Theoretical Insights into the Generation Mechanism of the Tyr 122 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 Tyr 122 β ↔ [Trp 48 β]? ↔ Tyr 356 β ↔ Tyr 731 α ↔ Tyr 730 α ↔ Cys 439 α. The formation of the Y 122 • radical initiates this long-range radical transfer process. However, the generation mechanism of Y 122 • 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 Y 122 • generation by density functional theory (DFT) calculations. Our examinations revealed that the generation of the Y 122 • 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 Y 122 and the second step of a proton-coupled long-range electron transfer reaction with the proton transfer from the Y 122 hydroxyl group to the terminal hydroxide ligand of Fe 1 III and simultaneously electron transfer from the side chain of Y 122 to Fe 2 IV . These findings provide an insight into the formation mechanism of Y 122 • catalyzed by the double-iron center of the β subunit of class Ia RNR.