KEGG   PATHWAY: ko00680Help
ko00680                     Pathway                                

Methane metabolism
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].
Metabolism; Energy metabolism
BRITE hierarchy
Pathway map
ko00680  Methane metabolism

Ortholog table
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]
M00346  Formaldehyde assimilation, serine pathway [PATH:ko00680]
M00356  Methanogenesis, methanol => methane [PATH:ko00680]
M00357  Methanogenesis, acetate => methane [PATH:ko00680]
M00358  Coenzyme M biosynthesis [PATH:ko00680]
M00378  F420 biosynthesis [PATH:ko00680]
M00422  Acetyl-CoA pathway, CO2 => acetyl-CoA [PATH:ko00680]
M00563  Methanogenesis, methylamine/dimethylamine/trimethylamine => methane [PATH:ko00680]
M00567  Methanogenesis, CO2 => methane [PATH:ko00680]
M00608  2-Oxocarboxylic acid chain extension, 2-oxoglutarate => 2-oxoadipate => 2-oxopimelate => 2-oxosuberate [PATH:ko00680]
H00203  Acatalasemia
Other DBs
BSID: 394
GO: 0015947
K16157  methane monooxygenase component A alpha chain [EC:]
K16158  methane monooxygenase component A beta chain [EC:]
K16159  methane monooxygenase component A gamma chain [EC:]
K16160  methane monooxygenase regulatory protein B
K16161  methane monooxygenase component C [EC:]
K16162  methane monooxygenase component D
K10944  methane/ammonia monooxygenase subunit A [EC:]
K10945  methane/ammonia monooxygenase subunit B
K10946  methane/ammonia monooxygenase subunit C
K14028  methanol dehydrogenase (cytochrome c) subunit 1 [EC:]
K16254  mxaJ protein
K16255  cytochrome c-L
K14029  methanol dehydrogenase (cytochrome c) subunit 2 [EC:]
K16256  mxaA protein
K16257  mxaC protein
K16258  mxaK protein
K16259  mxaL protein
K16260  mxaD protein
K17066  alcohol oxidase [EC:]
K00093  methanol dehydrogenase [EC:]
K00148  glutathione-independent formaldehyde dehydrogenase [EC:]
K17067  formaldehyde dismutase / methanol dehydrogenase [EC:]
K17068  formaldehyde dismutase [EC:]
K03396  S-(hydroxymethyl)glutathione synthase [EC:]
K00121  S-(hydroxymethyl)glutathione dehydrogenase / alcohol dehydrogenase [EC:]
K01070  S-formylglutathione hydrolase [EC:]
K00122  formate dehydrogenase [EC:]
K00123  formate dehydrogenase major subunit [EC:]
K22515  formate dehydrogenase beta subunit [EC:]
K00124  formate dehydrogenase iron-sulfur subunit
K00127  formate dehydrogenase subunit gamma
K00126  formate dehydrogenase subunit delta [EC:]
K22516  formate dehydrogenase (coenzyme F420) alpha subunit [EC:]
K00125  formate dehydrogenase (coenzyme F420) beta subunit [EC:]
K05299  formate dehydrogenase (NADP+) alpha subunit [EC:]
K15022  formate dehydrogenase (NADP+) beta subunit [EC:]
K00192  acetyl-CoA decarbonylase/synthase complex subunit alpha [EC:]
K00193  acetyl-CoA decarbonylase/synthase complex subunit beta [EC:2.3.1.-]
K00197  acetyl-CoA decarbonylase/synthase complex subunit gamma [EC:]
K00194  acetyl-CoA decarbonylase/synthase complex subunit delta [EC:]
K00195  acetyl-CoA decarbonylase/synthase complex subunit epsilon
