PATHWAY: rn00680 Help
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
Pathway map Ortholog table Module M00020 Serine biosynthesis, glycerate-3P => serine [PATH:rn00680 ]
M00174 Methane oxidation, methanotroph, methane => formaldehyde [PATH:rn00680 ]
M00344 Formaldehyde assimilation, xylulose monophosphate pathway [PATH:rn00680 ]
M00345 Formaldehyde assimilation, ribulose monophosphate pathway [PATH:rn00680 ]
M00563 Methanogenesis, methylamine/dimethylamine/trimethylamine => methane [PATH:rn00680 ]
M00608 2-Oxocarboxylic acid chain extension, 2-oxoglutarate => 2-oxoadipate => 2-oxopimelate => 2-oxosuberate [PATH:rn00680 ]
Other DBs Reaction R00134 formate:NADP+ oxidoreductase
R00199 ATP:pyruvate,water phosphotransferase
R00230 acetyl-CoA:phosphate acetyltransferase
R00235 Acetate:CoA ligase (AMP-forming)
R00315 ATP:acetate phosphotransferase
R00342 (S)-malate:NAD+ oxidoreductase
R00345 phosphate:oxaloacetate carboxy-lyase (adding phosphate;phosphoenolpyruvate-forming)
R00473 L-malyl-CoA glyoxylate-lyase (acetyl-CoA-forming)
R00519 formate:NAD+ oxidoreductase
R00527 S-Formylglutathione hydrolase
R00582 O-phospho-L-serine phosphohydrolase
R00588 L-Serine:glyoxylate aminotransferase
R00604 Formaldehyde:NAD+ oxidoreductase
R00605 methanol:NAD+ oxidoreductase
R00606 methylamine:amicyanin oxidoreductase (deaminating)
R00608 Methanol:oxygen oxidereductase
R00609 N-methyl-L-glutamate:acceptor oxidoreductase (demethylating)
R00614 formaldehyde:formaldehyde oxidoreductase
R00658 2-phospho-D-glycerate hydro-lyase (phosphoenolpyruvate-forming)
R00736 L-tyrosine carboxy-lyase (tyramine-forming)
R00756 ATP:D-fructose-6-phosphate 1-phosphotransferase
R00762 D-Fructose-1,6-bisphosphate 1-phosphohydrolase
R00945 5,10-Methylenetetrahydrofolate:glycine hydroxymethyltransferase
R01011 ATP:glycerone phosphotransferase
R01068 D-fructose-1,6-bisphosphate D-glyceraldehyde-3-phosphate-lyase (glycerone-phosphate-forming)
R01142 Methane,NADH:oxygen oxidoreductase (hydroxylating)
R01146 methanol:ferricytochrome-c oxidoreductase
R01196 pyruvate:ferredoxin 2-oxidoreductase (CoA-acetylating)
R01256 (S)-malate:CoA ligase (ADP-forming)
R01388 D-Glycerate:NAD+ 2-oxidoreductase
R01440 D-Xylulose-5-phosphate:formaldehyde glycolaldehydetransferase
R01513 3-Phospho-D-glycerate:NAD+ 2-oxidoreductase
R01518 D-phosphoglycerate 2,3-phosphomutase
R01586 L-glutamate:methylamine 1,3-dicarboxypropyltransferase (N-methyl-L-glutamate-forming)
R01588 dimethylamine:electron-transferring flavoprotein oxidoreductase
R02511 trimethylamine:electron-transferring flavoprotein oxidoreductase(demethylating)
R02512 Trimethylamine-N-oxide formaldehyde-lyase
R02560 trimethylamine:cytochrome c oxidoreductase
R03015 formylmethanofuran:ferredoxin oxidoreductase
R03025 Hydrogen:Coenzyme F420 oxidoreductase
R03390 Formylmethanofuran:5,6,7,8-tetrahydromethanopterin 5-formyltransferase
R03464 5,10-Methenyltetrahydromethanopterin 10-hydrolase (decyclizing)
R04173 3-Phosphoserine:2-oxoglutarate aminotransferase
R04347 5-methyl-5,6,7,8-tetrahydromethanopterin:2-mercaptoethanesulfonate 2-methyltransferas
R04455 hydrogen:N5,N10-methenyltetraydromethanopterin oxidoreductase
R04456 5,10-methylenetetrahydromethanopterin:coenzyme-F420 oxidoreductase
R04464 5,10-Methylenetetrahydromethanopterin:coenzyme-F420 oxidoreductase
R04540 Coenzyme B:coenzyme M:methanophenazine oxidoreductase
