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Entry
Name
Methane metabolism
Description
Methane is metabolized principally by methanotrophs and methanogens in the global carbon cycle. Methanotrophs consume methane as the only source of carbon, while methanogens produce methane as a metabolic byproduct. Methylotrophs, which are microorganisms that can obtain energy for growth by oxidizing one-carbon compounds, such as methanol and methane, are situated between methanotrophs and methanogens. Methanogens can obtain energy for growth by converting a limited number of substrates to methane under anaerobic conditions. Three types of methanogenic pathways are known: CO2 to methane [MD:
M00567 ], methanol to methane [MD:
M00356 ], and acetate to methane [MD:
M00357 ]. Methanogens use 2-mercaptoethanesulfonate (CoM; coenzyme M) as the terminal methyl carrier in methanogenesis and have four enzymes for CoM biosynthesis [MD:
M00358 ]. Coenzyme B-Coenzyme M heterodisulfide reductase (Hdr), requiring for the final reaction steps of methanogenic pathway, is divided into two types: cytoplasmic HdrABC in most methanogens and membrane-bound HdrED in Methanosarcina species. In methanotrophs and methyltrophs methane is oxidized to form formaldehyde, which is at the diverging point for further oxidation to CO2 for energy source and assimilation for biosynthesis. There are three pathways that convert formaldehyde to C2 or C3 compounds: serine pathway [MD:
M00346 ], ribulose monophosphate pathway [MD:
M00345 ], and xylulose monophosphate pathway [MD:
M00344 ]. The first two pathways are found in prokaryotes and the third is found in yeast. As a special case of methylotrophs, various amines can be used as carbon sources in trimethylamine metabolism [MD:
M00563 ].
Class
Metabolism; Energy metabolism
BRITE hierarchy
Pathway map
Ortholog table
Module
M00020 Serine biosynthesis, glycerate-3P => serine [PATH:ko00680 ]
M00174 Methane oxidation, methanotroph, methane => formaldehyde [PATH:ko00680 ]
M00344 Formaldehyde assimilation, xylulose monophosphate pathway [PATH:ko00680 ]
M00345 Formaldehyde assimilation, ribulose monophosphate pathway [PATH:ko00680 ]
M00563 Methanogenesis, methylamine/dimethylamine/trimethylamine => methane [PATH:ko00680 ]
M00608 2-Oxocarboxylic acid chain extension, 2-oxoglutarate => 2-oxoadipate => 2-oxopimelate => 2-oxosuberate [PATH:ko00680 ]
Other DBs
Orthology
K16160 methane monooxygenase regulatory protein B
K16162 methane monooxygenase component D
K10945 methane/ammonia monooxygenase subunit B
K10946 methane/ammonia monooxygenase subunit C
K14028 methanol dehydrogenase (cytochrome c) subunit 1 [EC:1.1.2.7 ]
K14029 methanol dehydrogenase (cytochrome c) subunit 2 [EC:1.1.2.7 ]
K00148 glutathione-independent formaldehyde dehydrogenase [EC:1.2.1.46 ]
K00124 formate dehydrogenase iron-sulfur subunit
K00127 formate dehydrogenase subunit gamma
K25123 iron hydrogenase HydA2 [EC:1.12.7.-]
K25124 FeS-containing electron transfer protein
K00192 anaerobic carbon-monoxide dehydrogenase, CODH/ACS complex subunit alpha [EC:1.2.7.4 ]
K00195 anaerobic carbon-monoxide dehydrogenase, CODH/ACS complex subunit epsilon
K00193 acetyl-CoA decarbonylase/synthase, CODH/ACS complex subunit beta [EC:2.3.1.169 ]
K00197 acetyl-CoA decarbonylase/synthase, CODH/ACS complex subunit gamma [EC:2.1.1.245 ]
