Spectroscopic and electronic structure description of the reduced binuclear non-heme iron active site in ribonucleotide reductase from E. coli

Comparison to reduced Δ9 desaturase and electronic structure contributions to differences in O2 reactivity

Yi Shan Yang, Jeffrey Baldwin, Brenda A. Ley, Joseph M. Bollinger, Jr., Edward I. Solomon

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47 Citations (Scopus)

Abstract

Ribonucleotide reductase (RR) catalyzes the first committed and rate-determining step in DNA biosynthesis, the reduction of ribonucleotides to deoxyribonucleotides. Fe(II) binding to the binuclear non-heme iron active site has been studied using a combination of circular dichroism (CD), magnetic circular dichroism (MCD), and variable-temperature variable-field (VTVH) MCD spectroscopies. These studies show that the two sites have significantly different metal binding affinities. This has also allowed a Mn(II)Fe(II) derivative to be prepared and studied by the above spectroscopies. The spectral features of the individual irons provide geometric and electronic structural insight into each metal site. Density functional calculations on reduced RR are correlated to the spectral features to obtain insight into its electronic structure. Parallel calculations are also performed on reduced stearoyl-acyl carier protein Δ9 desaturase (Δ9D) to correlate to prior spectral data and to the active site of RR. Differences in their dioxygen reactivities are investigated through reaction of these reduced sites with dioxygen, and possible electron-transfer pathways are evaluated. These results show that the active site of reduced RR consists of one 5- and one 4-coordinate iron with the 5C center having a higher binding affinity. Compared to reduced Δ9D, the presence of the 4C site energetically destabilizes reduced RR. Reaction of reduced RR with dioxygen to form a superoxide intermediate is energetically up hill as it results in an excited quartet state on the oxygenated iron, while the formation of a bridged peroxo intermediate is energetically favorable. Formation of peroxo-RR is more favorable than peroxo-Δ9D due to ligand field differences that can control the overlap of the redox active orbitals of the reduced sites with the π orbitals of dioxygen. This parallels experimental differences in the dioxygen reactivity of the reduced RR and Δ9D active sites.

Original languageEnglish (US)
Pages (from-to)8495-8510
Number of pages16
JournalJournal of the American Chemical Society
Volume122
Issue number35
DOIs
StatePublished - Sep 6 2000

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Ribonucleotide Reductases
Escherichia coli
Electronic structure
Catalytic Domain
Iron
Oxygen
Circular Dichroism
Dichroism
Spectrum Analysis
Metals
Deoxyribonucleotides
Circular dichroism spectroscopy
Ribonucleotides
Oxidoreductases
Biosynthesis
Magnetic Fields
Excited states
Superoxides
Oxidation-Reduction
Density functional theory

All Science Journal Classification (ASJC) codes

  • Catalysis
  • Chemistry(all)
  • Biochemistry
  • Colloid and Surface Chemistry

Cite this

@article{1bdd3196e43d49b4be475cb173e965a4,
title = "Spectroscopic and electronic structure description of the reduced binuclear non-heme iron active site in ribonucleotide reductase from E. coli: Comparison to reduced Δ9 desaturase and electronic structure contributions to differences in O2 reactivity",
abstract = "Ribonucleotide reductase (RR) catalyzes the first committed and rate-determining step in DNA biosynthesis, the reduction of ribonucleotides to deoxyribonucleotides. Fe(II) binding to the binuclear non-heme iron active site has been studied using a combination of circular dichroism (CD), magnetic circular dichroism (MCD), and variable-temperature variable-field (VTVH) MCD spectroscopies. These studies show that the two sites have significantly different metal binding affinities. This has also allowed a Mn(II)Fe(II) derivative to be prepared and studied by the above spectroscopies. The spectral features of the individual irons provide geometric and electronic structural insight into each metal site. Density functional calculations on reduced RR are correlated to the spectral features to obtain insight into its electronic structure. Parallel calculations are also performed on reduced stearoyl-acyl carier protein Δ9 desaturase (Δ9D) to correlate to prior spectral data and to the active site of RR. Differences in their dioxygen reactivities are investigated through reaction of these reduced sites with dioxygen, and possible electron-transfer pathways are evaluated. These results show that the active site of reduced RR consists of one 5- and one 4-coordinate iron with the 5C center having a higher binding affinity. Compared to reduced Δ9D, the presence of the 4C site energetically destabilizes reduced RR. Reaction of reduced RR with dioxygen to form a superoxide intermediate is energetically up hill as it results in an excited quartet state on the oxygenated iron, while the formation of a bridged peroxo intermediate is energetically favorable. Formation of peroxo-RR is more favorable than peroxo-Δ9D due to ligand field differences that can control the overlap of the redox active orbitals of the reduced sites with the π orbitals of dioxygen. This parallels experimental differences in the dioxygen reactivity of the reduced RR and Δ9D active sites.",
author = "Yang, {Yi Shan} and Jeffrey Baldwin and Ley, {Brenda A.} and {Bollinger, Jr.}, {Joseph M.} and Solomon, {Edward I.}",
year = "2000",
month = "9",
day = "6",
doi = "10.1021/ja994406r",
language = "English (US)",
volume = "122",
pages = "8495--8510",
journal = "Journal of the American Chemical Society",
issn = "0002-7863",
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TY - JOUR

