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 similar to 35 & Aring; long-range electron-hole transfer pathway during the catalytic process of class Ia RNR, which can be described as Tyr(122)beta <-> [Trp(48)beta]? <-> Tyr(356)beta <-> Tyr(731)alpha <-> Tyr(730)alpha <-> Cys(439)alpha. The formation of the Y-122(center dot) radical initiates this long-range radical transfer process. However, the generation mechanism of Y-122(center dot) 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(center dot) generation by density functional theory (DFT) calculations. Our examinations revealed that the generation of the Y-122(center dot) 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(center dot) catalyzed by the double-iron center of the beta subunit of class Ia RNR.