The radical mechanism of biological methane synthesis by methyl-coenzyme M reductase

Abstract

Methyl-coenzyme M reductase, the rate-limiting enzyme in methanogenesis and anaerobic methane oxidation, is responsible for the biological production of more than 1 billion tons of methane per year. The mechanism of methane synthesis is thought to involve either methyl-nickel(III) or methyl radical/Ni(II)-thiolate intermediates. We employed transient kinetic, spectroscopic, and computational approaches to study the reaction between the active Ni(I) enzyme and substrates. Consistent with the methyl radical-based mechanism, there was no evidence for a methyl-Ni(III) species; furthermore, magnetic circular dichroism spectroscopy identified the Ni(II)-thiolate intermediate. Temperature-dependent transient kinetics also closely matched density functional theory predictions of the methyl radical mechanism. Identifying the key intermediate in methanogenesis provides fundamental insights to develop better catalysts for producing and activating an important fuel and potent greenhouse gas.

Myoglobin Reconstituted with Ni Tetradehydrocorrin as a Methane‐Generating Model of Methyl‐coenzyme M Reductase

“…Theenzymatic reaction has been investigated in experimental and theoretical studies. [8] Although methane generation by F430 and its model complexes were demonstrated, [14][15][16][17] much stronger reductants,s uch as Ti III citrate and Na amalgam, were found to be required relative to the thiol-based reductant employed by native MCR. Tw od ifferent plausible pathways through aN i III ÀCH 3 intermediate or atransient methyl radical species and Ni II intermediate have been proposed.…”

“…Theenzymatic reaction has been investigated in experimental and theoretical studies. [3][4][5][6][7][8][9][10][11][12][13] However,t he large and complex structure of MCR complicates the elucidation of the reaction mechanism. Tw od ifferent plausible pathways through aN i III ÀCH 3 intermediate or atransient methyl radical species and Ni II intermediate have been proposed.…”

Methane—make it or break it

“…The MCR catalytic cycle begins with F 430 in the reduced Ni(I) form (4), but what happens next has been unclear. On page 953 of this issue, Wongnate et al (5) report evidence for a Ni(II)-thiolate intermediate.…”

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

“…In this mechanism, Ni I attacks methyl-S-CoM to produce am ethyl radical and CoM-S-Ni II (Figure 1b). [7] Thec atalytic mechanism actually used can be experimentally identified only by determining the presence or absence of possible key catalytic intermediates.S uch information had never been reported until the recent publication of Wongnate et al [7] Wongnate et al [7] identified CoM-S-Ni II after half at urnover of the MCR reaction by using spectroscopic methods. Thet hird catalytic mechanism proposed is av ariation of the second mechanism, in which Ni I attacks methyl-S-CoM to form am ethyl anion, and the methyl anion accepts ap roton from CoB-SH to produce methane.…”

“…Fore xample,t he crystal structure of the active MCR red1 form has to be solved. In the catalytic mechanism proposed by Wongnate et al, [7] theheterodisulfide CoM-S-S-CoB radical anion is bound to Ni at the CoM-sulfur. Furthermore,M CR contains many modified amino acids near the active site,namley,four methylated amino acids,d idehydroaspartate, [9] and thioglycine,t he main-chain carbonyl oxygen of which is exchanged with sulfur.…”