ArticleNature2013
The catalytic mechanism for aerobic formation of methane by bacteria.
Article in Nature, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
30 citing papers in PubMed, 101 citations in OpenAlex.
- Hydrogen bond reorganization activates water radical chemistry for COScience advances · 2026Article
- Phosphate scarcity governs methane production in the global open ocean.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Diverse marineMarine life science & technology · 2025Article
- Proteomic evidence for aerobic methane production in groundwater by methylotrophic Methylotenera.The ISME journal · 2025Article
- Discovery of a New Class of Aminoacyl Radical Enzymes Expands Nature's Known Radical Chemistry.Journal of the American Chemical Society · 2024Article
- Modeling the Initiation Phase of the Catalytic Cycle in the Glycyl-Radical Enzyme Benzylsuccinate Synthase.The journal of physical chemistry. B · 2024Article
- The Mechanism of Inhibition of Pyruvate Formate Lyase by Methacrylate.Journal of the American Chemical Society · 2023Article
- Structural remodelling of the carbon-phosphorus lyase machinery by a dual ABC ATPase.Nature communications · 2023Article
- An Unusual Oxidative Rearrangement Catalyzed by a Divergent Member of the 2-Oxoglutarate-Dependent Dioxygenase Superfamily during Biosynthesis of Dehydrofosmidomycin.Angewandte Chemie (International ed. in English) · 2022Article
- Article
- RadicalSAM.org: A Resource to Interpret Sequence-Function Space and Discover New Radical SAM Enzyme Chemistry.ACS bio & med chem Au · 2022Article
- Article
- Microbial drivers of methane emissions from unrestored industrial salt ponds.The ISME journal · 2022Article
- Phosphate-limited ocean regions select for bacterial populations enriched in the carbon-phosphorus lyase pathway for phosphonate degradation.Environmental microbiology · 2019Article
- Methylphosphonate Oxidation inApplied and environmental microbiology · 2019Article
- Detection of 2-aminoethylphosphonic acid in suspended particles in an ultraoligotrophic lake: a two-dimensional nuclear magnetic resonance (2D-NMR) study.Environmental science and pollution research international · 2018Article
- Structures of the Carbon-Phosphorus Lyase Complex Reveal the Binding Mode of the NBD-like PhnK.Structure (London, England : 1993) · 2016Article
- Article
- Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase.Nature communications · 2015Article
- Spore photoproduct lyase: the known, the controversial, and the unknown.The Journal of biological chemistry · 2015Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Methane is a potent greenhouse gas that is produced in significant quantities by aerobic marine organisms. These bacteria apparently catalyse the formation of methane through the cleavage of the highly unreactive carbon-phosphorus bond in methyl phosphonate (MPn), but the biological or terrestrial source of this compound is unclear. However, the ocean-dwelling bacterium Nitrosopumilus maritimus catalyses the biosynthesis of MPn from 2-hydroxyethyl phosphonate and the bacterial C-P lyase complex is known to convert MPn to methane. In addition to MPn, the bacterial C-P lyase complex catalyses C-P bond cleavage of many alkyl phosphonates when the environmental concentration of phosphate is low. PhnJ from the C-P lyase complex catalyses an unprecedented C-P bond cleavage reaction of ribose-1-phosphonate-5-phosphate to methane and ribose-1,2-cyclic-phosphate-5-phosphate. This reaction requires a redox-active [4Fe-4S]-cluster and S-adenosyl-L-methionine, which is reductively cleaved to L-methionine and 5'-deoxyadenosine. Here we show that PhnJ is a novel radical S-adenosyl-L-methionine enzyme that catalyses C-P bond cleavage through the initial formation of a 5'-deoxyadenosyl radical and two protein-based radicals localized at Gly 32 and Cys 272. During this transformation, the pro-R hydrogen from Gly 32 is transferred to the 5'-deoxyadenosyl radical to form 5'-deoxyadenosine and the pro-S hydrogen is transferred to the radical intermediate that ultimately generates methane. A comprehensive reaction mechanism is proposed for cleavage of the C-P bond by the C-P lyase complex that uses a covalent thiophosphate intermediate for methane and phosphate formation.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.