K00198  anaerobic carbon-monoxide dehydrogenase catalytic subunit [EC:]
K00196  anaerobic carbon-monoxide dehydrogenase iron sulfur subunit
K00600  glycine hydroxymethyltransferase [EC:]
K00830  alanine-glyoxylate transaminase / serine-glyoxylate transaminase / serine-pyruvate transaminase [EC:]
K00018  glycerate dehydrogenase [EC:]
K11529  glycerate 2-kinase [EC:]
K01689  enolase [EC:]
K01595  phosphoenolpyruvate carboxylase [EC:]
K00024  malate dehydrogenase [EC:]
K08692  malate-CoA ligase subunit alpha [EC:]
K14067  malate-CoA ligase subunit beta [EC:]
K08691  malyl-CoA/(S)-citramalyl-CoA lyase [EC:]
K17100  dihydroxyacetone synthase [EC:]
K00863  triose/dihydroxyacetone kinase / FAD-AMP lyase (cyclizing) [EC:]
K01623  fructose-bisphosphate aldolase, class I [EC:]
K11645  fructose-bisphosphate aldolase, class I [EC:]
K01624  fructose-bisphosphate aldolase, class II [EC:]
K01622  fructose 1,6-bisphosphate aldolase/phosphatase [EC:]
K16305  fructose-bisphosphate aldolase / 6-deoxy-5-ketofructose 1-phosphate synthase [EC:]
K16306  fructose-bisphosphate aldolase / 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase [EC:]
K03841  fructose-1,6-bisphosphatase I [EC:]
K02446  fructose-1,6-bisphosphatase II [EC:]
K11532  fructose-1,6-bisphosphatase II / sedoheptulose-1,7-bisphosphatase [EC:]
K01086  fructose-1,6-bisphosphatase I / sedoheptulose-1,7-bisphosphatase [EC:]
K04041  fructose-1,6-bisphosphatase III [EC:]
K00850  6-phosphofructokinase 1 [EC:]
K16370  6-phosphofructokinase 2 [EC:]
K21071  ATP-dependent phosphofructokinase / diphosphate-dependent phosphofructokinase [EC:]
K00918  ADP-dependent phosphofructokinase/glucokinase [EC:]
K08094  6-phospho-3-hexuloisomerase [EC:]
K08093  3-hexulose-6-phosphate synthase [EC:]
K13812  bifunctional enzyme Fae/Hps [EC:]
K13831  3-hexulose-6-phosphate synthase / 6-phospho-3-hexuloisomerase [EC:]
K00317  dimethylamine/trimethylamine dehydrogenase [EC:]
K18277  trimethylamine monooxygenase [EC:]
K07811  trimethylamine-N-oxide reductase (cytochrome c) [EC:]
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:]
K15228  methylamine dehydrogenase light chain [EC:]
K15229  methylamine dehydrogenase heavy chain [EC:]
K08685  quinohemoprotein amine dehydrogenase [EC:]
K22081  methylamine---glutamate N-methyltransferase subunit A [EC:]
K22082  methylamine---glutamate N-methyltransferase subunit B [EC:]
K22083  methylamine---glutamate N-methyltransferase subunit C [EC:]
K22084  methylglutamate dehydrogenase subunit A [EC:]
K22085  methylglutamate dehydrogenase subunit B [EC:]
K22086  methylglutamate dehydrogenase subunit C [EC:]
K22087  methylglutamate dehydrogenase subunit D [EC:]
K00200  formylmethanofuran dehydrogenase subunit A [EC:]
K00201  formylmethanofuran dehydrogenase subunit B [EC:]
K00202  formylmethanofuran dehydrogenase subunit C [EC:]
K00203  formylmethanofuran dehydrogenase subunit D [EC:]
K00204  4Fe-4S ferredoxin
K00205  4Fe-4S ferredoxin
K11260  4Fe-4S ferredoxin
K11261  formylmethanofuran dehydrogenase subunit E [EC:]
