KEGG   PATHWAY: mla00680Help
Entry
mla00680                    Pathway                                

Name
Methane metabolism - Methanocorpusculum labreanum
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
mla00680  Methane metabolism
mla00680

Ortholog table
Module
mla_M00378  F420 biosynthesis [PATH:mla00680]
mla_M00567  Methanogenesis, CO2 => methane [PATH:mla00680]
mla_M00608  2-Oxocarboxylic acid chain extension, 2-oxoglutarate => 2-oxoadipate => 2-oxopimelate => 2-oxosuberate [PATH:mla00680]
Other DBs
BSID: 46653
GO: 0015947
Organism
Methanocorpusculum labreanum [GN:mla]
Gene
Mlab_0463  formate dehydrogenase, alpha subunit (F420) [KO:K22516] [EC:1.8.98.6 1.17.98.3]
Mlab_1057  molybdopterin oxidoreductase Fe4S4 region [KO:K22516] [EC:1.8.98.6 1.17.98.3]
Mlab_0462  formate dehydrogenase, beta subunit (F420) [KO:K00125] [EC:1.8.98.6 1.17.98.3]
Mlab_1058  coenzyme F420 hydrogenase/dehydrogenase beta subunit domain protein [KO:K00125] [EC:1.8.98.6 1.17.98.3]
Mlab_1356  serine hydroxymethyltransferase [KO:K00600] [EC:2.1.2.1]
Mlab_1238  enolase [KO:K01689] [EC:4.2.1.11]
Mlab_1271  L-lactate dehydrogenase [KO:K00024] [EC:1.1.1.37]
Mlab_0615  Lactate/malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
Mlab_1327  hypothetical protein [KO:K01622] [EC:3.1.3.11 4.1.2.13]
Mlab_1135  fructose-bisphosphate aldolase [KO:K16305] [EC:2.2.1.11 4.1.2.13]
Mlab_1654  fructose-bisphosphate aldolase [KO:K16306] [EC:2.2.1.10 4.1.2.13]
Mlab_0600  fructose-bisphosphate aldolase [KO:K16306] [EC:2.2.1.10 4.1.2.13]
Mlab_1328  D-fructose 1,6-bisphosphatase [KO:K03841] [EC:3.1.3.11]
Mlab_0993  hexulose-6-phosphate isomerase [KO:K08094] [EC:5.3.1.27]
Mlab_0996  hexulose-6-phosphate synthase [KO:K13812] [EC:4.1.2.43 4.2.1.147]
Mlab_1453  hexulose-6-phosphate synthase [KO:K13831] [EC:5.3.1.27 4.1.2.43]
Mlab_0245  formylmethanofuran dehydrogenase, subunit A [KO:K00200] [EC:1.2.7.12]
Mlab_0574  formylmethanofuran dehydrogenase, subunit A [KO:K00200] [EC:1.2.7.12]
Mlab_0244  formylmethanofuran dehydrogenase, subunit B [KO:K00201] [EC:1.2.7.12]
Mlab_1389  formylmethanofuran dehydrogenase, subunit B [KO:K00201] [EC:1.2.7.12]
Mlab_0246  formylmethanofuran dehydrogenase, subunit C [KO:K00202] [EC:1.2.7.12]
Mlab_0575  formylmethanofuran dehydrogenase, subunit C [KO:K00202] [EC:1.2.7.12]
Mlab_0243  formylmethanofuran dehydrogenase, subunit D [KO:K00203] [EC:1.2.7.12]
Mlab_0238  formylmethanofuran dehydrogenase, subunit F [KO:K00205]
Mlab_0398  4Fe-4S ferredoxin, iron-sulfur binding domain protein [KO:K00205]
Mlab_0237  4Fe-4S ferredoxin, iron-sulfur binding domain protein [KO:K11260]
Mlab_1094  formylmethanofuran dehydrogenase, subunit E region [KO:K11261] [EC:1.2.7.12]
