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There is no single methane-oxidising enzyme for every environment. In oxygen, methane-oxidising bacteria use methane monooxygenase (MMO) to convert methane to methanol. Without oxygen, anaerobic methane-oxidising archaea use methyl-coenzyme M reductase (MCR) in reverse, oxidising methane through a different biochemical pathway. A 2025 study provided atomic-resolution structures of MCR from two groups of these archaea, revealing extensive chemical modifications—but it did not settle every question about how methane oxidation works.
Which enzyme oxidises methane?
The answer depends on whether the process is aerobic or anaerobic:
| Setting | Enzyme system | What it does |
|---|---|---|
| Aerobic, with oxygen | Methane monooxygenase (MMO) | Converts methane to methanol, inserting an oxygen atom into methane. |
| Anaerobic, without oxygen | Methyl-coenzyme M reductase (MCR) in anaerobic methanotrophic archaea (ANME) | Runs in reverse relative to its methane-producing relatives, oxidising methane in anoxic environments. |
These are distinct enzyme systems, not two names for the same enzyme. Anaerobic methane oxidation can occur as archaea transfer electrons to nitrate or metal oxides, or work in partnership with sulfate-reducing bacteria. The 2025 MCR structural study examined ANME enzymes from microbial enrichments; the organisms had not been isolated in culture, a constraint that has made their biochemistry difficult to study.
What the 2025 anaerobic MCR study discovered
Müller and colleagues reported atomic-resolution structures of MCR from freshwater nitrate-reducing ANME-2d and marine ANME-2c living with bacterial partners. Across the three MCR enzymes they studied, the authors identified seven post-translational modifications—chemical changes made to a protein after it is produced. Most notably, they found a previously unreported 3(S)-methylhistidine modification on the γ-chain of both ANME-2d enzymes. The study, published in Nature Communications on 5 September 2025, adds structural detail to an enzyme central to methane consumption in anoxic environments.
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What the structures say about the reaction
Krypton labelling did not reveal internal channels that would provide a route for alkanes to diffuse to the active site. The authors also propose that methanotrophic MCR uses the same radical reaction mechanism as methane-generating MCR homologues. That is a mechanistic inference based on the structural results and comparison with related enzymes—not experimental proof that every step of anaerobic methane oxidation is now understood.
Why a different 2025 MCR discovery is about methane production
A separate 2025 study examined how MCR is activated in methane-producing organisms. MCR is responsible for nearly all biological methane generation, and its active-site cofactor F430 contains nickel. Catalysis requires nickel in the Ni(I) state. The activation complex involves the small protein McrC and other methanogenic marker proteins, which activate MCR through an ATP-dependent process. The Nature paper reports three specialised iron-sulfur metal complexes involved in the activation mechanism.
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This activation result does not describe the newly resolved structure of methane-oxidising ANME MCR. Its relevance to oxidation is that MCR homologues in methanotrophs operate in reverse, as the Nature paper’s abstract notes. The authors also describe an evolutionary link between the activation machinery and nitrogenase; that is a relationship between systems with different functions, not evidence that methane oxidation and nitrogen fixation are the same process. TU Berlin’s account of the study explains the activation findings.
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How aerobic methane oxidation differs
In aerobic methanotrophic bacteria, MMO catalyses the conversion of methane to methanol. Work on soluble MMO has examined compound Q, an intermediate containing a pair of iron atoms in the Fe(IV) state. The intermediate reacts with methane and inserts one oxygen atom. A 2015 Nature study of compound Q discusses a methane C–H bond strength of 105 kcal mol−1 in this reaction context. That figure describes the bond discussed in that paper; it is not a rate, energy requirement for the whole reaction, or measurement of the 2025 MCR system.
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The 2015 paper also cited an estimate that MMO prevents approximately one billion tons of methane from entering the atmosphere annually. This is the paper’s published estimate, not a newly verified measurement of present-day methane flux. More recently, a 2026 study reported that copper acquisition from minerals promotes aerobic methane oxidation, with MMO identified as the enzyme catalysing the process. The Communications Earth & Environment paper concerns the aerobic pathway, not the anaerobic MCR structures.
Independent reader supportYour contribution helps us test, update, and keep practical guides available for everyone.What “mystery solved” does—and does not—mean
The strongest conclusion is specific: researchers obtained atomic-resolution structures for MCR from two groups of anaerobic methane-oxidising archaea and reported seven post-translational modifications across the three enzymes studied, including a novel modification on the ANME-2d γ-chain. The structures also provided evidence relevant to how the enzyme may work.
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They did not establish a single enzyme for all methane oxidation, nor experimentally settle the full reaction mechanism. MMO remains the relevant enzyme system for aerobic conversion of methane to methanol; the 2025 MCR structures concern anaerobic methane oxidation. Keeping those contexts separate is essential to understanding what has been resolved.
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