KEGG   PATHWAY: mvu00680Help
Entry
mvu00680                    Pathway                                

Name
Methane metabolism - Methanocaldococcus vulcanius
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
mvu00680  Methane metabolism
mvu00680

Ortholog table
Module
mvu_M00358  Coenzyme M biosynthesis [PATH:mvu00680]
mvu_M00378  F420 biosynthesis [PATH:mvu00680]
mvu_M00422  Acetyl-CoA pathway, CO2 => acetyl-CoA [PATH:mvu00680]
mvu_M00567  Methanogenesis, CO2 => methane [PATH:mvu00680]
mvu_M00608  2-Oxocarboxylic acid chain extension, 2-oxoglutarate => 2-oxoadipate => 2-oxopimelate => 2-oxosuberate [PATH:mvu00680]
Other DBs
BSID: 126846
GO: 0015947
Organism
Methanocaldococcus vulcanius [GN:mvu]
Gene
Metvu_1163  formate dehydrogenase, alpha subunit [KO:K22516] [EC:1.8.98.6 1.17.98.3]
Metvu_0711  molybdopterin oxidoreductase [KO:K22516] [EC:1.8.98.6 1.17.98.3]
Metvu_0710  coenzyme F420 hydrogenase/dehydrogenase beta subunit domain protein [KO:K00125] [EC:1.8.98.6 1.17.98.3]
Metvu_1187  CO dehydrogenase/acetyl-CoA synthase complex, epsilon subunit [KO:K00192] [EC:1.2.7.4]
Metvu_0967  CO dehydrogenase/acetyl-CoA synthase complex, beta subunit [KO:K00192 K00193] [EC:1.2.7.4 2.3.1.-]
Metvu_1184  CO dehydrogenase/acetyl-CoA synthase complex, beta subunit [KO:K00193] [EC:2.3.1.-]
Metvu_1053  CO dehydrogenase/acetyl-CoA synthase delta subunit, TIM barrel [KO:K00197] [EC:2.1.1.245]
Metvu_1052  CO dehydrogenase/acetyl-CoA synthase, delta subunit [KO:K00194] [EC:2.1.1.245]
Metvu_1186  CO dehydrogenase/acetyl-CoA synthase complex, epsilon subunit [KO:K00195]
Metvu_0628  carbon-monoxide dehydrogenase, catalytic subunit [KO:K00198] [EC:1.2.7.4]
Metvu_1161  4Fe-4S ferredoxin iron-sulfur binding domain protein [KO:K00196]
Metvu_1162  4Fe-4S ferredoxin iron-sulfur binding domain protein [KO:K00196]
Metvu_0753  Glycine hydroxymethyltransferase [KO:K00600] [EC:2.1.2.1]
Metvu_1625  enolase [KO:K01689] [EC:4.2.1.11]
Metvu_0361  Malate dehydrogenase (NADP(+)) [KO:K00024] [EC:1.1.1.37]
Metvu_0943  protein of unknown function DUF100 [KO:K01622] [EC:3.1.3.11 4.1.2.13]
Metvu_0368  Fructose-bisphosphate aldolase [KO:K16305] [EC:2.2.1.11 4.1.2.13]
Metvu_1437  predicted phospho-2-dehydro-3-deoxyheptonate aldolase [KO:K16306] [EC:2.2.1.10 4.1.2.13]
Metvu_0786  ADP-specific phosphofructokinase [KO:K00918] [EC:2.7.1.147 2.7.1.146]
Metvu_0392  6-phospho 3-hexuloisomerase [KO:K08094] [EC:5.3.1.27]
Metvu_0541  Dimethylmenaquinone methyltransferase [KO:K08093] [EC:4.1.2.43]
Metvu_1176  Formaldehyde-activating enzyme (Fae) [KO:K13812] [EC:4.1.2.43 4.2.1.147]
Metvu_0799  formylmethanofuran dehydrogenase subunit A [KO:K00200] [EC:1.2.7.12]
Metvu_0713  formylmethanofuran dehydrogenase subunit B [KO:K00201] [EC:1.2.7.12]
Metvu_1491  formylmethanofuran dehydrogenase subunit B [KO:K00201] [EC:1.2.7.12]
Metvu_0919  conserved hypothetical protein [KO:K00202] [EC:1.2.7.12]
Metvu_0797  formylmethanofuran dehydrogenase subunit C [KO:K00202] [EC:1.2.7.12]
Metvu_0800  molybdopterin dinucleotide-binding region [KO:K00203] [EC:1.2.7.12]
Metvu_0803  4Fe-4S ferredoxin iron-sulfur binding domain protein [KO:K00204]
Metvu_0802  4Fe-4S ferredoxin iron-sulfur binding domain protein [KO:K00205]
Metvu_0801  4Fe-4S ferredoxin iron-sulfur binding domain protein [KO:K11260]
