KEGG   PATHWAY: rn00680
Entry
rn00680                     Pathway                                
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
rn00680  Methane metabolism
rn00680

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]
M00346  Formaldehyde assimilation, serine pathway [PATH:rn00680]
M00356  Methanogenesis, methanol => methane [PATH:rn00680]
M00357  Methanogenesis, acetate => methane [PATH:rn00680]
M00358  Coenzyme M biosynthesis [PATH:rn00680]
M00378  F420 biosynthesis, archaea [PATH:rn00680]
M00422  Acetyl-CoA pathway, CO2 => acetyl-CoA [PATH:rn00680]
M00563  Methanogenesis, methylamine/dimethylamine/trimethylamine => methane [PATH:rn00680]
M00567  Methanogenesis, CO2 => methane [PATH:rn00680]
M00608  2-Oxocarboxylic acid chain extension, 2-oxoglutarate => 2-oxoadipate => 2-oxopimelate => 2-oxosuberate [PATH:rn00680]
M00935  Methanofuran biosynthesis [PATH:rn00680]
Other DBs
GO: 0015947
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)
R08059   
R08060   
R08214  (-)-threo-iso(homo)2-citrate:NAD+ oxidoreductase (decarboxylating)
R08215  (-)-threo-iso(homo)3-citrate:NAD+ oxidoreductase (decarboxylating)
R08217  ATP:7-mercaptoheptanoylthreonine 3-phosphotransferase
R08323   
R08328   
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
R09096   
R09098  methanol:coenzyme M methyltransferase
R09099  5,10-methylenetetrahydromethanopterin:glycine hydroxymethyltransferase
R09124  trimethylamine:coenzyme M methyltransferase
R09153   
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
R10219   
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
R10397   
R10797  formate:coenzyme-F420 oxidoreductase
R10902  tyramine:L-glutamate gamma-ligase (ADP-forming)
R10935   
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
R12720   
R12754   
Compound
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
C18799  5-Methyl-H4SPT
C18802  Tetrahydrosarcinapterin
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
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
J Biol Chem 277:13421-9 (2002)
DOI:10.1074/jbc.M201011200
Reference
  Authors
Deppenmeier U
  Title
The membrane-bound electron transport system of Methanosarcina species.
  Journal
J Bioenerg Biomembr 36:55-64 (2004)
DOI:10.1023/B:JOBB.0000019598.64642.97
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
Science 305:1457-62 (2004)
DOI:10.1126/science.1100025
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
Proc Natl Acad Sci U S A 102:10664-9 (2005)
DOI:10.1073/pnas.0502623102
Reference
  Authors
Yurimoto H, Kato N, Sakai Y
  Title
Assimilation, dissimilation, and detoxification of formaldehyde, a central metabolic intermediate of methylotrophic metabolism.
  Journal
Chem Rec 5:367-75 (2005)
DOI:10.1002/tcr.20056
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
J Bacteriol 188:642-58 (2006)
DOI:10.1128/JB.188.2.642-658.2006
Reference
  Authors
Kato N, Yurimoto H, Thauer RK
  Title
The physiological role of the ribulose monophosphate pathway in bacteria and archaea.
  Journal
Biosci Biotechnol Biochem 70:10-21 (2006)
DOI:10.1271/bbb.70.10
Reference
  Authors
Thauer RK, Kaster AK, Seedorf H, Buckel W, Hedderich R
  Title
Methanogenic archaea: ecologically relevant differences in energy conservation.
  Journal
Nat Rev Microbiol 6:579-91 (2008)
DOI:10.1038/nrmicro1931
Reference
  Authors
Liffourrena AS, Salvano MA, Lucchesi GI
  Title
Pseudomonas putida A ATCC 12633 oxidizes trimethylamine aerobically via two different pathways.
  Journal
Arch Microbiol 192:471-6 (2010)
DOI:10.1007/s00203-010-0577-5
Related
pathway
rn00010  Glycolysis / Gluconeogenesis
rn00030  Pentose phosphate pathway
rn00260  Glycine, serine and threonine metabolism
rn00300  Lysine biosynthesis
rn00630  Glyoxylate and dicarboxylate metabolism
rn00720  Carbon fixation pathways in prokaryotes
rn00740  Riboflavin metabolism
rn00790  Folate biosynthesis
rn00910  Nitrogen metabolism
rn00920  Sulfur metabolism
KO pathway
ko00680   
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