KEGG   PATHWAY: ave00680
Entry
ave00680                    Pathway                                
Name
Methane metabolism - Archaeoglobus veneficus
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
ave00680  Methane metabolism
ave00680

Module
ave_M00378  F420 biosynthesis, archaea [PATH:ave00680]
ave_M00422  Acetyl-CoA pathway, CO2 => acetyl-CoA [PATH:ave00680]
Other DBs
GO: 0015947
Organism
Archaeoglobus veneficus [GN:ave]
Gene
Arcve_0721  Nitrate reductase [KO:K00123] [EC:1.17.1.9]
Arcve_1249  4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [KO:K00124]
Arcve_0720  4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [KO:K00124]
Arcve_2107  4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [KO:K00125] [EC:1.17.98.3 1.8.98.6]
Arcve_1121  Acetyl-CoA decarbonylase/synthase complex subunit alpha [KO:K00192] [EC:1.2.7.4]
Arcve_1122  CO dehydrogenase/acetyl-CoA synthase complex, epsilon subunit [KO:K00195]
Arcve_1123  CO dehydrogenase/acetyl-CoA synthase complex, beta subunit [KO:K00193] [EC:2.3.1.169]
Arcve_1126  CO dehydrogenase/acetyl-CoA synthase delta subunit, TIM barrel [KO:K00197] [EC:2.1.1.245]
Arcve_1125  CO dehydrogenase/acetyl-CoA synthase, delta subunit [KO:K00194] [EC:2.1.1.245]
Arcve_0327  Glycine hydroxymethyltransferase [KO:K00600] [EC:2.1.2.1]
Arcve_1098  Glycine hydroxymethyltransferase [KO:K00600] [EC:2.1.2.1]
Arcve_1595  Enolase [KO:K01689] [EC:4.2.1.11]
Arcve_2006  Phosphoenolpyruvate carboxylase [KO:K01595] [EC:4.1.1.31]
Arcve_1885  Malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
Arcve_0430  phospho-2-dehydro-3-deoxyheptonate aldolase [KO:K11645] [EC:4.1.2.13]
Arcve_0905  protein of unknown function DUF100 [KO:K01622] [EC:4.1.2.13 3.1.3.11]
Arcve_1168  phospho-2-dehydro-3-deoxyheptonate aldolase [KO:K16306] [EC:4.1.2.13 2.2.1.10]
Arcve_0921  6-phospho 3-hexuloisomerase [KO:K08094] [EC:5.3.1.27]
Arcve_1411  Bifunctional enzyme fae/hps [KO:K13812] [EC:4.2.1.147 4.1.2.43]
Arcve_1683  3-hexulose-6-phosphate synthase [KO:K13831] [EC:4.1.2.43 5.3.1.27]
Arcve_0372  formylmethanofuran dehydrogenase subunit A [KO:K00200] [EC:1.2.7.12]
Arcve_1115  formylmethanofuran dehydrogenase subunit A [KO:K00200] [EC:1.2.7.12]
Arcve_0373  formylmethanofuran dehydrogenase subunit B [KO:K00201] [EC:1.2.7.12]
Arcve_1110  formylmethanofuran dehydrogenase subunit B [KO:K00201] [EC:1.2.7.12]
Arcve_1113  formylmethanofuran dehydrogenase subunit B [KO:K00201] [EC:1.2.7.12]
Arcve_0371  formylmethanofuran dehydrogenase subunit C [KO:K00202] [EC:1.2.7.12]
Arcve_1114  formylmethanofuran dehydrogenase subunit C [KO:K00202] [EC:1.2.7.12]
Arcve_0374  molybdopterin dinucleotide-binding region [KO:K00203] [EC:1.2.7.12]
Arcve_1111  tungsten formylmethanofuran dehydrogenase, subunit D (FwdD-1) [KO:K00203] [EC:1.2.7.12]
Arcve_1077  4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [KO:K00205]
Arcve_1118  4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [KO:K00205]
Arcve_1109  Fe-S cluster domain protein [KO:K11260]
Arcve_0336  Formylmethanofuran--tetrahydromethanopterin N-formyltransferase [KO:K00672] [EC:2.3.1.101]
Arcve_1202  formylmethanofuran/tetrahydromethanopterin N-formyltransferase [KO:K00672] [EC:2.3.1.101]
Arcve_2011  Methenyltetrahydromethanopterin cyclohydrolase [KO:K01499] [EC:3.5.4.27]
Arcve_1338  F420-dependent methylenetetrahydromethanopterin dehydrogenase [KO:K00319] [EC:1.5.98.1]
Arcve_1117  coenzyme F420 hydrogenase/dehydrogenase beta subunit domain protein [KO:K00441] [EC:1.12.98.1]
Arcve_1055  hypothetical protein [KO:K00320] [EC:1.5.98.2]
Arcve_0808  5,10-methylenetetrahydromethanopterin reductase [KO:K00320] [EC:1.5.98.2]
Arcve_1567  4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [KO:K03388] [EC:1.8.7.3 1.8.98.4 1.8.98.5 1.8.98.6]
Arcve_1076  methyl-viologen-reducing hydrogenase delta subunit [KO:K03388] [EC:1.8.7.3 1.8.98.4 1.8.98.5 1.8.98.6]