Metvu_0708  formylmethanofuran dehydrogenase subunit E region [KO:K11261] [EC:1.2.7.12]
Metvu_0497  formylmethanofuran/tetrahydromethanopterin N-formyltransferase [KO:K00672] [EC:2.3.1.101]
Metvu_1361  methenyltetrahydromethanopterin cyclohydrolase [KO:K01499] [EC:3.5.4.27]
Metvu_0302  Methylenetetrahydromethanopterin dehydrogenase [KO:K00319] [EC:1.5.98.1]
Metvu_1282  coenzyme F420 hydrogenase, subunit alpha [KO:K00440] [EC:1.12.98.1]
Metvu_0629  coenzyme F420-reducing hydrogenase, alpha subunit [KO:K00440] [EC:1.12.98.1]
Metvu_1285  coenzyme F420 hydrogenase, subunit beta [KO:K00441] [EC:1.12.98.1]
Metvu_0895  Coenzyme F420 hydrogenase [KO:K00441] [EC:1.12.98.1]
Metvu_0631  coenzyme F420 hydrogenase/dehydrogenase beta subunit domain protein [KO:K00441] [EC:1.12.98.1]
Metvu_0700  coenzyme F420-reducing hydrogenase delta subunit [KO:K00442]
Metvu_1283  coenzyme F420-reducing hydrogenase delta subunit [KO:K00442]
Metvu_1284  coenzyme F420 hydrogenase, subunit gamma [KO:K00443] [EC:1.12.98.1]
Metvu_0630  NADH ubiquinone oxidoreductase 20 kDa subunit [KO:K00443] [EC:1.12.98.1]
Metvu_0027  coenzyme F420-dependent N(5),N(10)-methenyltetrahydromethanopterin reductase [KO:K13942] [EC:1.12.98.2]
Metvu_0160  5,10-methylenetetrahydromethanopterin reductase [KO:K00320] [EC:1.5.98.2]
Metvu_0154  tetrahydromethanopterin S-methyltransferase, subunit A [KO:K00577] [EC:2.1.1.86]
Metvu_0153  Tetrahydromethanopterin S-methyltransferase [KO:K00578] [EC:2.1.1.86]
Metvu_0152  tetrahydromethanopterin S-methyltransferase, subunit C [KO:K00579] [EC:2.1.1.86]
Metvu_0151  tetrahydromethanopterin S-methyltransferase, subunit D [KO:K00580] [EC:2.1.1.86]
Metvu_0150  tetrahydromethanopterin S-methyltransferase, subunit E [KO:K00581] [EC:2.1.1.86]
Metvu_0155  tetrahydromethanopterin S-methyltransferase, F subunit [KO:K00582] [EC:2.1.1.86]
Metvu_0156  tetrahydromethanopterin S-methyltransferase, subunit G [KO:K00583] [EC:2.1.1.86]
Metvu_0157  tetrahydromethanopterin S-methyltransferase, MtrH subunit [KO:K00584] [EC:2.1.1.86]
Metvu_0149  methyl-coenzyme M reductase, alpha subunit [KO:K00399] [EC:2.8.4.1]
Metvu_1194  methyl-coenzyme M reductase, alpha subunit [KO:K00399] [EC:2.8.4.1]
Metvu_1123  methyl coenzyme M reductase system, component A2 [KO:K00400]
Metvu_1469  ABC transporter releated protein [KO:K00400]
Metvu_0145  methyl-coenzyme M reductase, beta subunit [KO:K00401] [EC:2.8.4.1]
Metvu_1192  methyl-coenzyme M reductase, beta subunit [KO:K00401] [EC:2.8.4.1]
Metvu_0148  methyl-coenzyme M reductase, gamma subunit [KO:K00402] [EC:2.8.4.1]
Metvu_1193  methyl-coenzyme M reductase, gamma subunit [KO:K00402] [EC:2.8.4.1]
Metvu_0147  methyl-coenzyme M reductase I operon protein C [KO:K03421]
Metvu_0146  methyl-coenzyme M reductase operon protein D [KO:K03422]
Metvu_1195  methyl-coenzyme M reductase operon protein D [KO:K03422]
Metvu_1485  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]
Metvu_0714  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]
Metvu_0280  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]
Metvu_0442  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]
Metvu_0443  CoB/CoM heterodisulfide reductase, subunit C [KO:K03390] [EC:1.8.98.6 1.8.98.5 1.8.98.4 1.8.7.3]
Metvu_0281  CoB/CoM heterodisulfide reductase, subunit C [KO:K03390] [EC:1.8.98.6 1.8.98.5 1.8.98.4 1.8.7.3]
