KEGG   PATHWAY: mhz00680
Entry
mhz00680                    Pathway                                
Name
Methane metabolism - Methanomethylovorans hollandica
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
mhz00680  Methane metabolism
mhz00680

Module
mhz_M00356  Methanogenesis, methanol => methane [PATH:mhz00680]
mhz_M00357  Methanogenesis, acetate => methane [PATH:mhz00680]
mhz_M00378  F420 biosynthesis, archaea [PATH:mhz00680]
mhz_M00422  Acetyl-CoA pathway, CO2 => acetyl-CoA [PATH:mhz00680]
mhz_M00563  Methanogenesis, methylamine/dimethylamine/trimethylamine => methane [PATH:mhz00680]
mhz_M00567  Methanogenesis, CO2 => methane [PATH:mhz00680]
mhz_M00608  2-Oxocarboxylic acid chain extension, 2-oxoglutarate => 2-oxoadipate => 2-oxopimelate => 2-oxosuberate [PATH:mhz00680]
mhz_M00935  Methanofuran biosynthesis [PATH:mhz00680]
Other DBs
GO: 0015947
Organism
Methanomethylovorans hollandica [GN:mhz]
Gene
Metho_0975  CO dehydrogenase/acetyl-CoA synthase complex, epsilon subunit [KO:K00192] [EC:1.2.7.4]
Metho_0976  CO dehydrogenase/acetyl-CoA synthase complex, epsilon subunit [KO:K00195]
Metho_0977  CO dehydrogenase/CO-methylating acetyl-CoA synthase complex, beta subunit [KO:K00193] [EC:2.3.1.169]
Metho_0980  CO dehydrogenase/acetyl-CoA synthase gamma subunit (corrinoid Fe-S protein) [KO:K00197] [EC:2.1.1.245]
Metho_0979  CO dehydrogenase/acetyl-CoA synthase, delta subunit [KO:K00194] [EC:2.1.1.245]
Metho_1412  carbon-monoxide dehydrogenase, catalytic subunit [KO:K00198] [EC:1.2.7.4]
Metho_2321  glycine/serine hydroxymethyltransferase [KO:K00600] [EC:2.1.2.1]
Metho_1939  putative glycerate kinase [KO:K11529] [EC:2.7.1.165]
Metho_0369  phosphopyruvate hydratase [KO:K01689] [EC:4.2.1.11]
Metho_2062  malate dehydrogenase, NAD-dependent [KO:K00024] [EC:1.1.1.37]
Metho_0427  DhnA-type fructose-1,6-bisphosphate aldolase-like enzyme [KO:K16305] [EC:4.1.2.13 2.2.1.11]
Metho_0254  putative phospho-2-dehydro-3-deoxyheptonate aldolase [KO:K16306] [EC:4.1.2.13 2.2.1.10]
Metho_0268  putative phospho-2-dehydro-3-deoxyheptonate aldolase [KO:K16306] [EC:4.1.2.13 2.2.1.10]
Metho_0581  fructose-1,6-bisphosphatase, class II [KO:K02446] [EC:3.1.3.11]
Metho_0565  hexose kinase, 1-phosphofructokinase family [KO:K16370] [EC:2.7.1.11]
Metho_2034  archaeal ADP-dependent phosphofructokinase/glucokinase [KO:K00918] [EC:2.7.1.146 2.7.1.147]
Metho_2035  ADP-specific phosphofructokinase [KO:K00918] [EC:2.7.1.146 2.7.1.147]
Metho_0199  6-phospho 3-hexuloisomerase [KO:K08094] [EC:5.3.1.27]
Metho_0261  formaldehyde-activating enzyme [KO:K13812] [EC:4.2.1.147 4.1.2.43]
Metho_0283  Demethylmenaquinone methyltransferase [KO:K13831] [EC:4.1.2.43 5.3.1.27]
Metho_0729  formylmethanofuran dehydrogenase subunit A [KO:K00200] [EC:1.2.7.12]
