Structural basis of half-site reactivity in the catalytic α-subunit of Class Ib ribonucleotide reductases

Abstract

Ribonucleotide reductases (RNRs) employ radical chemistry to generate deoxyribonucleotides required for DNA synthesis and repair. A notable feature of RNRs is half-site reactivity, where, despite the enzyme being a symmetric 2 dimer, only one active site is catalytically active at a time while the other remains in a "poised" state for substrate binding. This phenomenon is tightly linked to the asymmetric 2{beta}2 interaction required for radical transfer. Here, we determined cryo-EM structures of the -subunit in the apo and holo states, i.e., the complex bound to TTP (effector) and GDP (substrate). The structures reveal asymmetric binding of the effector TTP and the substrate GDP across the dimer, with concomitant stabilization of loops surrounding the ligand-binding site. Interestingly, this asymmetry leads to well-resolved N-terminal density for [~]150 residues in the substrate-bound subunit, but weak density for this region in the effector-bound monomer. N-terminal domains are unresolved in both monomers of the apo structure. Isothermal titration calorimetry supports asymmetric binding of pyrimidine effectors with micromolar affinities. Molecular dynamics simulations and three-dimensional variability analysis reveal synchronous motions of loop 2, which together with the N-terminal domain drive alternate opening and closing of the active sites in the two monomers. These conformational dynamics provide key insights into the mechanistic basis of half-site reactivity. Together, these findings provide new insights into the structural dynamics and thermodynamic principles governing regulation and half-site activity in Class Ib RNRs. Significance statementRibonucleotide reductases (RNRs) are essential enzymes that supply the building blocks required for DNA synthesis and repair, yet the structural basis of their half-site reactivity has remained unclear. Using cryo-electron microscopy, calorimetry, molecular dynamics simulations, and conformational variability analysis, we show that the catalytic -subunit of a Class Ib RNR exhibits asymmetric nucleotide binding and coordinated conformational dynamics between the two monomers. These motions drive alternating opening and closing of the active sites and are linked to differential stabilization of the N-terminal region. Our findings suggest that asymmetric conformational gating and N-terminal sampling regulate productive interaction with the radical-generating {beta}-subunit, providing a mechanistic framework for understanding half-site reactivity and allosteric regulation in RNRs.