Metvu_1486  methyl-viologen-reducing hydrogenase delta subunit [KO:K14127] [EC:1.8.98.6 1.8.98.5 1.12.99.-]
Metvu_0718  methyl-viologen-reducing hydrogenase delta subunit [KO:K14127] [EC:1.8.98.6 1.8.98.5 1.12.99.-]
Metvu_1488  nickel-dependent hydrogenase large subunit [KO:K14126] [EC:1.8.98.5 1.12.99.-]
Metvu_0716  nickel-dependent hydrogenase large subunit [KO:K14126] [EC:1.8.98.5 1.12.99.-]
Metvu_0717  NADH ubiquinone oxidoreductase 20 kDa subunit [KO:K14128] [EC:1.8.98.5 1.12.99.-]
Metvu_1487  NADH ubiquinone oxidoreductase 20 kDa subunit [KO:K14128] [EC:1.8.98.5 1.12.99.-]
Metvu_1159  pyruvate flavodoxin/ferredoxin oxidoreductase domain protein [KO:K00169] [EC:1.2.7.1]
Metvu_1160  thiamine pyrophosphate protein domain protein TPP-binding protein [KO:K00170] [EC:1.2.7.1]
Metvu_1157  pyruvate/ketoisovalerate oxidoreductase, gamma subunit [KO:K00172] [EC:1.2.7.1]
Metvu_1158  pyruvate ferredoxin/flavodoxin oxidoreductase, delta subunit [KO:K00171] [EC:1.2.7.1]
Metvu_0945  phosphoenolpyruvate synthase [KO:K01007] [EC:2.7.9.2]
Metvu_0722  phosphonopyruvate decarboxylase-related protein [KO:K15635] [EC:5.4.2.12]
Metvu_0779  phosphonopyruvate decarboxylase-related protein [KO:K15635] [EC:5.4.2.12]
Metvu_1427  D-3-phosphoglycerate dehydrogenase [KO:K00058] [EC:1.1.1.399 1.1.1.95]
Metvu_1678  phosphoserine phosphatase SerB [KO:K01079] [EC:3.1.3.3]
Metvu_1522  Phosphosulfolactate synthase [KO:K08097] [EC:4.4.1.19]
Metvu_0374  2-phosphosulfolactate phosphatase [KO:K05979] [EC:3.1.3.71]
Metvu_0738  (R)-2-hydroxyacid dehydrogenase [KO:K05884] [EC:1.1.1.337]
Metvu_1521  sulfopyruvate decarboxylase subunit ComD [KO:K06034] [EC:4.1.1.79]
Metvu_1181  thiamine pyrophosphate protein domain protein TPP-binding protein [KO:K13039] [EC:4.1.1.79]
Metvu_0187  7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofG subunit [KO:K11780] [EC:2.5.1.77]
Metvu_0742  7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofH subunit [KO:K11781] [EC:2.5.1.77]
Metvu_0088  2-phospho-L-lactate guanylyltransferase CofC [KO:K14941] [EC:2.7.7.68]
Metvu_0809  LPPG domain protein containing protein [KO:K11212] [EC:2.7.8.28]
Metvu_1689  F420-dependent oxidoreductase [KO:K12234] [EC:6.3.2.34 6.3.2.31]
Metvu_1301  RimK domain protein ATP-grasp [KO:K14940] [EC:6.3.2.32]
Metvu_1576  isopropylmalate/citramalate/homocitrate synthase [KO:K10977] [EC:2.3.3.- 2.3.3.14]
Metvu_1303  homoaconitate hydratase family protein [KO:K16792] [EC:4.2.1.114]
Metvu_0677  3-isopropylmalate dehydratase, small subunit [KO:K16793] [EC:4.2.1.114]
Metvu_0864  3-isopropylmalate dehydratase, small subunit [KO:K16793] [EC:4.2.1.114]
Metvu_0752  isopropylmalate/isohomocitrate dehydrogenase [KO:K10978] [EC:1.1.1.- 1.1.1.87]
Metvu_1091  Pyridoxal-dependent decarboxylase [KO:K18933] [EC:4.1.1.11 4.1.1.25]
Metvu_0080  protein of unknown function DUF201 [KO:K06914] [EC:6.3.4.24]
Metvu_1271  protein of unknown function DUF556 [KO:K09733] [EC:4.2.3.153]
Metvu_0344  aminotransferase class I and II [KO:K19793] [EC:2.6.1.108]
Metvu_0230  aspartate/glutamate/uridylate kinase [KO:K07144] [EC:2.7.4.31]
Metvu_0143  H4MPT-linked C1 transfer pathway 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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