Metho_0732  formylmethanofuran dehydrogenase subunit B [KO:K00201] [EC:1.2.7.12]
Metho_1809  formylmethanofuran dehydrogenase subunit B [KO:K00201] [EC:1.2.7.12]
Metho_0730  formylmethanofuran dehydrogenase subunit C [KO:K00202] [EC:1.2.7.12]
Metho_0731  formylmethanofuran dehydrogenase subunit D [KO:K00203] [EC:1.2.7.12]
Metho_1808  formylmethanofuran dehydrogenase subunit D [KO:K00203] [EC:1.2.7.12]
Metho_0728  NADH:ubiquinone oxidoreductase chain I-like protein [KO:K00205]
Metho_1080  NADH:ubiquinone oxidoreductase chain I-like protein [KO:K00205]
Metho_1810  CO dehydrogenase/acetyl-CoA synthase gamma subunit (corrinoid Fe-S protein) [KO:K11260]
Metho_1571  formylmethanofuran dehydrogenase subunit E [KO:K11261] [EC:1.2.7.12]
Metho_2457  formylmethanofuran--tetrahydromethanopterin N-formyltransferase [KO:K00672] [EC:2.3.1.101]
Metho_1529  methenyltetrahydromethanopterin cyclohydrolase [KO:K01499] [EC:3.5.4.27]
Metho_0243  coenzyme F420-dependent N(5),N(10)-methenyltetrahydromethanopterin dehydrogenase [KO:K00319] [EC:1.5.98.1]
Metho_0305  coenzyme F420-reducing hydrogenase, beta subunit [KO:K00441] [EC:1.12.98.1]
Metho_1361  coenzyme F420-reducing hydrogenase, beta subunit [KO:K00441] [EC:1.12.98.1]
Metho_1162  formaldehyde-activating enzyme [KO:K10713] [EC:4.2.1.147]
Metho_2247  5,10-methylenetetrahydromethanopterin reductase [KO:K00320] [EC:1.5.98.2]
Metho_2092  N5-methyltetrahydromethanopterin:coenzyme M methyltransferase subunit A [KO:K00577] [EC:7.2.1.4]
Metho_0912  tetrahydromethanopterin S-methyltransferase, subunit A [KO:K00577] [EC:7.2.1.4]
Metho_2093  tetrahydromethanopterin S-methyltransferase, subunit B [KO:K00578] [EC:7.2.1.4]
Metho_2094  N5-methyltetrahydromethanopterin:coenzyme M methyltransferase subunit C [KO:K00579] [EC:7.2.1.4]
Metho_2095  N5-methyltetrahydromethanopterin:coenzyme M methyltransferase subunit D [KO:K00580] [EC:7.2.1.4]
Metho_2096  N5-methyltetrahydromethanopterin:coenzyme M methyltransferase subunit E [KO:K00581] [EC:7.2.1.4]
Metho_2091  tetrahydromethanopterin S-methyltransferase, F subunit [KO:K00582] [EC:7.2.1.4]
Metho_2090  N5-methyltetrahydromethanopterin:coenzyme M methyltransferase subunit G [KO:K00583] [EC:7.2.1.4]
Metho_2089  N5-methyltetrahydromethanopterin:coenzyme M methyltransferase subunit H [KO:K00584] [EC:7.2.1.4]
Metho_1670  methyl-coenzyme M reductase, alpha subunit [KO:K00399] [EC:2.8.4.1]
Metho_0164  methyl coenzyme M reductase system, component A2 [KO:K00400]
Metho_0328  ATPase component of various ABC-type transport systems with duplicated ATPase domain [KO:K00400]
Metho_1666  methyl-coenzyme M reductase, beta subunit [KO:K00401] [EC:2.8.4.1]
Metho_1669  methyl-coenzyme M reductase, gamma subunit [KO:K00402] [EC:2.8.4.1]
Metho_1668  methyl-coenzyme M reductase I operon protein C [KO:K03421]