K00194 acetyl-CoA decarbonylase/synthase, CODH/ACS complex subunit delta [EC:2.1.1.245 ]
K00198 anaerobic carbon-monoxide dehydrogenase catalytic subunit [EC:1.2.7.4 ]
K00196 anaerobic carbon-monoxide dehydrogenase iron sulfur subunit
K16306 fructose-bisphosphate aldolase / 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase [EC:4.1.2.13 2.2.1.10 ]
K07811 trimethylamine-N-oxide reductase (cytochrome c) [EC:1.7.2.3 ]
K03532 trimethylamine-N-oxide reductase (cytochrome c), cytochrome c-type subunit TorC
K03533 TorA specific chaperone
K07821 trimethylamine-N-oxide reductase (cytochrome c), cytochrome c-type subunit TorY
K07812 trimethylamine-N-oxide reductase (cytochrome c) [EC:1.7.2.3 ]
K22081 methylamine---glutamate N-methyltransferase subunit A [EC:2.1.1.21 ]
K22082 methylamine---glutamate N-methyltransferase subunit B [EC:2.1.1.21 ]
K22083 methylamine---glutamate N-methyltransferase subunit C [EC:2.1.1.21 ]
K00672 formylmethanofuran--tetrahydromethanopterin N-formyltransferase [EC:2.3.1.101 ]
K00442 coenzyme F420 hydrogenase subunit delta
K00300 methylenetetrahydrofolate/methylenetetrahydromethanopterin dehydrogenase (NADP+) [EC:1.5.1.5 1.5.1.-]
K10714 methylene-tetrahydromethanopterin dehydrogenase [EC:1.5.1.-]
K00577 tetrahydromethanopterin S-methyltransferase subunit A [EC:7.2.1.4 ]
K00578 tetrahydromethanopterin S-methyltransferase subunit B [EC:7.2.1.4 ]
K00579 tetrahydromethanopterin S-methyltransferase subunit C [EC:7.2.1.4 ]
K00580 tetrahydromethanopterin S-methyltransferase subunit D [EC:7.2.1.4 ]
K00581 tetrahydromethanopterin S-methyltransferase subunit E [EC:7.2.1.4 ]
K00582 tetrahydromethanopterin S-methyltransferase subunit F [EC:7.2.1.4 ]
K00583 tetrahydromethanopterin S-methyltransferase subunit G [EC:7.2.1.4 ]
K00584 tetrahydromethanopterin S-methyltransferase subunit H [EC:7.2.1.4 ]
K00400 methyl coenzyme M reductase system, component A2
K03421 methyl-coenzyme M reductase subunit C
K03422 methyl-coenzyme M reductase subunit D
K14126 F420-non-reducing hydrogenase large subunit [EC:1.12.99.- 1.8.98.5 ]
K14128 F420-non-reducing hydrogenase small subunit [EC:1.12.99.- 1.8.98.5 ]
K00169 pyruvate ferredoxin oxidoreductase alpha subunit [EC:1.2.7.1 ]
K00170 pyruvate ferredoxin oxidoreductase beta subunit [EC:1.2.7.1 ]
K00172 pyruvate ferredoxin oxidoreductase gamma subunit [EC:1.2.7.1 ]
K00171 pyruvate ferredoxin oxidoreductase delta subunit [EC:1.2.7.1 ]
K01834 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase [EC:5.4.2.11 ]
K15634 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase [EC:5.4.2.11 ]
K15633 2,3-bisphosphoglycerate-independent phosphoglycerate mutase [EC:5.4.2.12 ]
K15635 2,3-bisphosphoglycerate-independent phosphoglycerate mutase [EC:5.4.2.12 ]
K14080 [methyl-Co(III) methanol/glycine betaine-specific corrinoid protein]:coenzyme M methyltransferase [EC:2.1.1.246 2.1.1.377 ]
K04480 methanol---5-hydroxybenzimidazolylcobamide Co-methyltransferase [EC:2.1.1.90 ]
K14081 methanol corrinoid protein
K14082 [methyl-Co(III) methylamine-specific corrinoid protein]:coenzyme M methyltransferase [EC:2.1.1.247 ]
K14083 trimethylamine---corrinoid protein Co-methyltransferase [EC:2.1.1.250 ]
K14084 trimethylamine corrinoid protein
K16177 monomethylamine corrinoid protein
K16178 dimethylamine---corrinoid protein Co-methyltransferase [EC:2.1.1.249 ]
K16179 dimethylamine corrinoid protein
