Peroxo-type intermediates in class I ribonucleotide reductase and related binuclear non-heme iron enzymes.
We have performed a systematic study of chemically possible peroxo-type intermediates occurring in the non-heme di-iron enzyme class Ia ribonucleotide reductase, using spectroscopically calibrated computational chemistry. Density functional computations of equilibrium structures, Fe-O and O-O stretch frequencies, Mossbauer isomer shifts, absorption spectra, J-coupling constants, electron affinities, and free energies of O(2) and proton or water binding are presented for a series of possible intermediates. The results enable structure-property correlations and a new rationale for the changes in carboxylate conformations occurring during the O(2) reaction of this class of non-heme iron enzymes. Our procedure identifies and characterizes various possible candidates for peroxo intermediates experimentally observed along the ribonucleotide reductase dioxygen activation reaction. The study explores how water or a proton can bind to the di-iron site of ribonucleotide reductase and facilitate changes that affect the electronic structure of the iron sites and activate the site for further reaction. Two potential reaction pathways are presented: one where water adds to Fe1 of the cis-mu-1,2 peroxo intermediate P causing opening of a bridging carboxylate to form intermediate P' that has an increased electron affinity and is activated for proton-coupled electron transfer to form the Fe(III)Fe(IV) intermediate X; and one that is more energetically favorable where the P to P' conversion involves addition of a proton to a terminal carboxylate ligand in the site which increases the electron affinity and triggers electron transfer to form X. Both pathways provide a mechanism for the activation of peroxy intermediates in binuclear non-heme iron enzymes for reactivity. The studies further show that water coordination can induce the conformational changes observed in crystal structures of the met state.
Jensen
Kasper P
KP
DTU-Chemistry, Technical University of Denmark, Building 207, DK 2800 Kgs. Lyngby, Denmark.
Bell
Caleb B
CB
Clay
Michael D
MD
Solomon
Edward I
EI
D000042:Absorption; D003198:Computer Simulation; D006418:Heme; D006878:Hydroxides / Q000737:chemistry; D007501:Iron / Q000378:metabolism*; D007536:Isomerism; D008958:Models, Molecular; D008968:Molecular Conformation; D010084:Oxidation-Reduction; D010100:Oxygen / Q000737:chemistry; D010545:Peroxides / Q000737:chemistry; D011522:Protons; D012264:Ribonucleotide Reductases / Q000737:chemistry* / Q000378:metabolism*; D013056:Spectrophotometry, Ultraviolet; D015204:Spectroscopy, Mossbauer; D013816:Thermodynamics; D014732:Vibration; D014867:Water / Q000737:chemistry
D006878:Hydroxides; D010545:Peroxides; D011522:Protons; D014867:Water; D006418:Heme; C031356:hydroxide ion; D007501:Iron; D012264:Ribonucleotide Reductases; D010100:Oxygen