Metho_1667  methyl-coenzyme M reductase operon protein D [KO:K03422]
Metho_1079  polyferredoxin, heterodixulfide reductase subunit A [KO:K03388] [EC:1.8.7.3 1.8.98.4 1.8.98.5 1.8.98.6]
Metho_0299  CoB--CoM heterodisulfide reductase, subunit B [KO:K03389] [EC:1.8.7.3 1.8.98.4 1.8.98.5 1.8.98.6]
Metho_0300  CoB--CoM heterodisulfide reductase, subunit C [KO:K03390] [EC:1.8.7.3 1.8.98.4 1.8.98.5 1.8.98.6]
Metho_1506  Fe-S oxidoreductase [KO:K08264] [EC:1.8.98.1]
Metho_1043  Fe-S oxidoreductase [KO:K08264] [EC:1.8.98.1]
Metho_1505  nitrate reductase gamma subunit [KO:K08265] [EC:1.8.98.1]
Metho_1338  DNA-binding protein, excisionase family [KO:K01895] [EC:6.2.1.1]
Metho_2047  acyl-CoA synthetase/AMP-acid ligase [KO:K01895] [EC:6.2.1.1]
Metho_2385  acetate--CoA ligase [KO:K01895] [EC:6.2.1.1]
Metho_2440  2-oxoacid:ferredoxin oxidoreductase, alpha subunit [KO:K00169] [EC:1.2.7.1]
Metho_2441  2-oxoacid:ferredoxin oxidoreductase, beta subunit [KO:K00170] [EC:1.2.7.1]
Metho_2438  2-oxoacid:acceptor oxidoreductase, gamma subunit, pyruvate/2-ketoisovalerate family [KO:K00172] [EC:1.2.7.1]
Metho_2439  2-oxoacid:acceptor oxidoreductase, delta subunit, pyruvate/2-ketoisovalerate family [KO:K00171] [EC:1.2.7.1]
Metho_1310  phosphoenolpyruvate synthase [KO:K01007] [EC:2.7.9.2]
Metho_0756  phosphoenolpyruvate synthase/pyruvate phosphate dikinase [KO:K01007] [EC:2.7.9.2]
Metho_0146  2,3-bisphosphoglycerate-independent phosphoglycerate mutase [KO:K15633] [EC:5.4.2.12]
Metho_1170  phosphoglyceromutase [KO:K15633] [EC:5.4.2.12]
Metho_2081  putative homoserine kinase [KO:K15635] [EC:5.4.2.12]
Metho_1646  D-3-phosphoglycerate dehydrogenase [KO:K00058] [EC:1.1.1.95 1.1.1.399]
Metho_0242  phosphoserine phosphatase SerB [KO:K01079] [EC:3.1.3.3]
Metho_0761  methyltransferase, MtaA/CmuA family [KO:K14080] [EC:2.1.1.246 2.1.1.377]
Metho_0776  methyltransferase, MtaA/CmuA family [KO:K14080] [EC:2.1.1.246 2.1.1.377]
Metho_1260  methyltransferase, MtaA/CmuA family [KO:K14080] [EC:2.1.1.246 2.1.1.377]
Metho_0775  Methanol-cobalamin methyltransferase B subunit [KO:K04480] [EC:2.1.1.90]
Metho_1601  Methanol-cobalamin methyltransferase B subunit [KO:K04480] [EC:2.1.1.90]
Metho_0774  methyltransferase cognate corrinoid protein [KO:K14081]
Metho_1599  methyltransferase cognate corrinoid protein [KO:K14081]
Metho_1600  methyltransferase cognate corrinoid protein [KO:K14081]
Metho_0007  methyltransferase, MtaA/CmuA family [KO:K14082] [EC:2.1.1.247]
Metho_0037  methyltransferase, MtaA/CmuA family [KO:K14082] [EC:2.1.1.247]
Metho_0355  methyltransferase, MtaA/CmuA family [KO:K14082] [EC:2.1.1.247]
Metho_0027  trimethylamine:corrinoid methyltransferase [KO:K14083] [EC:2.1.1.250]
Metho_0028  methyltransferase cognate corrinoid protein [KO:K14084]
Metho_0131  putative cobalamin binding protein [KO:K14084]