K11781 5-amino-6-(D-ribitylamino)uracil---L-tyrosine 4-hydroxyphenyl transferase [EC:2.5.1.147 ]
K11780 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase [EC:4.3.1.32 ]
K24998 dehydro coenzyme F420 reductase / coenzyme F420-0:L-glutamate ligase / coenzyme F420-1:gamma-L-glutamate ligase [EC:1.3.8.17 6.3.2.31 6.3.2.34 ]
K07072 (4-(4-[2-(gamma-L-glutamylamino)ethyl]phenoxymethyl)furan-2-yl)methanamine synthase [EC:2.5.1.131 ]
Compound
C00118 D-Glyceraldehyde 3-phosphate
C00143 5,10-Methylenetetrahydrofolate
C00354 D-Fructose 1,6-bisphosphate
C01217 5,6,7,8-Tetrahydromethanopterin
C01274 5-Formyl-5,6,7,8-tetrahydromethanopterin
C03920 2-(Methylthio)ethanesulfonate
C04330 5,10-Methenyltetrahydromethanopterin
C04377 5,10-Methylenetetrahydromethanopterin
C04488 5-Methyl-5,6,7,8-tetrahydromethanopterin
C04732 5-Amino-6-(1-D-ribitylamino)uracil
C04832 Coenzyme M 7-mercaptoheptanoylthreonine-phosphate heterodisulfide
C06019 D-arabino-Hex-3-ulose 6-phosphate
C11536 (2R)-O-Phospho-3-sulfolactate
C14180 S-(Hydroxymethyl)glutathione
C16593 7-Mercaptoheptanoic acid
C16594 7-Mercaptoheptanoylthreonine
C16597 (-)-threo-Iso(homo)2-citrate
C16600 (-)-threo-Iso(homo)3-citrate
C18802 Tetrahydrosarcinapterin
C19154 7,8-Didemethyl-8-hydroxy-5-deazariboflavin
C19155 (2S)-Lactyl-2-diphospho-5'-guanosine
C20954 (5-Formylfuran-3-yl)methyl phosphate
C21068 [5-(Aminomethyl)furan-3-yl]methyl phosphate
C21069 [5-(Aminomethyl)furan-3-yl]methyl diphosphate
C21070 (4-{4-[2-(gamma-L-Glutamylamino)ethyl]phenoxymethyl}furan-2-yl)methanamine
C21971 5-Amino-5-(4-hydroxybenzyl)-6-(D-ribitylimino)-5,6-dihydrouracil
C22277 Dehydro coenzyme F420-0
C22297 Enolpyruvoyl-2-diphospho-5'-guanosine
Reference
Authors
Graham DE, Xu H, White RH
Title
Identification of coenzyme M biosynthetic phosphosulfolactate synthase: a new family of sulfonate-biosynthesizing enzymes.
Journal
Reference
Authors
Deppenmeier U
Title
The membrane-bound electron transport system of Methanosarcina species.
Journal
Reference
Authors
Hallam SJ, Putnam N, Preston CM, Detter JC, Rokhsar D, Richardson PM, DeLong EF
Title
Reverse methanogenesis: testing the hypothesis with environmental genomics.
Journal
Reference
Authors
Welander PV, Metcalf WW
Title
Loss of the mtr operon in Methanosarcina blocks growth on methanol, but not methanogenesis, and reveals an unknown methanogenic pathway.
Journal
Reference
Authors
Yurimoto H, Kato N, Sakai Y
Title
Assimilation, dissimilation, and detoxification of formaldehyde, a central metabolic intermediate of methylotrophic metabolism.
Journal
Reference
Authors
Fricke WF, Seedorf H, Henne A, Kruer M, Liesegang H, Hedderich R, Gottschalk G, Thauer RK.
Title
The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis.
Journal
Reference
Authors
Kato N, Yurimoto H, Thauer RK
Title
The physiological role of the ribulose monophosphate pathway in bacteria and archaea.
Journal
Reference
Authors
Thauer RK, Kaster AK, Seedorf H, Buckel W, Hedderich R
Title
Methanogenic archaea: ecologically relevant differences in energy conservation.
Journal
Reference
Authors
Liffourrena AS, Salvano MA, Lucchesi GI
Title
Pseudomonas putida A ATCC 12633 oxidizes trimethylamine aerobically via two different pathways.
Journal
Related pathway
ko00010 Glycolysis / Gluconeogenesis
ko00260 Glycine, serine and threonine metabolism
ko00630 Glyoxylate and dicarboxylate metabolism
ko00720 Carbon fixation pathways in prokaryotes