysis has been a long-standing goal of structural biology. A wide range of motions, from small side-chain fluctuations to large domain rearrangements, have been implicated in enzyme function by experimental and computational studies. However, because structural techniques generally depend on averaging, direct visualization of conformational landscapes during turnover has been challenging. Here, we report the conformational landscapes of a class I ribonucleotide reductase (RNR) in various stages of turnover using single-particle cryo-electron microscopy (cryo-EM) and a combination of classification and deep-learning-based analyses. RNRs are responsible for the conversion of ribonucleotides to deoxyribonucleotides, a reaction that is essential for all DNA-based life. Class I RNRs, used by humans and other aerobic organisms, perform a complex series of chemical steps that are coupled with the dynamics of two highly mobile subunits, which can be resolved by EM. We demonstrate that despite the dimeric nature of the enzyme and its intrinsic dynamics, remarkable asymmetry is maintained across the class I RNR complex that physically segregates the two halves of its turnover cycle.