T1 - Spectroscopic and electronic structure description of the reduced binuclear non-heme iron active site in ribonucleotide reductase from E. coli

T2 - Comparison to reduced Δ9 desaturase and electronic structure contributions to differences in O2 reactivity

AU - Yang, Yi Shan

AU - Baldwin, Jeffrey

AU - Ley, Brenda A.

AU - Bollinger, Jr., Joseph M.

AU - Solomon, Edward I.

PY - 2000/9/6

Y1 - 2000/9/6

N2 - Ribonucleotide reductase (RR) catalyzes the first committed and rate-determining step in DNA biosynthesis, the reduction of ribonucleotides to deoxyribonucleotides. Fe(II) binding to the binuclear non-heme iron active site has been studied using a combination of circular dichroism (CD), magnetic circular dichroism (MCD), and variable-temperature variable-field (VTVH) MCD spectroscopies. These studies show that the two sites have significantly different metal binding affinities. This has also allowed a Mn(II)Fe(II) derivative to be prepared and studied by the above spectroscopies. The spectral features of the individual irons provide geometric and electronic structural insight into each metal site. Density functional calculations on reduced RR are correlated to the spectral features to obtain insight into its electronic structure. Parallel calculations are also performed on reduced stearoyl-acyl carier protein Δ9 desaturase (Δ9D) to correlate to prior spectral data and to the active site of RR. Differences in their dioxygen reactivities are investigated through reaction of these reduced sites with dioxygen, and possible electron-transfer pathways are evaluated. These results show that the active site of reduced RR consists of one 5- and one 4-coordinate iron with the 5C center having a higher binding affinity. Compared to reduced Δ9D, the presence of the 4C site energetically destabilizes reduced RR. Reaction of reduced RR with dioxygen to form a superoxide intermediate is energetically up hill as it results in an excited quartet state on the oxygenated iron, while the formation of a bridged peroxo intermediate is energetically favorable. Formation of peroxo-RR is more favorable than peroxo-Δ9D due to ligand field differences that can control the overlap of the redox active orbitals of the reduced sites with the π orbitals of dioxygen. This parallels experimental differences in the dioxygen reactivity of the reduced RR and Δ9D active sites.

AB - Ribonucleotide reductase (RR) catalyzes the first committed and rate-determining step in DNA biosynthesis, the reduction of ribonucleotides to deoxyribonucleotides. Fe(II) binding to the binuclear non-heme iron active site has been studied using a combination of circular dichroism (CD), magnetic circular dichroism (MCD), and variable-temperature variable-field (VTVH) MCD spectroscopies. These studies show that the two sites have significantly different metal binding affinities. This has also allowed a Mn(II)Fe(II) derivative to be prepared and studied by the above spectroscopies. The spectral features of the individual irons provide geometric and electronic structural insight into each metal site. Density functional calculations on reduced RR are correlated to the spectral features to obtain insight into its electronic structure. Parallel calculations are also performed on reduced stearoyl-acyl carier protein Δ9 desaturase (Δ9D) to correlate to prior spectral data and to the active site of RR. Differences in their dioxygen reactivities are investigated through reaction of these reduced sites with dioxygen, and possible electron-transfer pathways are evaluated. These results show that the active site of reduced RR consists of one 5- and one 4-coordinate iron with the 5C center having a higher binding affinity. Compared to reduced Δ9D, the presence of the 4C site energetically destabilizes reduced RR. Reaction of reduced RR with dioxygen to form a superoxide intermediate is energetically up hill as it results in an excited quartet state on the oxygenated iron, while the formation of a bridged peroxo intermediate is energetically favorable. Formation of peroxo-RR is more favorable than peroxo-Δ9D due to ligand field differences that can control the overlap of the redox active orbitals of the reduced sites with the π orbitals of dioxygen. This parallels experimental differences in the dioxygen reactivity of the reduced RR and Δ9D active sites.

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