K00672  formylmethanofuran--tetrahydromethanopterin N-formyltransferase [EC:]
K01499  methenyltetrahydromethanopterin cyclohydrolase [EC:]
K00319  methylenetetrahydromethanopterin dehydrogenase [EC:]
K00440  coenzyme F420 hydrogenase subunit alpha [EC:]
K00441  coenzyme F420 hydrogenase subunit beta [EC:]
K00442  coenzyme F420 hydrogenase subunit delta
K00443  coenzyme F420 hydrogenase subunit gamma [EC:]
K00300  methylenetetrahydrofolate/methylenetetrahydromethanopterin dehydrogenase (NADP+) [EC:1.5.1.-]
K10714  methylene-tetrahydromethanopterin dehydrogenase [EC:1.5.1.-]
K13942  5,10-methenyltetrahydromethanopterin hydrogenase [EC:]
K10713  5,6,7,8-tetrahydromethanopterin hydro-lyase [EC:]
K00320  5,10-methylenetetrahydromethanopterin reductase [EC:]
K00577  tetrahydromethanopterin S-methyltransferase subunit A [EC:]
K00578  tetrahydromethanopterin S-methyltransferase subunit B [EC:]
K00579  tetrahydromethanopterin S-methyltransferase subunit C [EC:]
K00580  tetrahydromethanopterin S-methyltransferase subunit D [EC:]
K00581  tetrahydromethanopterin S-methyltransferase subunit E [EC:]
K00582  tetrahydromethanopterin S-methyltransferase subunit F [EC:]
K00583  tetrahydromethanopterin S-methyltransferase subunit G [EC:]
K00584  tetrahydromethanopterin S-methyltransferase subunit H [EC:]
K00399  methyl-coenzyme M reductase alpha subunit [EC:]
K00400  methyl coenzyme M reductase system, component A2
K00401  methyl-coenzyme M reductase beta subunit [EC:]
K00402  methyl-coenzyme M reductase gamma subunit [EC:]
K03421  methyl-coenzyme M reductase subunit C
K03422  methyl-coenzyme M reductase subunit D
K22480  heterodisulfide reductase subunit A1 [EC:]
K22481  heterodisulfide reductase subunit B1 [EC:]
K22482  heterodisulfide reductase subunit C1 [EC:]
K03388  heterodisulfide reductase subunit A2 [EC:]
K03389  heterodisulfide reductase subunit B2 [EC:]
K03390  heterodisulfide reductase subunit C2 [EC:]
K08264  heterodisulfide reductase subunit D [EC:]
K08265  heterodisulfide reductase subunit E [EC:]
K14127  F420-non-reducing hydrogenase iron-sulfur subunit [EC: 1.12.99.-]
K14126  F420-non-reducing hydrogenase large subunit [EC: 1.12.99.-]
K14128  F420-non-reducing hydrogenase small subunit [EC: 1.12.99.-]
K00925  acetate kinase [EC:]
K00625  phosphate acetyltransferase [EC:]
K13788  phosphate acetyltransferase [EC:]
K01895  acetyl-CoA synthetase [EC:]
K00169  pyruvate ferredoxin oxidoreductase alpha subunit [EC:]
K00170  pyruvate ferredoxin oxidoreductase beta subunit [EC:]
K00172  pyruvate ferredoxin oxidoreductase gamma subunit [EC:]
K00171  pyruvate ferredoxin oxidoreductase delta subunit [EC:]
K01007  pyruvate, water dikinase [EC:]
K01834  2,3-bisphosphoglycerate-dependent phosphoglycerate mutase [EC:]
K15633  2,3-bisphosphoglycerate-independent phosphoglycerate mutase [EC:]
K15634  probable phosphoglycerate mutase [EC:]
K15635  2,3-bisphosphoglycerate-independent phosphoglycerate mutase [EC:]
K00058  D-3-phosphoglycerate dehydrogenase / 2-oxoglutarate reductase [EC:]
