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Activation of Dimanganese Class Ib Ribonucleotide Reductase by Hydrogen Peroxide: Mechanistic Insights from Density Functional Theory
Stockholm University, Faculty of Science, Department of Physics.
Stockholm University, Faculty of Science, Department of Physics.
2013 (English)In: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 52, no 8, 4173-4184 p.Article in journal (Refereed) Published
Abstract [en]

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 Nrdl, 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 Nrdl may be to provide H2O2 on the correct time scale.

Place, publisher, year, edition, pages
2013. Vol. 52, no 8, 4173-4184 p.
National Category
Chemical Sciences
Research subject
Chemical Physics
Identifiers
URN: urn:nbn:se:su:diva-90370DOI: 10.1021/ic3008427ISI: 000317712000015OAI: oai:DiVA.org:su-90370DiVA: diva2:627710
Note

AuthorCount:2;

Available from: 2013-06-12 Created: 2013-06-03 Last updated: 2017-12-06Bibliographically approved
In thesis
1. Manganese and Iron Heterodimers and Homodimers in Enzymes: Insights from Density Functional Theory
Open this publication in new window or tab >>Manganese and Iron Heterodimers and Homodimers in Enzymes: Insights from Density Functional Theory
2012 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The enzyme ribonucleotide reductase (RNR) catalyzes the reduction of ribonucleotides to deoxyribonucleotides, the building blocks of DNA, and is essential for all organisms. Canonical class I RNR R2 proteins use a diiron cofactor to generate a tyrosyl radical, which is required for catalysis. Recent discoveries have established that the different subgroups of class I RNR employ different metal cofactors. Class Ib R2 (R2F) utilizes a dimanganese cofactor and a flavoprotein to generate the tyrosyl radical. Class Ic R2 (R2c) lacks the radical-bearing tyrosine, and instead has an oxidized heterodinuclear manganese-iron center, the first known redox active MnFe cofactor. A second group of MnFe proteins with different functions, denoted R2-like ligand binding oxidases (R2lox), was later identified. R2lox proteins are capable of performing two-electron oxidations and are believed to be hydrocarbon oxidases. In the present thesis density functional theory, a quantum mechanical method, is employed to study the manganese and iron heterodimers and homodimers in the R2 and R2lox proteins, with the aim to shed light on the mechanistic details and stress the main features of the alternative metal centers. Some of the questions addressed are the radical generation with the homodimers and heterodimer in R2, the radical transfer between R2 and the RNR catalytic subunit, and the function of R2lox. A Mn(IV)Fe(III) state is shown to be an equally strong oxidant as a tyrosyl radical, giving a rationalization for the presence of the heterodimer in R2c. A reaction mechanism for the formation of an unprecedented tyrosine-valine crosslink catalyzed by the heterodimer in R2lox is modeled, and the potential of the protein to perform hydroxylations of hydrocarbons based on calculated barriers for methane hydroxylation is discussed. An energetically possible reaction mechanism is suggested for activation of dimanganese R2F by hydrogen peroxide, and a hypothetical role of the flavoprotein in radical generation is proposed.

Place, publisher, year, edition, pages
Stockholm: Department of Physics, Stockholm University, 2012. 86 p.
Keyword
Ribonucleotide reductase, manganese, iron, density functional theory
National Category
Theoretical Chemistry Biochemistry and Molecular Biology Inorganic Chemistry
Research subject
Chemical Physics
Identifiers
urn:nbn:se:su:diva-78814 (URN)978-91-7447-543-2 (ISBN)
Public defence
2012-09-14, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 10:00 (English)
Opponent
Supervisors
Note

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4: Submitted. Paper 5: Manuscript.

Available from: 2012-08-23 Created: 2012-08-13 Last updated: 2015-10-27Bibliographically approved

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