Mlab_0215  formylmethanofuran-tetrahydromethanopterin formyltransferase [KO:K00672] [EC:2.3.1.101]
Mlab_0399  methenyltetrahydromethanopterin cyclohydrolase [KO:K01499] [EC:3.5.4.27]
Mlab_0079  methylenetetrahydromethanopterin dehydrogenase [KO:K00319] [EC:1.5.98.1]
Mlab_0015  coenzyme F420-reducing hydrogenase, alpha subunit [KO:K00440] [EC:1.12.98.1]
Mlab_0012  coenzyme F420-reducing hydrogenase, beta subunit [KO:K00441] [EC:1.12.98.1]
Mlab_0014  coenzyme F420-reducing hydrogenase, delta subunit [KO:K00442]
Mlab_0013  coenzyme F420-reducing hydrogenase, gamma subunit [KO:K00443] [EC:1.12.98.1]
Mlab_1744  H2-forming methylenetetrahydromethanopterin dehydrogenase [KO:K13942] [EC:1.12.98.2]
Mlab_0076  methylenetetrahydromethanopterin reductase [KO:K00320] [EC:1.5.98.2]
Mlab_1554  tetrahydromethanopterin S-methyltransferase, subunit A [KO:K00577] [EC:2.1.1.86]
Mlab_1556  tetrahydromethanopterin S-methyltransferase, subunit A [KO:K00577] [EC:2.1.1.86]
Mlab_1557  tetrahydromethanopterin S-methyltransferase, subunit B [KO:K00578] [EC:2.1.1.86]
Mlab_1558  tetrahydromethanopterin S-methyltransferase, subunit C [KO:K00579] [EC:2.1.1.86]
Mlab_1559  tetrahydromethanopterin S-methyltransferase, subunit D [KO:K00580] [EC:2.1.1.86]
Mlab_1560  tetrahydromethanopterin S-methyltransferase, subunit E [KO:K00581] [EC:2.1.1.86]
Mlab_1555  tetrahydromethanopterin S-methyltransferase, F subunit [KO:K00582] [EC:2.1.1.86]
Mlab_1553  tetrahydromethanopterin S-methyltransferase, subunit H [KO:K00584] [EC:2.1.1.86]
Mlab_1068  methyl-coenzyme M reductase, alpha subunit [KO:K00399] [EC:2.8.4.1]
Mlab_1561  methyl-coenzyme M reductase, alpha subunit [KO:K00399] [EC:2.8.4.1]
Mlab_0555  ABC transporter related protein [KO:K00400]
Mlab_0729  ABC transporter related protein [KO:K00400]
Mlab_1565  methyl-coenzyme M reductase, beta subunit [KO:K00401] [EC:2.8.4.1]
Mlab_1066  Coenzyme-B sulfoethylthiotransferase [KO:K00401] [EC:2.8.4.1]
Mlab_1562  methyl-coenzyme M reductase, gamma subunit [KO:K00402] [EC:2.8.4.1]
Mlab_1067  methyl-coenzyme M reductase, gamma subunit [KO:K00402] [EC:2.8.4.1]
Mlab_1563  Methyl-coenzyme M reductase operon protein C [KO:K03421]
Mlab_1564  Methyl-coenzyme M reductase, protein D [KO:K03422]
Mlab_0241  CoB--CoM heterodisulfide reductase subunit A [KO:K03388] [EC:1.8.98.6 1.8.98.5 1.8.98.4 1.8.7.3]
Mlab_0979  4Fe-4S ferredoxin, iron-sulfur binding domain protein [KO:K03388] [EC:1.8.98.6 1.8.98.5 1.8.98.4 1.8.7.3]
Mlab_0240  CoB--CoM heterodisulfide reductase subunit B [KO:K03389] [EC:1.8.98.6 1.8.98.5 1.8.98.4 1.8.7.3]
Mlab_0239  Heterodisulfide reductase subunit C-like protein [KO:K03390] [EC:1.8.98.6 1.8.98.5 1.8.98.4 1.8.7.3]
