Mechanistic Investigation of Oxidative Decarboxylation Catalyzed by Two Iron(II)- and 2-Oxoglutarate-Dependent Enzymes

Huang, Jhih‐Liang; Tang, Yijie; Yu, Cheng-Ping; Sanyal, Dev; Jia, Xinglin; Liu, Xinyu; Guo, Yisong; Chang, Wei‐chen

doi:10.1021/acs.biochem.8b00115

Cited by 34 publications

(40 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Herein, we employ a complementary approach including mechanistic probe design, transient kinetics, CW EPR, 2D pulsed EPR hyperfine sublevel correlation spectroscopy (HYSCORE), Mössbauer, and LC-UV/MS to elucidate the plausible pathways of this novel reaction. Different from the originally proposed hydroxylation and CO 2 elimination pathway, 12,13 our results suggest that alternate pathways involving a benzylic carbocation or an electron transfer coupled decarboxylation is likely to be utilized to trigger the olefination (Scheme 1).…”

contrasting

confidence: 89%

Elucidating the Reaction Pathway of Decarboxylation-Assisted Olefination Catalyzed by a Mononuclear Non-Heme Iron Enzyme

Tang

Cha

et al. 2018

J. Am. Chem. Soc.

Self Cite

View full text Add to dashboard Cite

Installation of olefins into molecules is a key transformation in organic synthesis. The recently discovered decarboxylation-assisted olefination in the biosynthesis of rhabduscin by a mononuclear non-heme iron enzyme (P.IsnB) represents a novel approach in olefin construction. This method is commonly employed in natural product biosynthesis. Herein, we demonstrate that a ferryl intermediate is used for C–H activation at the benzylic position of the substrate. We further establish that P.IsnB reactivity can be switched from olefination to hydroxylation using electron-withdrawing groups appended on the phenyl moiety of the analogues. These experimental observations imply that a pathway involving an initial C–H activation followed by a benzylic carbocation species or by electron transfer coupled β- scission is likely utilized to complete C=C bond formation.

show abstract

contrasting

confidence: 89%

Elucidating the Reaction Pathway of Decarboxylation-Assisted Olefination Catalyzed by a Mononuclear Non-Heme Iron Enzyme

Tang

Cha

et al. 2018

J. Am. Chem. Soc.

Self Cite

View full text Add to dashboard Cite

show abstract

“…The general knowledge about the catalytic mechanism of non-heme dioxygenases is constantly expanding with new results. Multiple kinetic and spectroscopic studies have evaluated the rate of the formation and decay of the Fe(IV)−oxo intermediate [29][30][31][32] and the efficiency of the binding of co-substrate αKG, co-product Suc, and metal ion to the enzyme [12,15,33]. Some authors have shown the importance of protein dynamics for efficient co-substrate binding and catalysis [16,17].…”

Section: Discussionmentioning

confidence: 99%

A Single-Turnover Kinetic Study of DNA Demethylation Catalyzed by Fe(II)/α-Ketoglutarate-Dependent Dioxygenase AlkB

2019

View full text Add to dashboard Cite

AlkB is a Fe(II)/α-ketoglutarate-dependent dioxygenase that repairs some alkylated bases of DNA and RNA in Escherichia coli. In the course of catalysis, oxidation of a co-substrate (α-ketoglutarate, αKG) leads to the formation of a highly reactive 'oxyferryl' enzyme-bound intermediate, Fe(IV) = O, ensuring hydroxylation of the alkyl nucleobase adducts. Previous studies have revealed that AlkB is a flexible protein and can adopt different conformations during interactions with cofactors and DNA. To assess the conformational dynamics of the enzyme in complex with single-or double-stranded DNA in real-time mode, we employed the stopped-flow fluorescence method. N 1 -Methyladenine (m 1 A) introduced into a sequence of 15-mer oligonucleotides was chosen as the specific damage. Single-turnover kinetics were monitored by means of intrinsic fluorescence of the protein's Trp residues, fluorescent base analogue 2-aminopurine (2aPu), and a dye-quencher pair (FAM/BHQ1). For all the fluorescent labels, the fluorescent traces showed several phases of consistent conformational changes, which were assigned to specific steps of the enzymatic process. These data offer an overall picture of the structural dynamics of AlkB and DNA during their interaction.

show abstract

“…An oxidative decarboxylation by an Fe/ α -KG-dependent dioxygenase has been characterized recently. 475 A proposed mechanism is presented in Figure 151.…”

Section: C-c Bond Breaking Reactionsmentioning

confidence: 99%

Formation and Cleavage of C–C Bonds by Enzymatic Oxidation–Reduction Reactions

2018

View full text Add to dashboard Cite

Many oxidation-reduction (redox) enzymes, particularly oxygenases, have roles in reactions that make and break C-C bonds. The list includes cytochrome P450 and other heme-based monooxygenases, heme-based dioxygenases, nonheme iron mono- and dioxygenases, flavoproteins, radical S-adenosylmethionine enzymes, copper enzymes, and peroxidases. Reactions involve steroids, intermediary metabolism, secondary natural products, drugs, and industrial and agricultural chemicals. Many C-C bonds are formed via either (i) coupling of diradicals or (ii) generation of unstable products that rearrange. C-C cleavage reactions involve several themes: (i) rearrangement of unstable oxidized products produced by the enzymes, (ii) oxidation and collapse of radicals or cations via rearrangement, (iii) oxygenation to yield products that are readily hydrolyzed by other enzymes, and (iv) activation of O in systems in which the binding of a substrate facilitates O activation. Many of the enzymes involve metals, but of these, iron is clearly predominant.

show abstract

Mechanistic Investigation of Oxidative Decarboxylation Catalyzed by Two Iron(II)- and 2-Oxoglutarate-Dependent Enzymes

Cited by 34 publications

References 24 publications

Elucidating the Reaction Pathway of Decarboxylation-Assisted Olefination Catalyzed by a Mononuclear Non-Heme Iron Enzyme

Elucidating the Reaction Pathway of Decarboxylation-Assisted Olefination Catalyzed by a Mononuclear Non-Heme Iron Enzyme

A Single-Turnover Kinetic Study of DNA Demethylation Catalyzed by Fe(II)/α-Ketoglutarate-Dependent Dioxygenase AlkB

Formation and Cleavage of C–C Bonds by Enzymatic Oxidation–Reduction Reactions

Contact Info

Product

Resources

About