Theoretical Insights into the Generation Mechanism of the Tyr₁₂₂ Radical Catalyzed by Intermediate X in Class Ia Ribonucleotide Reductase

Ribonucleotide reductase (RNR) catalyzes the reduction of ribonucleotides to deoxyribonucleotides in all organisms. There is an ∼35 Å long-range electron-hole transfer pathway during the catalytic process of class Ia RNR, which can be described as Tyr₁₂₂β ↔ [Trp₄₈β]? ↔ Tyr₃₅₆β ↔ Tyr₇₃₁α ↔ Tyr₇₃₀α ↔ Cys₄₃₉α. The formation of the Y₁₂₂^• radical initiates this long-range radical transfer process. However, the generation mechanism of Y₁₂₂^• is not yet clear due to confusion over the intermediate X structures. Based on the two reported X structures, we examined the possible mechanisms of Y₁₂₂^• generation by density functional theory (DFT) calculations. Our examinations revealed that the generation of the Y₁₂₂^• radical from the two different core structures of X was via a similar two-step reaction, with the first step of proton transfer for the formation of the proton receptor of Y₁₂₂ and the second step of a proton-coupled long-range electron transfer reaction with the proton transfer from the Y₁₂₂ hydroxyl group to the terminal hydroxide ligand of Fe₁^III and simultaneously electron transfer from the side chain of Y₁₂₂ to Fe₂^IV. These findings provide an insight into the formation mechanism of Y₁₂₂^• catalyzed by the double-iron center of the β subunit of class Ia RNR.