KEGG   PATHWAY: nho00720
Entry
nho00720                    Pathway                                
Name
Carbon fixation pathways in prokaryotes - Natronomonas halophila
Description
Carbon fixation is an important pathway for autotrophs living in various environments. Plants and cyanobacteria fix CO2 as organic compounds using solar energy mainly by the reductive pentose phosphate cycle (also called Calvin cycle, Calvin-Benson cycle, or Calvin-Benson-Bassham cycle) [MD:M00165]. There are, at least, five additional carbon fixation pathways known to exist in autotrophic bacteria and archaea, which differ in reducing compounds, energy source, and oxygen sensitivity of enzymes. (i) The reductive citric acid cycle (Arnon-Buchanan cycle) [MD:M00173] is found in microaerophiles and anaerobes, such as green sulfur bacteria. In one complete turn of this cycle, four molecules of CO2 are fixed by the enzymes that are sensitive to oxygen, resulting in the production of one molecule of oxaloacetate, which is itself an intermediate of the cycle. (ii) The reductive acetyl-CoA pathway (Wood-Ljungdahl pathway) [MD:M00377] is found in strictly anaerobic bacteria and archaea (Proteobacteria, Planctomycetes, Spirochaetes, and Euryarchaeota), some of which are methane-forming. A bifunctional enzyme, carbon monoxide dehydrogenase/acetyl-CoA synthase, catalyzes the reactions from CO2 to CO and from CO2 to a methyl group, and then to generate acetyl-CoA. (iii) The 3-hydroxypropionate bicycle [MD:M00376] is found in some green non-sulphur bacteria of the family Chloroflexaceae. In one complete turn of this bicycle, three molecules of bicarbonate are converted into one molecule of pyruvate. In addition, this bicycle provides the secondary benefit of useful intermediates for biosynthesis: acetyl-CoA, glyoxylate, and succinyl-CoA. (iv) The hydroxypropionate-hydroxybutyrate cycle [MD:M00375] is found in aerobic Crenarchaeota, Acidianus, Metallosphaera, and Sulfolobales. Some of the intermediates and the carboxylation reactions are the same as in the 3-hydroxypropionate bicycle. One complete turn of this cycle generates two molecules of acetyl-CoA, one of which is reutilized in the the cycle and the other is removed for cell material biosynthesis. (v) The dicarboxylate-hydroxybutyrate cycle [MD:M00374] was named after its intermediates: succinate (a kind of dicarboxylate) and hydroxybutyrate. This cycle has been found only in Ignicoccus hospitals, a strictly anaerobic hyperthermophilic archaea. Recent genome study suggests that this cycle may exist in Desulfurococcales (to which Ignicoccus belongs) and Thermoproteales (a taxon close to the origin of archaea). The first half of the cycle, from acetyl-CoA to succinate-CoA, corresponds to the reductive citric acid cycle and the latter half of the cycle, from succinate-CoA to two molecules of acetyl-CoA, corresponds to the hydroxypropionate-hydroxybutyrate cycle.
Class
Metabolism; Energy metabolism
Pathway map
nho00720  Carbon fixation pathways in prokaryotes
nho00720

Other DBs
GO: 0015977
Organism
Natronomonas halophila [GN:nho]
Gene
HWV23_04715  2-oxoacid:acceptor oxidoreductase subunit alpha [KO:K00169] [EC:1.2.7.1]
HWV23_04710  2-ketoglutarate ferredoxin oxidoreductase subunit beta [KO:K00170] [EC:1.2.7.1]
HWV23_12180  ppsA; phosphoenolpyruvate synthase [KO:K01007] [EC:2.7.9.2]
HWV23_08970  malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
HWV23_04075  class II fumarate hydratase [KO:K01679] [EC:4.2.1.2]
HWV23_16365  FAD-binding protein [KO:K00239] [EC:1.3.5.1]
HWV23_16360  succinate dehydrogenase/fumarate reductase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
HWV23_16350  sdhC; succinate dehydrogenase, cytochrome b556 subunit [KO:K00241]
HWV23_16355  succinate dehydrogenase hydrophobic membrane anchor subunit [KO:K00242]
HWV23_03510  sucD; succinate--CoA ligase subunit alpha [KO:K01902] [EC:6.2.1.5]
HWV23_03505  sucC; ADP-forming succinate--CoA ligase subunit beta [KO:K01903] [EC:6.2.1.5]
HWV23_04500  enoyl-CoA hydratase/isomerase family protein [KO:K15016] [EC:4.2.1.17 1.1.1.35]
