Activation of Dimanganese Class Ib Ribonucleotide Reductase by Hydrogen Peroxide: Mechanistic Insights from Density Functional Theory

Activation of manganese-dependent class Ib ribonucleotide reductase by hydrogen peroxide was modeled using B3LYP* hybrid density functional theory. Class Ib ribonucleotide reductase R2 subunit (R2F) does not react with molecular oxygen. Instead R2F is proposed to react with H₂O₂ or HO₂^–, provided by the unusual flavodoxin protein NrdI, to generate the observed manganese­(III) manganese­(III) tyrosyl-radical state. On the basis of the calculations, an energetically feasible reaction mechanism is suggested for activation by H₂O₂, which proceeds through two reductive half-reactions. In the first reductive half-reaction, H₂O₂ is cleaved with a barrier of 13.1 kcal mol^–1 [Mn­(II)­Mn­(II) → Mn­(III)­Mn­(III)], and in the second reductive half-reaction, H₂O₂ is cleaved with a barrier of 17.0 kcal mol^–1 [Mn­(III)­Mn­(III) → Mn­(IV)­Mn­(IV)]. Tyrosyl-radical formation from both the Mn­(IV)­Mn­(IV) state and a Mn­(III)­Mn­(IV) state, where an electron and proton have been taken up, is both kinetically and thermodynamically accessible. Hence, chemically, H₂O₂ is a possible oxidant for the manganese-dependent R2F. The selectivity between the second reductive half-reaction and a competing oxidative reaction, as in manganese catalase, may be the time scale for the availability of H₂O₂. The role of NrdI may be to provide H₂O₂ on the correct time scale