Mlab_0844  AMP-dependent synthetase and ligase [KO:K01895] [EC:6.2.1.1]
Mlab_1256  AMP-dependent synthetase and ligase [KO:K01895] [EC:6.2.1.1]
Mlab_1417  pyruvate ferredoxin oxidoreductase, alpha subunit [KO:K00169] [EC:1.2.7.1]
Mlab_0049  pyruvate flavodoxin/ferredoxin oxidoreductase domain protein [KO:K00169] [EC:1.2.7.1]
Mlab_1418  pyruvate ferredoxin oxidoreductase, beta subunit [KO:K00170] [EC:1.2.7.1]
Mlab_0050  thiamine pyrophosphate enzyme domain protein TPP-binding protein [KO:K00170] [EC:1.2.7.1]
Mlab_1415  pyruvate ferredoxin oxidoreductase, gamma subunit [KO:K00172] [EC:1.2.7.1]
Mlab_0048  pyruvate ferredoxin oxidoreductase, gamma subunit [KO:K00172] [EC:1.2.7.1]
Mlab_0047  pyruvate ferredoxin/flavodoxin oxidoreductase, delta subunit [KO:K00171] [EC:1.2.7.1]
Mlab_1416  pyruvate ferredoxin oxidoreductase, delta subunit [KO:K00171] [EC:1.2.7.1]
Mlab_1544  phosphoenolpyruvate synthase [KO:K01007] [EC:2.7.9.2]
Mlab_0839  phosphoglycerate mutase [KO:K15635] [EC:5.4.2.12]
Mlab_0645  phosphoglycerate mutase [KO:K15635] [EC:5.4.2.12]
Mlab_1543  D-3-phosphoglycerate dehydrogenase [KO:K00058] [EC:1.1.1.399 1.1.1.95]
Mlab_0504  sulfopyruvate decarboxylase subunit beta / sulfopyruvate decarboxylase subunit alpha [KO:K13039] [EC:4.1.1.79]
Mlab_1590  Radical SAM domain protein [KO:K11780] [EC:2.5.1.77]
Mlab_0123  Radical SAM domain protein [KO:K11781] [EC:2.5.1.77]
Mlab_1358  protein of unknown function DUF121 [KO:K14941] [EC:2.7.7.68]
Mlab_0152  LPPG:FO 2-phospho-L-lactate transferase [KO:K11212] [EC:2.7.8.28]
Mlab_1332  coenzyme F420-0 gamma-glutamyl ligase [KO:K12234] [EC:6.3.2.34 6.3.2.31]
Mlab_0232  2-isopropylmalate synthase [KO:K10977] [EC:2.3.3.- 2.3.3.14]
Mlab_0233  3-isopropylmalate dehydratase [KO:K16792] [EC:4.2.1.114]
Mlab_0234  3-isopropylmalate dehydratase, small subunit [KO:K16793] [EC:4.2.1.114]
Mlab_0235  3-isopropylmalate dehydrogenase [KO:K10978] [EC:1.1.1.- 1.1.1.87]
Mlab_1545  Pyridoxal-dependent decarboxylase [KO:K18933] [EC:4.1.1.11 4.1.1.25]
Mlab_0268  protein of unknown function DUF201 [KO:K06914] [EC:6.3.4.24]
Mlab_1383  protein of unknown function DUF556 [KO:K09733] [EC:4.2.3.153]
Mlab_0628  Uncharacterized kinase related to aspartokinase uridylate kinase-like protein [KO:K07144] [EC:2.7.4.31]
Mlab_0269  transcriptional regulator/sugar kinase-like protein [KO:K07072] [EC:2.5.1.131]
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
C01179  3-(4-Hydroxyphenyl)pyruvate
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
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
KO pathway
ko00680   

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