Metho_1575  putative cobalamin binding protein [KO:K14084]
Metho_0607  putative cobalamin binding protein [KO:K14084]
Metho_0036  Monomethylamine methyltransferase MtmB [KO:K16176] [EC:2.1.1.248]
Metho_0013  Monomethylamine methyltransferase MtmB [KO:K16176] [EC:2.1.1.248]
Metho_0035  Monomethylamine methyltransferase MtmB [KO:K16176] [EC:2.1.1.248]
Metho_0014  methyltransferase cognate corrinoid protein [KO:K16177]
Metho_0034  methyltransferase cognate corrinoid protein [KO:K16177]
Metho_0033  dimethylamine:corrinoid methyltransferase [KO:K16178] [EC:2.1.1.249]
Metho_1026  dimethylamine:corrinoid methyltransferase [KO:K16178] [EC:2.1.1.249]
Metho_0032  methyltransferase cognate corrinoid protein [KO:K16179]
Metho_1027  methyltransferase cognate corrinoid protein [KO:K16179]
Metho_1758  sulfopyruvate decarboxylase, alpha subunit [KO:K06034] [EC:4.1.1.79]
Metho_1757  sulfopyruvate decarboxylase, beta subunit [KO:K13039] [EC:4.1.1.79]
Metho_0950  radical SAM domain protein, CofH subfamily [KO:K11781] [EC:2.5.1.147]
Metho_0951  radical SAM domain protein, CofH subfamily [KO:K11781] [EC:2.5.1.147]
Metho_0952  7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofG subunit [KO:K11780] [EC:4.3.1.32]
Metho_0949  2-phospho-L-lactate guanylyltransferase [KO:K14941] [EC:2.7.7.68 2.7.7.105]
Metho_2233  LPPG:FO 2-phospho-L-lactate transferase [KO:K11212] [EC:2.7.8.28]
Metho_2079  F420-0:gamma-glutamyl ligase [KO:K12234] [EC:6.3.2.31 6.3.2.34]
Metho_0886  isopropylmalate/homocitrate/citramalate synthase [KO:K10977] [EC:2.3.3.14 2.3.3.-]
Metho_0694  homoaconitate hydratase family protein/3-isopropylmalate dehydratase, large subunit [KO:K16792] [EC:4.2.1.114]
Metho_0481  3-isopropylmalate dehydratase, small subunit [KO:K16793] [EC:4.2.1.114]
Metho_0479  isopropylmalate/isohomocitrate dehydrogenase [KO:K10978] [EC:1.1.1.87 1.1.1.-]
Metho_2460  tyrosine decarboxylase MnfA [KO:K18933] [EC:4.1.1.25 4.1.1.11]
Metho_0940  putative ATP-utilizing enzyme (ATP-grasp superfamily) [KO:K06914] [EC:6.3.4.24]
Metho_1723  hypothetical protein [KO:K09733] [EC:4.2.3.153]
Metho_0766  aspartate/tyrosine/aromatic aminotransferase [KO:K19793] [EC:2.6.1.108]
Metho_0938  putative kinase, aspartokinase/uridylate kinase [KO:K07144] [EC:2.7.4.31]
Metho_0939  putative 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
mhz00010  Glycolysis / Gluconeogenesis
mhz00030  Pentose phosphate pathway
mhz00260  Glycine, serine and threonine metabolism
mhz00300  Lysine biosynthesis
mhz00630  Glyoxylate and dicarboxylate metabolism
mhz00720  Other carbon fixation pathways
mhz00740  Riboflavin metabolism
mhz00790  Folate biosynthesis
mhz00910  Nitrogen metabolism
mhz00920  Sulfur metabolism
KO pathway
ko00680   
LinkDB

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