Literature DB >> 22511515

Electronic structure analysis of the oxygen-activation mechanism by Fe(II)- and α-ketoglutarate (αKG)-dependent dioxygenases.

Shengfa Ye1, Christoph Riplinger, Andreas Hansen, Carsten Krebs, J Martin Bollinger, Frank Neese.   

Abstract

α-Ketoglutarate (αKG)-dependent nonheme iron enzymes utilize a high-spin (HS) ferrous center to couple the activation of oxygen to the decarboxylation of the cosubstrate αKG to yield succinate and CO(2), and to generate a high-valent ferryl species that then acts as an oxidant to functionalize the target C-H bond. Herein a detailed analysis of the electronic-structure changes that occur in the oxygen activation by this enzyme was performed. The rate-limiting step, which is identical on the septet and quintet surfaces, is the nucleophilic attack of the distal O atom of the O(2) adduct on the carbonyl group in αKG through a bicyclic transition state ((5, 7) TS1). Due to the different electronic structures in (5, 7) TS1, the decay of (7)TS1 leads to a ferric oxyl species, which undergoes a rapid intersystem crossing to form the ferryl intermediate. By contrast, a HS ferrous center ligated by a peroxosuccinate is obtained on the quintet surface following (5)TS1. Thus, additional two single-electron transfer steps are required to afford the same Fe(IV)-oxo species. However, the triplet reaction channel is catalytically irrelevant. The biological role of αKG played in the oxygen-activation reaction is dual. The αKG LUMO (C=O π*) serves as an electron acceptor for the nucleophilic attack of the superoxide monoanion. On the other hand, the αKG HOMO (C1-C2 σ) provides the second and third electrons for the further reduction of the superoxide. In addition to density functional theory, high-level ab initio calculations have been used to calculate the accurate energies of the critical points on the alternative potential-energy surfaces. Overall, the results delivered by the ab initio calculations are largely parallel to those obtained with the B3LYP density functional, thus lending credence to our conclusions.
Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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Year:  2012        PMID: 22511515      PMCID: PMC3955955          DOI: 10.1002/chem.201102829

Source DB:  PubMed          Journal:  Chemistry        ISSN: 0947-6539            Impact factor:   5.236


  72 in total

1.  Mechanistic Studies of the Formation and Decay of Diiron(III) Peroxo Complexes in the Reaction of Diiron(II) Precursors with Dioxygen.

Authors:  Andrew L. Feig; Michael Becker; Siegfried Schindler; Rudi van Eldik; Stephen J. Lippard
Journal:  Inorg Chem       Date:  1996-04-24       Impact factor: 5.165

2.  Histone demethylation by a family of JmjC domain-containing proteins.

Authors:  Yu-ichi Tsukada; Jia Fang; Hediye Erdjument-Bromage; Maria E Warren; Christoph H Borchers; Paul Tempst; Yi Zhang
Journal:  Nature       Date:  2005-12-18       Impact factor: 49.962

3.  Insight into the mechanism of an iron dioxygenase by resolution of steps following the FeIV=HO species.

Authors:  Piotr K Grzyska; Evan H Appelman; Robert P Hausinger; Denis A Proshlyakov
Journal:  Proc Natl Acad Sci U S A       Date:  2010-02-10       Impact factor: 11.205

4.  Targeting of HIF-alpha to the von Hippel-Lindau ubiquitylation complex by O2-regulated prolyl hydroxylation.

Authors:  P Jaakkola; D R Mole; Y M Tian; M I Wilson; J Gielbert; S J Gaskell; A von Kriegsheim; H F Hebestreit; M Mukherji; C J Schofield; P H Maxwell; C W Pugh; P J Ratcliffe
Journal:  Science       Date:  2001-04-05       Impact factor: 47.728

5.  Intermediates in the oxygenation of a nonheme diiron(II) complex, including the first evidence for a bound superoxo species.

Authors:  Xiaopeng Shan; Lawrence Que
Journal:  Proc Natl Acad Sci U S A       Date:  2005-03-31       Impact factor: 11.205

6.  Requirements for alpha-ketoglutarate, ferrous ion and ascorbate by collagen proline hydroxylase.

Authors:  J J Hutton; A L Trappel; S Udenfriend
Journal:  Biochem Biophys Res Commun       Date:  1966-07-20       Impact factor: 3.575

7.  X-ray crystal structure of Escherichia coli taurine/alpha-ketoglutarate dioxygenase complexed to ferrous iron and substrates.

Authors:  Jonathan M Elkins; Matthew J Ryle; Ian J Clifton; Julie C Dunning Hotopp; John S Lloyd; Nicolai I Burzlaff; Jack E Baldwin; Robert P Hausinger; Peter L Roach
Journal:  Biochemistry       Date:  2002-04-23       Impact factor: 3.162

8.  Mechanism of dioxygen activation in 2-oxoglutarate-dependent enzymes: a hybrid DFT study.

Authors:  Tomasz Borowski; Arianna Bassan; Per E M Siegbahn
Journal:  Chemistry       Date:  2004-02-20       Impact factor: 5.236

9.  Substrate positioning controls the partition between halogenation and hydroxylation in the aliphatic halogenase, SyrB2.

