KEGG   PATHWAY: rpb00680Help
Entry
rpb00680                    Pathway                                

Name
Methane metabolism - Rhodopseudomonas palustris HaA2
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
rpb00680  Methane metabolism
rpb00680

Ortholog table
Module
rpb_M00378  F420 biosynthesis [PATH:rpb00680]
Other DBs
BSID: 31245
GO: 0015947
Organism
Rhodopseudomonas palustris HaA2 [GN:rpb]
Gene
RPB_3418  Alcohol dehydrogenase superfamily, zinc-containing [KO:K00121] [EC:1.1.1.1 1.1.1.284]
RPB_0724  formate dehydrogenase, alpha subunit [KO:K00123] [EC:1.17.1.9]
RPB_0725  NADH dehydrogenase (quinone) [KO:K00124]
RPB_0726  NADH dehydrogenase (ubiquinone), 24 kDa subunit [KO:K00127]
RPB_0722  formate dehydrogenase delta subunit [KO:K00126] [EC:1.17.1.9]
RPB_2634  serine hydroxymethyltransferase [KO:K00600] [EC:2.1.2.1]
RPB_4629  Serine--glyoxylate transaminase [KO:K00830] [EC:2.6.1.51 2.6.1.45 2.6.1.44]
RPB_3567  Hydroxypyruvate reductase [KO:K11529] [EC:2.7.1.165]
RPB_2778  enolase [KO:K01689] [EC:4.2.1.11]
RPB_3592  Phosphoenolpyruvate carboxylase [KO:K01595] [EC:4.1.1.31]
RPB_0281  malate dehydrogenase (NAD) [KO:K00024] [EC:1.1.1.37]
RPB_4471  fructose-bisphosphate aldolase [KO:K01623] [EC:4.1.2.13]
RPB_0950  fructose-bisphosphate aldolase [KO:K01624] [EC:4.1.2.13]
RPB_0947  D-fructose 1,6-bisphosphatase [KO:K03841] [EC:3.1.3.11]
RPB_2965  fructose-1,6-bisphosphatase, class II [KO:K11532] [EC:3.1.3.37 3.1.3.11]
RPB_0444  6-phosphofructokinase [KO:K16370] [EC:2.7.1.11]
RPB_1138  glutamate synthase (NADPH) GltB1 subunit [KO:K22081] [EC:2.1.1.21]
RPB_1137  glutamate synthase (NADPH) GltB3 subunit [KO:K22082] [EC:2.1.1.21]
RPB_1136  ferredoxin-dependent glutamate synthase [KO:K22083] [EC:2.1.1.21]
RPB_1141  sarcosine oxidase, beta subunit family [KO:K22084] [EC:1.5.99.5]
RPB_1142  Sarcosine oxidase, delta subunit, heterotetrameric [KO:K22085] [EC:1.5.99.5]
RPB_1143  sarcosine oxidase, alpha subunit family [KO:K22086] [EC:1.5.99.5]
RPB_1144  Sarcosine oxidase, gamma subunit [KO:K22087] [EC:1.5.99.5]
RPB_4023  Coenzyme F420 hydrogenase/dehydrogenase beta subunit-like [KO:K00441] [EC:1.12.98.1]
RPB_4431  methylenetetrahydromethanopterin reductase [KO:K00320] [EC:1.5.98.2]
RPB_1027  acetate kinase [KO:K00925] [EC:2.7.2.1]
RPB_0319  acetyl-coenzyme A synthetase [KO:K01895] [EC:6.2.1.1]
RPB_2123  AMP-dependent synthetase and ligase [KO:K01895] [EC:6.2.1.1]
RPB_0436  phosphoglycerate mutase [KO:K15633] [EC:5.4.2.12]
RPB_1315  D-3-phosphoglycerate dehydrogenase [KO:K00058] [EC:1.1.1.399 1.1.1.95]
RPB_4226  D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding [KO:K00058] [EC:1.1.1.399 1.1.1.95]
RPB_1314  phosphoserine aminotransferase [KO:K00831] [EC:2.6.1.52]
RPB_3347  phosphoserine phosphatase [KO:K01079] [EC:3.1.3.3]
RPB_4423  FO synthase subunit 2 / FO synthase subunit 1 [KO:K11779] [EC:2.5.1.77]
RPB_4422  Protein of unknown function DUF121 [KO:K14941] [EC:2.7.7.68]
RPB_4407  LPPG:FO 2-phospho-L-lactate transferase [KO:K11212] [EC:2.7.8.28]
RPB_4408  coenzyme F420-0 gamma-glutamyl ligase [KO:K12234] [EC:6.3.2.34 6.3.2.31]
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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