R04541 2-(methylthio)ethanesulfonate:N-(7-thioheptanoyl)-3-O-phosphothreonine S-(2-sulfoethyl)thiotransferase
R05338 D-arabino-hex-3-ulose-6-phosphate formaldehyde-lyase (D-ribulose-5-phosphate-forming)
R05339 D-arabino-hex-3-ulose-6-phosphate isomerase
R05623 N,N,N-trimethylamine,NADPH:oxygen oxidoreductase (N-oxide-forming)
R05774 sulfopyruvate carboxy-lyase
R05789 (R)-2-phospho-3-sulfolactate phosphohydrolase
R05805 ADP:D-fructose-6-phosphate 1-phosphotransferase
R06982 S-(hydroxymethyl)glutathione formaldehyde-lyase (glutathione-forming)
R06983 S-(hydroxymethyl)glutathione dehydrogenase
R07136 (2R)-3-sulfolactate:NAD+ oxidoreductase
R07157 carbon-monoxide,water:ferredoxin oxidoreductase
R07476 (2R)-O-phospho-3-sulfolactate sulfo-lyase
R08058 5,6,7,8-tetrahydromethanopterin hydro-lyase (formaldehyde-adding, 5,10-methylenetetrahydromethanopterin-forming)
R08214 (-)-threo-iso(homo)2-citrate:NAD+ oxidoreductase (decarboxylating)
R08215 (-)-threo-iso(homo)3-citrate:NAD+ oxidoreductase (decarboxylating)
R08217 ATP:7-mercaptoheptanoylthreonine 3-phosphotransferase
R08331 acetyl-CoA:2-oxoadipate C-acetyltransferase (thioester-hydrolysing, carboxymethyl forming)
R08332 acetyl-CoA:2-oxopimelate C-acetyltransferase (thioester-hydrolysing, carboxymethyl forming)
R08572 ATP:(R)-glycerate 2-phosphotransferase
R09098 methanol:coenzyme M methyltransferase
R09099 5,10-methylenetetrahydromethanopterin:glycine hydroxymethyltransferase
R09124 trimethylamine:coenzyme M methyltransferase
R09397 GTP:2-phospho-L-lactate guanylyltransferase
R09398 (2S)-lactyl-2-diphospho-5'-guanosine:7,8-didemethyl-8-hydroxy-5-deazariboflavin 2-phospho-L-lactate transferase
R09399 L-glutamate:coenzyme F420-0 ligase (GDP-forming)
R09400 L-glutamate:coenzyme F420-1 ligase (GDP-forming)
R09401 L-glutamate:coenzyme gamma-F420-2 (ADP-forming)
R09518 methane,quinol:oxygen oxidoreductase
R09998 methylamine:coenzyme M methyltransferase
R09999 dimethylamine:coenzyme M methyltransferase
R10392 (R)-(homo)2-citrate hydro-lyase
R10393 (-)-threo-iso(homo)2-citrate hydro-lyase
R10395 (R)-(homo)3-citrate hydro-lyase
R10396 (-)-threo-iso(homo)3-citrate hydro-lyase
R10797 formate:coenzyme-F420 oxidoreductase
R10902 tyramine:L-glutamate gamma-ligase (ADP-forming)
R11038 L-alanine:(5-formylfuran-3-yl)methyl-phosphate aminotransferase
R11039 [5-(aminomethyl)furan-3-yl]methyl phosphate kinase
R11040 (4-{4-[2-(gamma-L-glutamylamino)ethyl]phenoxymethyl}furan-2-yl)methanamine synthase
R11928 CoB,CoM,ferredoxin:coenzyme F420 oxidoreductase
R11931 CoB,CoM:ferredoxin oxidoreductase
R11943 CoB,CoM,ferredoxin:H2 oxidoreductase
R11944 coenzyme B,coenzyme M,ferredoxin:formate oxidoreductase
R12161 5-amino-6-(D-ribitylamino)uracil:L-tyrosine 4-hydroxybenzyltransferase
R12162 5-amino-5-(4-hydroxybenzyl)-6-(D-ribitylimino)-5,6-dihydrouracil ammonia-lyase (7,8-didemethyl-8-hydroxy-5-deazariboflavin-forming)
R12291 5-methyltetrahydrosarcinapterin:CoM 2-methyltransferase
R12646 GTP:phosphoenolpyruvate guanylyltransferase
R12648 enolpyruvoyl-2-diphospho-5'-guanosine:7,8-didemethyl-8-hydroxy-5-deazariboflavin 2-phosphoenolpyruvate transferase
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 rn00010 Glycolysis / Gluconeogenesis
rn00260 Glycine, serine and threonine metabolism
rn00630 Glyoxylate and dicarboxylate metabolism
rn00720 Carbon fixation pathways in prokaryotes
KO pathway