Arcve_0533  4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [KO:K03388] [EC:1.8.7.3 1.8.98.4 1.8.98.5 1.8.98.6]
Arcve_1116  methyl-viologen-reducing hydrogenase delta subunit [KO:K03388] [EC:1.8.7.3 1.8.98.4 1.8.98.5 1.8.98.6]
Arcve_1853  methyl-viologen-reducing hydrogenase delta subunit [KO:K03388] [EC:1.8.7.3 1.8.98.4 1.8.98.5 1.8.98.6]
Arcve_1120  CoB--CoM heterodisulfide reductase [KO:K03389] [EC:1.8.7.3 1.8.98.4 1.8.98.5 1.8.98.6]
Arcve_1119  putative heterodisulfide reductase, C subunit [KO:K03390] [EC:1.8.7.3 1.8.98.4 1.8.98.5 1.8.98.6]
Arcve_0532  methyl-viologen-reducing hydrogenase delta subunit [KO:K14127] [EC:1.12.99.- 1.8.98.5 1.8.98.6]
Arcve_1568  methyl-viologen-reducing hydrogenase delta subunit [KO:K14127] [EC:1.12.99.- 1.8.98.5 1.8.98.6]
Arcve_2108  methyl-viologen-reducing hydrogenase delta subunit [KO:K14127] [EC:1.12.99.- 1.8.98.5 1.8.98.6]
Arcve_1570  Hydrogen dehydrogenase [KO:K14126] [EC:1.12.99.- 1.8.98.5]
Arcve_1855  Hydrogen dehydrogenase [KO:K14126] [EC:1.12.99.- 1.8.98.5]
Arcve_1569  NADH ubiquinone oxidoreductase 20 kDa subunit [KO:K14128] [EC:1.12.99.- 1.8.98.5]
Arcve_1854  NADH ubiquinone oxidoreductase 20 kDa subunit [KO:K14128] [EC:1.12.99.- 1.8.98.5]
Arcve_0328  Acetyl-coenzyme A synthetase [KO:K01895] [EC:6.2.1.1]
Arcve_0887  Acetyl-coenzyme A synthetase [KO:K01895] [EC:6.2.1.1]
Arcve_0797  Pyruvate synthase [KO:K00169] [EC:1.2.7.1]
Arcve_1207  Pyruvate synthase [KO:K00169] [EC:1.2.7.1]
Arcve_1545  Pyruvate synthase [KO:K00169] [EC:1.2.7.1]
Arcve_1208  Pyruvate synthase [KO:K00170] [EC:1.2.7.1]
Arcve_1546  Pyruvate synthase [KO:K00170] [EC:1.2.7.1]
Arcve_0796  Pyruvate synthase [KO:K00170] [EC:1.2.7.1]
Arcve_1205  pyruvate/ketoisovalerate oxidoreductase, gamma subunit [KO:K00172] [EC:1.2.7.1]
Arcve_0802  pyruvate ferredoxin oxidoreductase subunit gamma/delta [KO:K00172] [EC:1.2.7.1]
Arcve_0801  pyruvate/ketoisovalerate oxidoreductase, gamma subunit [KO:K00172] [EC:1.2.7.1]
Arcve_1543  pyruvate/ketoisovalerate oxidoreductase, gamma subunit [KO:K00172] [EC:1.2.7.1]
Arcve_1544  pyruvate ferredoxin/flavodoxin oxidoreductase, delta subunit [KO:K00171] [EC:1.2.7.1]
Arcve_1206  pyruvate ferredoxin/flavodoxin oxidoreductase, delta subunit [KO:K00171] [EC:1.2.7.1]
Arcve_1512  phosphoenolpyruvate synthase [KO:K01007] [EC:2.7.9.2]
Arcve_0617  proposed homoserine kinase [KO:K15635] [EC:5.4.2.12]
Arcve_0410  phosphonopyruvate decarboxylase-related protein [KO:K15635] [EC:5.4.2.12]
Arcve_1526  D-3-phosphoglycerate dehydrogenase [KO:K00058] [EC:1.1.1.95 1.1.1.399]
Arcve_1074  phosphoserine phosphatase SerB [KO:K01079] [EC:3.1.3.3]
Arcve_1610  FO synthase subunit 2 [KO:K11781] [EC:2.5.1.147]
Arcve_1611  FO synthase subunit 1 [KO:K11780] [EC:4.3.1.32]
Arcve_1619  2-phospho-L-lactate guanylyltransferase CofC [KO:K14941] [EC:2.7.7.68 2.7.7.105]
Arcve_0317  LPPG:FO 2-phospho-L-lactate transferase [KO:K11212] [EC:2.7.8.28]
Arcve_0767  F420-0:gamma-glutamyl ligase [KO:K12234] [EC:6.3.2.31 6.3.2.34]
Arcve_0276  L-tyrosine decarboxylase [KO:K18933] [EC:4.1.1.25 4.1.1.11]
Arcve_1368  ATP-grasp fold domain protein, DUF201-type [KO:K06914] [EC:6.3.4.24]
Arcve_1618  UPF0264 protein [KO:K09733] [EC:4.2.3.153]
Arcve_1964  aspartate/glutamate/uridylate kinase [KO:K07144] [EC:2.7.4.31]
Arcve_1963  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
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
ave00010  Glycolysis / Gluconeogenesis
ave00030  Pentose phosphate pathway
ave00260  Glycine, serine and threonine metabolism
ave00300  Lysine biosynthesis
ave00630  Glyoxylate and dicarboxylate metabolism
ave00720  Other carbon fixation pathways
ave00740  Riboflavin metabolism
ave00790  Folate biosynthesis
ave00910  Nitrogen metabolism
ave00920  Sulfur metabolism
KO pathway
ko00680   
LinkDB

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