Electronic and spectroscopic studies of the non-heme reduced binuclear iron sites of two ribonucleotide reductase variants: comparison to reduced methane monooxygenase and contributions to O2 reactivity.
Circular dichroism (CD), magnetic circular dichroism (MCD), and variable-temperature variable-field (VTVH) MCD have been used to probe the biferrous active site of two variants of ribonucleotide reductase. The aspartate to glutamate substitution (R2-D84E) at the binuclear iron site modifies the endogenous ligand set of ribonucleotide reductase to match that of the binuclear center in the hydroxylase component of methane monooxygenase (MMOH). The crystal structure of chemically reduced R2-D84E suggests that the active-site structure parallels that of MMOH. However, CD, MCD, and VTVH MCD data combined with spin-Hamiltonian analysis of reduced R2-D84E indicate a different coordination environment relative to reduced MMOH, with no mu-(1,1)(eta(1),eta(2)) carboxylate bridge. To further understand the variations in geometry of the active site, which lead to differences in reactivity, density functional theory (DFT) calculations have been carried out to identify active-site structures for R2-wt and R2-D84E consistent with these spectroscopic data. The effects of varying the ligand set, positions of bound and free waters, and additional protein constraints on the geometry and energy of the binuclear site of both R2-wt and variant R2s are also explored to identify the contributions to their structural differences and their relation to reduced MMOH.
Wei
Pin-Pin
PP
Department of Chemistry, Stanford University, Stanford, California 94305, USA.
Skulan
Andrew J
AJ
Mitić
Natasa
N
Yang
Yi-Shan
YS
Saleh
Lana
L
Bollinger
J Martin
JM
Solomon
Edward I
EI
D001665:Binding Sites; D002942:Circular Dichroism; D005296:Ferrous Compounds / Q000737:chemistry*; D008956:Models, Chemical; D008958:Models, Molecular; D019159:Nonheme Iron Proteins / Q000737:chemistry*; D010100:Oxygen / Q000737:chemistry*; D010105:Oxygenases / Q000737:chemistry*; D017433:Protein Structure, Secondary; D012264:Ribonucleotide Reductases / Q000737:chemistry*; D019265:Spectroscopy, Near-Infrared
D005296:Ferrous Compounds; D019159:Nonheme Iron Proteins; D010105:Oxygenases; C021555:methane monooxygenase; D012264:Ribonucleotide Reductases; C108427:ribonucleotide reductase R2 subunit; D010100:Oxygen