K00831  phosphoserine aminotransferase [EC:]
K01079  phosphoserine phosphatase [EC:]
K02203  phosphoserine / homoserine phosphotransferase [EC:]
K22305  phosphoserine phosphatase [EC:]
K14080  [methyl-Co(III) methanol-specific corrinoid protein]:coenzyme M methyltransferase [EC:]
K04480  methanol---5-hydroxybenzimidazolylcobamide Co-methyltransferase [EC:]
K14081  methanol corrinoid protein
K14082  [methyl-Co(III) methylamine-specific corrinoid protein]:coenzyme M methyltransferase [EC:]
K14083  trimethylamine---corrinoid protein Co-methyltransferase [EC:]
K14084  trimethylamine corrinoid protein
K16176  methylamine---corrinoid protein Co-methyltransferase [EC:]
K16177  monomethylamine corrinoid protein
K16178  dimethylamine---corrinoid protein Co-methyltransferase [EC:]
K16179  dimethylamine corrinoid protein
K08097  phosphosulfolactate synthase [EC:]
K05979  2-phosphosulfolactate phosphatase [EC:]
K05884  L-2-hydroxycarboxylate dehydrogenase (NAD+) [EC:]
K06034  sulfopyruvate decarboxylase subunit alpha [EC:]
K13039  sulfopyruvate decarboxylase subunit beta [EC:]
K11779  FO synthase [EC:]
K11781  5-amino-6-(D-ribitylamino)uracil---L-tyrosine 4-hydroxyphenyl transferase [EC:]
K11780  7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase [EC:]
K14941  2-phospho-L-lactate guanylyltransferase [EC:]
K11212  LPPG:FO 2-phospho-L-lactate transferase [EC:]
K12234  coenzyme F420-0:L-glutamate ligase / coenzyme F420-1:gamma-L-glutamate ligase [EC:]
K14940  gamma-F420-2:alpha-L-glutamate ligase [EC:]
K10977  methanogen homocitrate synthase [EC:2.3.3.-]
K16792  methanogen homoaconitase large subunit [EC:]
K16793  methanogen homoaconitase small subunit [EC:]
K10978  methanogen homoisocitrate dehydrogenase [EC:1.1.1.-]
K18933  tyrosine decarboxylase / aspartate 1-decarboxylase [EC:]
K06914  tyramine---L-glutamate ligase [EC:]
K09733  (5-formylfuran-3-yl)methyl phosphate synthase [EC:]
K19793  (5-formylfuran-3-yl)methyl phosphate transaminase [EC:]
K07144  5-(aminomethyl)-3-furanmethanol phosphate kinase [EC:]
K07072  (4-(4-[2-(gamma-L-glutamylamino)ethyl]phenoxymethyl)furan-2-yl)methanamine synthase [EC:]
C00011  CO2
C00022  Pyruvate
C00024  Acetyl-CoA
C00033  Acetate
C00036  Oxaloacetate
C00037  Glycine
C00048  Glyoxylate
C00058  Formate
C00065  L-Serine
C00067  Formaldehyde
C00074  Phosphoenolpyruvate
C00082  L-Tyrosine
C00085  D-Fructose 6-phosphate
C00101  Tetrahydrofolate
C00111  Glycerone phosphate
C00118  D-Glyceraldehyde 3-phosphate
C00132  Methanol
C00143  5,10-Methylenetetrahydrofolate
C00149  (S)-Malate
C00168  Hydroxypyruvate
C00184  Glycerone
C00197  3-Phospho-D-glycerate
C00199  D-Ribulose 5-phosphate
C00218  Methylamine
C00227  Acetyl phosphate
C00231  D-Xylulose 5-phosphate
C00237  CO
C00258  D-Glycerate
C00322  2-Oxoadipate
C00354  D-Fructose 1,6-bisphosphate
C00483  Tyramine
C00543  Dimethylamine
C00565  Trimethylamine
C00593  Sulfoacetaldehyde
C00631  2-Phospho-D-glycerate
C00862  Methanofuran
C00876  Coenzyme F420
C01001  Formylmethanofuran
