Crystal structure of the ribonucleotide reductase R2 mutant that accumulates a μ-1,2-peroxodiiron(III) intermediate during oxygen activation

The R2 subunit of Escherichia coli (aerobic) ribonucleotide reductase activates molecular oxygen at its diiron center to produce a functionally essential stable tyrosyl radical from residue Y122. It was previously shown that the D84E site-directed mutant of R2 (R2-D84E) accumulates a μ-1,2- peroxodiiron(III) intermediate on the pathway to tyrosyl radical formation. This intermediate does not accumulate in the reaction of wildtype (wt) R2, but an analogous complex does accumulate during oxygen activation by the structurally similar diiron protein, methane monooxygenase hydroxylase (MMOH). Herein we describe the crystallographically determined three- dimensional structures of the reduced, diiron(II) reactant and oxidized, diiron(III) product forms of R2-D84E. The reduced R2-D84E structure differs from that of reduced wt R2 in the conformations of three carboxylate ligands, E84, E204, and E238. The adjustments in these ligands render the coordination sphere of the diiron(II) center very similar to that in reduced MMOH. In addition, a water molecule not observed in reduced wt R2 is coordinated to Fe2 in reduced R2-D84E. The oxidized R2-D84E structure is similar to that of oxidized wt R2 except in the coordination mode of E84. In R2-D84E, E84 coordinates to Fe1 in a monodentate, terminal mode and is hydrogen bonded to a water molecule also coordinated to Fe1. In wt R2, D84 is a bidentate, chelating ligand. In both R2-D84E structures, Y122 is shifted away from Fe1 such that a hydrogen bonding interaction with E84 is not possible. The observed structural adjustments suggest possible rationales for the stability of the μ-1,2-peroxodiiron(III) complex in R2-D84E. In addition, the structures expand the experimental foundation for computational investigations aimed at defining the detailed mechanistic pathways for O₂ activation at diiron(II) centers.