The Reaction Mechanism of Methyl-Coenzyme M Reductase

Wongnate, Thanyaporn; Ragsdale, Stephen W.

doi:10.1074/jbc.m115.636761

Cited by 54 publications

(42 citation statements)

References 46 publications

(87 reference statements)

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“…To do this we employed high-throughput amplicon sequencing of mcrA gene cDNA. Methyl co-enzyme reductase (MCR) is a multi-subunit enzyme of methanogenic archaea which catalyses the final step in CH 4 formation and the initial step in anaerobic CH 4 oxidation 15 . It reduces methyl-coenzyme M (CH3-S-CoM) by 7-mercaptoheptanoylthreonine phosphate (H-S-HTP) 16 .…”

Section: Introductionmentioning

confidence: 99%

Plane of nutrition affects the phylogenetic diversity and relative abundance of transcriptionally active methanogens in the bovine rumen

McGovern¹,

McCabe²,

Cormican³

et al. 2017

Sci Rep

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Methane generated during enteric fermentation in ruminant livestock species is a major contributor to global anthropogenic greenhouse gas emissions. A period of moderate feed restriction followed by ad libitum access to feed is widely applied in cattle management to exploit the animal’s compensatory growth potential and reduce feed costs. In the present study, we utilised microbial RNA from rumen digesta samples to assess the phylogenetic diversity of transcriptionally active methanogens from feed-restricted and non-restricted animals. To determine the contribution of different rumen methanogens to methanogenesis during dietary restriction of cattle, we conducted high-throughput mcrA cDNA amplicon sequencing on an Illumina MiSeq and analysed both the abundance and phylogenetic origin of different mcrA cDNA sequences. When compared to their unrestricted contemporaries, in feed-restricted animals, the methanogenic activity, based on mcrA transcript abundance, of Methanobrevibacter gottschalkii clade increased while the methanogenic activity of the Methanobrevibacter ruminantium clade and members of the Methanomassiliicoccaceae family decreased. This study shows that the quantity of feed consumed can evoke large effects on the composition of methanogenically active species in the rumen of cattle. These data potentially have major implications for targeted CH4 mitigation approaches such as anti-methanogen vaccines and/or tailored dietary management.

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Section: Introductionmentioning

confidence: 99%

Plane of nutrition affects the phylogenetic diversity and relative abundance of transcriptionally active methanogens in the bovine rumen

McGovern¹,

McCabe²,

Cormican³

et al. 2017

Sci Rep

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“…Understanding the mechanisms of mMCR and aMCR is critical to realizing this possibility. The mMCR catalytic cycle begins with F 430 in the reduced Ni(I) form, MCR red1 , and it is known that methyl-SCoM, the methyl donor, binds first followed by CoBSH, the electron donor, yielding the CoBS-SCoM heterodisulfide and methane [25,46]. Following binding of methyl-SCoM to the electron paramagnetic resonance (EPR)-active MCR red1 state, two possible Ni-bound intermediates have been proposed, an EPR-active methyl-Ni(III) species (mechanism I) and an EPR-silent Ni(II)-thiolate (mechanism II) (Figure 3) [14,25,29].…”

Section: Mcr: Advances In Recombinant Expression and Mechanismmentioning

confidence: 99%

Biocatalysts for methane conversion: big progress on breaking a small substrate

Lawton

Rosenzweig

2016

Current Opinion in Chemical Biology

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Nature utilizes two groups of enzymes to catalyze methane conversions, methyl-coenzyme M reductases (MCRs) and methane monooxygenases (MMOs). These enzymes have been difficult to incorporate into industrial processes due to their complexity, poor stability, and lack of recombinant tractability. Despite these issues, new ways of preparing and stabilizing these enzymes have recently been discovered, and new mechanistic insight into how MCRs and MMOs break the C-H bond in nature’s most inert hydrocarbon haved been obtained. This review focuses on recent findings in the methane biocatalysis field, and discusses the impact of these finding on designing MMO and MCR-based biotechnologies.

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“…Methanogenic Mcrs are (αβγ) 2 hexamers that include two highly conserved active sites, where the nickel-containing cyclic tetrapyrrole prosthetic group known as cofactor F 430 is noncovalently bound (Ermler et al, 1997;Grabarse et al, 2000). For methanogenesis, CH 3 -S-CoM must bind prior to HS-CoB to form a ternary complex (Wongnate and Ragsdale, 2015), and the nickel of cofactor F 430 must be present in the Ni(I) state . The ordered binding for Mcr is facilitated through numerous important enzyme conformational changes (Grabarse et al, 2001;Cedervall et al, 2010;Ebner et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

“…In a second case study (CS2), we considered that Mcr may be limited by formation of the methyl radical at high temperatures (>45 • C; Wongnate et al, 2016). In the third study (CS3), published Mcr binding and reaction rates were used to postulate that Mcr kinetics is limited by CH 3 -S-CoM unbinding (Ellermann et al, 1988;Scheller et al, 2010;Chen et al, 2012;Wongnate and Ragsdale, 2015;Wongnate et al, 2016). A final investigation (CS4) examined the possibility that AOM is limited by the second step of the reverse aceticlastic pathway involving a methyl-tetrahydrosarcinapterin:coenzyme M (CH 3 -H 4 SPT:HS-CoM) methyltransferase (Mtr) (Benedict et al, 2012;Vepachedu and Ferry, 2012;Nazem-Bokaee et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Computationally Exploring and Alleviating the Kinetic Bottlenecks of Anaerobic Methane Oxidation

Grisewood

Ferry

Maranas

2018

Front. Environ. Sci.

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The anaerobic oxidation of methane (AOM) by methanotrophic archaea offers a carbon-and electron-efficient route for the production of acetate, which can be further processed to yield liquid fuels. This acetate production pathway is initiated by methyl-coenzyme M reductase, but this enzyme can only oxidize trace amounts of methane ex situ. Efforts to improve the kinetics of methyl-coenzyme M reductase through enzyme engineering have been, in part, limited by low-throughput assays. Computational enzyme engineering can circumvent this limitation through the design of smaller, more focused libraries, which have a higher probability of success. By drawing from a new consensus reaction mechanism for Mcr and newly published data, the first complete kinetic characterization of the Mcr reaction mechanism is proposed. In the developed kinetic description, the rate of methyl-coenzyme M unbinding is proposed to limit Mcr overall kinetics. A revised computational method was devised to improve the rate of product release while not disrupting the reaction's activated complex. Large, hydrophobic amino acids that can assume multiple conformations were predicted to be most effective at reaching this design goal. Other rate-limiting scenarios were examined, such as (i) high-temperature (>45 • C), (ii) methyltransferase-limiting, and (iii) ineffective cofactor F 430 binding. A separate library of designs is put forth for each one of these cases. These efforts mark the first computational attempt at redesigning methyl-coenzyme M reductase for reversed or improved activity, which if experimentally validated, would have a cross-cutting impact across the biotechnology and biochemistry fields by debottlenecking anaerobic methane oxidation.

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The Reaction Mechanism of Methyl-Coenzyme M Reductase

Cited by 54 publications

References 46 publications

Plane of nutrition affects the phylogenetic diversity and relative abundance of transcriptionally active methanogens in the bovine rumen

Plane of nutrition affects the phylogenetic diversity and relative abundance of transcriptionally active methanogens in the bovine rumen

Biocatalysts for methane conversion: big progress on breaking a small substrate

Computationally Exploring and Alleviating the Kinetic Bottlenecks of Anaerobic Methane Oxidation

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