C01005  O-Phospho-L-serine
C01031  S-Formylglutathione
C01046  N-Methyl-L-glutamate
C01080  Reduced coenzyme F420
C01104  Trimethylamine N-oxide
C01217  5,6,7,8-Tetrahydromethanopterin
C01274  5-Formyl-5,6,7,8-tetrahydromethanopterin
C01438  Methane
C03232  3-Phosphonooxypyruvate
C03576  Coenzyme M
C03920  2-(Methylthio)ethanesulfonate
C04330  5,10-Methenyltetrahydromethanopterin
C04348  L-Malyl-CoA
C04377  5,10-Methylenetetrahydromethanopterin
C04488  5-Methyl-5,6,7,8-tetrahydromethanopterin
C04628  Coenzyme B
C04732  5-Amino-6-(1-D-ribitylamino)uracil
C04832  Coenzyme M 7-mercaptoheptanoylthreonine-phosphate heterodisulfide
C05528  3-Sulfopyruvate
C06019  D-arabino-Hex-3-ulose 6-phosphate
C11536  (2R)-O-Phospho-3-sulfolactate
C11537  (2R)-3-Sulfolactate
C14180  S-(Hydroxymethyl)glutathione
C16583  (R)-(Homo)2-citrate
C16588  2-Oxopimelate
C16589  2-Oxosuberate
C16590  7-Oxoheptanoic acid
C16593  7-Mercaptoheptanoic acid
C16594  7-Mercaptoheptanoylthreonine
C16597  (-)-threo-Iso(homo)2-citrate
C16598  (R)-(Homo)3-citrate
C16600  (-)-threo-Iso(homo)3-citrate
C19151  Coenzyme F420-3
C19152  Coenzyme F420-1
C19153  Coenzyme F420-0
C19154  7,8-Didemethyl-8-hydroxy-5-deazariboflavin
C19155  (2S)-Lactyl-2-diphospho-5'-guanosine
C19156  (2S)-2-Phospholactate
C20581  cis-(Homo)2-aconitate
C20582  cis-(Homo)3-aconitate
C20926  gamma-Glutamyltyramine
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
Graham DE, Xu H, White RH
Identification of coenzyme M biosynthetic phosphosulfolactate synthase: a new family of sulfonate-biosynthesizing enzymes.
J Biol Chem 277:13421-9 (2002)
Deppenmeier U
The membrane-bound electron transport system of Methanosarcina species.
J Bioenerg Biomembr 36:55-64 (2004)
Hallam SJ, Putnam N, Preston CM, Detter JC, Rokhsar D, Richardson PM, DeLong EF
Reverse methanogenesis: testing the hypothesis with environmental genomics.
Science 305:1457-62 (2004)
Welander PV, Metcalf WW
Loss of the mtr operon in Methanosarcina blocks growth on methanol, but not methanogenesis, and reveals an unknown methanogenic pathway.
Proc Natl Acad Sci U S A 102:10664-9 (2005)
Yurimoto H, Kato N, Sakai Y
Assimilation, dissimilation, and detoxification of formaldehyde, a central metabolic intermediate of methylotrophic metabolism.
Chem Rec 5:367-75 (2005)
Fricke WF, Seedorf H, Henne A, Kruer M, Liesegang H, Hedderich R, Gottschalk G, Thauer RK.
The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis.
J Bacteriol 188:642-58 (2006)
Kato N, Yurimoto H, Thauer RK
The physiological role of the ribulose monophosphate pathway in bacteria and archaea.
Biosci Biotechnol Biochem 70:10-21 (2006)
Thauer RK, Kaster AK, Seedorf H, Buckel W, Hedderich R
Methanogenic archaea: ecologically relevant differences in energy conservation.
Nat Rev Microbiol 6:579-91 (2008)
Liffourrena AS, Salvano MA, Lucchesi GI
Pseudomonas putida A ATCC 12633 oxidizes trimethylamine aerobically via two different pathways.
Arch Microbiol 192:471-6 (2010)

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