Authors:  Megan L Matthews; Christopher S Neumann; Linde A Miles; Tyler L Grove; Squire J Booker; Carsten Krebs; Christopher T Walsh; J Martin Bollinger
Journal:  Proc Natl Acad Sci U S A       Date:  2009-10-06       Impact factor: 11.205

10.  Substrate-triggered formation and remarkable stability of the C-H bond-cleaving chloroferryl intermediate in the aliphatic halogenase, SyrB2.

Authors:  Megan L Matthews; Courtney M Krest; Eric W Barr; Frédéric H Vaillancourt; Christopher T Walsh; Michael T Green; Carsten Krebs; J Martin Bollinger
Journal:  Biochemistry       Date:  2009-05-26       Impact factor: 3.162

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  25 in total

1.  Two Distinct Mechanisms for C-C Desaturation by Iron(II)- and 2-(Oxo)glutarate-Dependent Oxygenases: Importance of α-Heteroatom Assistance.

Authors:  Noah P Dunham; Wei-Chen Chang; Andrew J Mitchell; Ryan J Martinie; Bo Zhang; Jonathan A Bergman; Lauren J Rajakovich; Bo Wang; Alexey Silakov; Carsten Krebs; Amie K Boal; J Martin Bollinger
Journal:  J Am Chem Soc       Date:  2018-06-04       Impact factor: 15.419

2.  Epoxidation Catalyzed by the Nonheme Iron(II)- and 2-Oxoglutarate-Dependent Oxygenase, AsqJ: Mechanistic Elucidation of Oxygen Atom Transfer by a Ferryl Intermediate.

Authors:  Jikun Li; Hsuan-Jen Liao; Yijie Tang; Jhih-Liang Huang; Lide Cha; Te-Sheng Lin; Justin L Lee; Igor V Kurnikov; Maria G Kurnikova; Wei-Chen Chang; Nei-Li Chan; Yisong Guo
Journal:  J Am Chem Soc       Date:  2020-03-16       Impact factor: 15.419

3.  Evidence that the fosfomycin-producing epoxidase, HppE, is a non-heme-iron peroxidase.

Authors:  Chen Wang; Wei-chen Chang; Yisong Guo; Hui Huang; Spencer C Peck; Maria E Pandelia; Geng-min Lin; Hung-wen Liu; Carsten Krebs; J Martin Bollinger
Journal:  Science       Date:  2013-10-10       Impact factor: 47.728

Review 4.  Mono- and binuclear non-heme iron chemistry from a theoretical perspective.

Authors:  Tibor András Rokob; Jakub Chalupský; Daniel Bím; Prokopis C Andrikopoulos; Martin Srnec; Lubomír Rulíšek
Journal:  J Biol Inorg Chem       Date:  2016-05-26       Impact factor: 3.358

5.  Evidence for Modulation of Oxygen Rebound Rate in Control of Outcome by Iron(II)- and 2-Oxoglutarate-Dependent Oxygenases.

Authors:  Juan Pan; Eliott S Wenger; Megan L Matthews; Christopher J Pollock; Minakshi Bhardwaj; Amelia J Kim; Benjamin D Allen; Robert B Grossman; Carsten Krebs; J Martin Bollinger
Journal:  J Am Chem Soc       Date:  2019-09-16       Impact factor: 15.419

6.  Visualizing the Reaction Cycle in an Iron(II)- and 2-(Oxo)-glutarate-Dependent Hydroxylase.

Authors:  Andrew J Mitchell; Noah P Dunham; Ryan J Martinie; Jonathan A Bergman; Christopher J Pollock; Kai Hu; Benjamin D Allen; Wei-Chen Chang; Alexey Silakov; J Martin Bollinger; Carsten Krebs; Amie K Boal
Journal:  J Am Chem Soc       Date:  2017-09-20       Impact factor: 15.419

7.  Hydrogen-bonding effects on the reactivity of [X-Fe(III)-O-Fe(IV)═O] (X = OH, F) complexes toward C-H bond cleavage.

Authors:  Genqiang Xue; Caiyun Geng; Shengfa Ye; Adam T Fiedler; Frank Neese; Lawrence Que
Journal:  Inorg Chem       Date:  2013-03-15       Impact factor: 5.165

8.  Spectroscopic Evidence for the Two C-H-Cleaving Intermediates of Aspergillus nidulans Isopenicillin N Synthase.

Authors:  Esta Tamanaha; Bo Zhang; Yisong Guo; Wei-Chen Chang; Eric W Barr; Gang Xing; Jennifer St Clair; Shengfa Ye; Frank Neese; J Martin Bollinger; Carsten Krebs
Journal:  J Am Chem Soc       Date:  2016-07-05       Impact factor: 15.419

Review 9.  Imposing function down a (cupin)-barrel: secondary structure and metal stereochemistry in the αKG-dependent oxygenases.

Authors:  John A Hangasky; Cornelius Y Taabazuing; Meaghan A Valliere; Michael J Knapp
Journal:  Metallomics       Date:  2013-04       Impact factor: 4.526

Review 10.  Mechanisms of tryptophan and tyrosine hydroxylase.

Authors:  Kenneth M Roberts; Paul F Fitzpatrick
Journal:  IUBMB Life       Date:  2013-02-26       Impact factor: 3.885

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