The Biological Methane‐Forming Reaction: Mechanism Confirmed Through Spectroscopic Characterization of a Key Intermediate

Shima, Seigo

doi:10.1002/anie.201606269

Cited by 10 publications

(5 citation statements)

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“…The key difference between them is how Ni(I) attacks methyl-S-CoM 82) (Figure 6c). Recent biochemical and spectroscopic analyses detected the latter intermediate, which strongly supports the methyl-radical mechanism (95,130). EPR and UV/visible spectroscopic data showed that only one of the two active sites of Mcr is active, suggesting cooperativity between them similar to that in an opposed piston engine (32,116).…”

Section: Catalytic Mechanismmentioning

confidence: 63%

Structural Basis of Hydrogenotrophic Methanogenesis

Shima

Huang

Wagner

et al. 2020

Annu. Rev. Microbiol.

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Most methanogenic archaea use the rudimentary hydrogenotrophic pathway—from CO2 and H2 to methane—as the terminal step of microbial biomass degradation in anoxic habitats. The barely exergonic process that just conserves sufficient energy for a modest lifestyle involves chemically challenging reactions catalyzed by complex enzyme machineries with unique metal-containing cofactors. The basic strategy of the methanogenic energy metabolism is to covalently bind C1 species to the C1 carriers methanofuran, tetrahydromethanopterin, and coenzyme M at different oxidation states. The four reduction reactions from CO2 to methane involve one molybdopterin-based two-electron reduction, two coenzyme F420–based hydride transfers, and one coenzyme F430–based radical process. For energy conservation, one ion-gradient-forming methyl transfer reaction is sufficient, albeit supported by a sophisticated energy-coupling process termed flavin-based electron bifurcation for driving the endergonic CO2 reduction and fixation. Here, we review the knowledge about the structure-based catalytic mechanism of each enzyme of hydrogenotrophic methanogenesis. Expected final online publication date for the Annual Review of Microbiology, Volume 74 is September 8, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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Section: Catalytic Mechanismmentioning

confidence: 63%

Structural Basis of Hydrogenotrophic Methanogenesis

Shima

Huang

Wagner

et al. 2020

Annu. Rev. Microbiol.

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“…Moreover, they did not find any spectroscopic evidence for the methyl‐Ni III species, which is related to mechanism I. As discussed previously, the mechanistic picture of MCR is still incomplete and awaits further clarification.…”

Section: Ni‐dependent Enzymesmentioning

confidence: 86%

Computational Insights into the Reaction Mechanisms of Nickel‐Catalyzed Hydrofunctionalizations and Nickel‐Dependent Enzymes

Zhang

Chung

2018

Asian J Org Chem

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For several decades, transition-metal catalysis has been ap opular methodf or many functional group transformations in organicc hemistry.R ecent developments in sustainability and applicationso fe arth-abundant metals have resulted in as ynthetic renaissance and have attracted considerable interest in less toxic and inexpensive first-row transition-metal catalysts such as nickel. Herein, we highlight some recent computationali nsights into the reactionm ech-anismso fN i-catalyzed hydrofunctionalizations (i.e.,h ydrogenation,h ydrovinylation, hydroacylation, hydroheteroarylation, hydrosilylation, and hydroalkoxylation) and Ni-dependent enzymes (i.e.,l actater acemase, methyl-CoM reductase, and [NiFe]-hydrogenase). These computational studies provide insightsi nto these reactionm echanisms and thus assist in the developmentand design of sustainable catalysts.Scheme3.Ni-catalyzed asymmetric hydrogenationofb-amino nitroolefins (TFE = 2,2,2-trifluoroethanol, TON = turnover number).Scheme4.Computedf avorable catalytic cycle for the Ni-catalyzed asymmetric hydrogenation in the presence of the (S)-binapine ligand. Relative Gibbs free energy valuesare shown.Scheme5.Computedf ree energies of proposed key catalyticcycle for the Ni-catalyzed hydrogenation in the presence of ad imeric Ni speciesa nd the (S)-binapine ligand (only the key transition states were computed).Scheme6.[Si II (Xant)Si II ]Ni(h 2 -1,3-cod)-catalyzedolefin hydrogenation.Scheme20. The proposed proton-coupled electron transfer mechanism for lactate racemization (see Ref.[35]). Scheme21. (a) Methane formation reaction catalyzed by MCR and (b) the active-site structure of F 430 .Scheme22. Different proposed mechanisms for methanef ormation catalyzed by MCR (see Ref. [49]).

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“…Carbon-nickel bonds had also been discussed as possible reaction intermediates in the mechanism of methyl coenzyme M reductase [103,104], but recent findings reveal a methyl radical intermediate [104,105]. Carbon-metal bonds have also been proposed in O 2 -tolerant, Cu-and Mo-dependent CO-oxidizing enzymes [106], which are unrelated to the anaerobic CODH depicted in Figure 1, but the case is unresolved.…”

Section: Carbon-metal Bonds In Ancient Metabolic Pathwaysmentioning

confidence: 99%

Carbon–Metal Bonds: Rare and Primordial in Metabolism

Martin

2019

Trends in Biochemical Sciences

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The Biological Methane‐Forming Reaction: Mechanism Confirmed Through Spectroscopic Characterization of a Key Intermediate

Cited by 10 publications

References 11 publications

Structural Basis of Hydrogenotrophic Methanogenesis

Structural Basis of Hydrogenotrophic Methanogenesis

Computational Insights into the Reaction Mechanisms of Nickel‐Catalyzed Hydrofunctionalizations and Nickel‐Dependent Enzymes

Carbon–Metal Bonds: Rare and Primordial in Metabolism

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