HWV23_00735  enoyl-CoA hydratase/isomerase family protein [KO:K15016] [EC:4.2.1.17 1.1.1.35]
HWV23_00880  NAD-binding protein [KO:K15016] [EC:4.2.1.17 1.1.1.35]
HWV23_05045  thiolase domain-containing protein [KO:K00626] [EC:2.3.1.9]
HWV23_15115  acetyl-CoA acyltransferase [KO:K00626] [EC:2.3.1.9]
HWV23_16210  thiolase domain-containing protein [KO:K00626] [EC:2.3.1.9]
HWV23_01085  thiolase family protein [KO:K00626] [EC:2.3.1.9]
HWV23_12730  2-oxoacid:acceptor oxidoreductase subunit alpha [KO:K00174] [EC:1.2.7.3 1.2.7.11]
HWV23_12725  2-oxoacid:ferredoxin oxidoreductase subunit beta [KO:K00175] [EC:1.2.7.3 1.2.7.11]
HWV23_01205  icd; isocitrate dehydrogenase (NADP(+)) [KO:K00031] [EC:1.1.1.42]
HWV23_08285  aconitate hydratase [KO:K01681] [EC:4.2.1.3]
HWV23_12745  mce; methylmalonyl-CoA epimerase [KO:K05606] [EC:5.1.99.1]
HWV23_00340  VOC family protein [KO:K05606] [EC:5.1.99.1]
HWV23_05310  methylmalonyl-CoA mutase family protein [KO:K01848] [EC:5.4.99.2]
HWV23_12750  methylmalonyl-CoA mutase family protein [KO:K01848] [EC:5.4.99.2]
HWV23_05070  cobalamin B12-binding domain-containing protein [KO:K01849] [EC:5.4.99.2]
HWV23_03555  folD; bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD [KO:K01491] [EC:1.5.1.5 3.5.4.9]
HWV23_10085  acs; acetate--CoA ligase [KO:K01895] [EC:6.2.1.1]
HWV23_10095  acs; acetate--CoA ligase [KO:K01895] [EC:6.2.1.1]
HWV23_11590  AMP-binding protein [KO:K01895] [EC:6.2.1.1]
HWV23_12810  AMP-binding protein [KO:K01895] [EC:6.2.1.1]
HWV23_00330  AMP-binding protein [KO:K01895] [EC:6.2.1.1]
HWV23_00395  AMP-binding protein [KO:K01895] [EC:6.2.1.1]
HWV23_00425  AMP-binding protein [KO:K01895] [EC:6.2.1.1]
Compound
C00011  CO2
C00022  Pyruvate
C00024  Acetyl-CoA
C00026  2-Oxoglutarate
C00033  Acetate
C00036  Oxaloacetate
C00042  Succinate
C00048  Glyoxylate
C00058  Formate
C00074  Phosphoenolpyruvate
C00083  Malonyl-CoA
C00091  Succinyl-CoA
C00100  Propanoyl-CoA
C00101  Tetrahydrofolate
C00122  Fumarate
C00143  5,10-Methylenetetrahydrofolate
C00149  (S)-Malate
C00158  Citrate
C00222  3-Oxopropanoate
C00227  Acetyl phosphate
C00232  Succinate semialdehyde
C00234  10-Formyltetrahydrofolate
C00237  CO
C00288  HCO3-
C00311  Isocitrate
C00332  Acetoacetyl-CoA
C00417  cis-Aconitate
C00440  5-Methyltetrahydrofolate
C00445  5,10-Methenyltetrahydrofolate
C00566  (3S)-Citryl-CoA
C00683  (S)-Methylmalonyl-CoA
C00877  Crotonoyl-CoA
C00894  Propenoyl-CoA
C00989  4-Hydroxybutanoic acid
C01011  (3S)-Citramalyl-CoA
C01013  3-Hydroxypropanoate
C01144  (S)-3-Hydroxybutanoyl-CoA
C01213  (R)-Methylmalonyl-CoA
C04348  L-Malyl-CoA
C05668  3-Hydroxypropionyl-CoA
C06027  L-erythro-3-Methylmalyl-CoA
C06028  2-Methylfumaryl-CoA
C11062  4-Hydroxybutyryl-CoA
C18323  3-Methylfumaryl-CoA
Reference
  Authors
Zarzycki J, Brecht V, Muller M, Fuchs G
  Title
Identifying the missing steps of the autotrophic 3-hydroxypropionate CO2 fixation cycle in Chloroflexus aurantiacus.
  Journal
Proc Natl Acad Sci U S A 106:21317-22 (2009)
DOI:10.1073/pnas.0908356106
Reference
  Authors
Teufel R, Kung JW, Kockelkorn D, Alber BE, Fuchs G
  Title
3-hydroxypropionyl-coenzyme A dehydratase and acryloyl-coenzyme A reductase, enzymes of the autotrophic 3-hydroxypropionate/4-hydroxybutyrate cycle in the Sulfolobales.
  Journal
J Bacteriol 191:4572-81 (2009)
DOI:10.1128/JB.00068-09
Reference
  Authors
Huber H, Gallenberger M, Jahn U, Eylert E, Berg IA, Kockelkorn D, Eisenreich W, Fuchs G
  Title
A dicarboxylate/4-hydroxybutyrate autotrophic carbon assimilation cycle in the hyperthermophilic Archaeum Ignicoccus hospitalis.
  Journal
Proc Natl Acad Sci U S A 105:7851-6 (2008)
DOI:10.1073/pnas.0801043105
Reference
  Authors
Hugler M, Wirsen CO, Fuchs G, Taylor CD, Sievert SM
  Title
Evidence for autotrophic CO2 fixation via the reductive tricarboxylic acid cycle by members of the epsilon subdivision of proteobacteria.
  Journal
J Bacteriol 187:3020-7 (2005)
DOI:10.1128/JB.187.9.3020-3027.2005
Reference
  Authors
Seravalli J, Kumar M, Ragsdale SW
  Title
Rapid kinetic studies of acetyl-CoA synthesis: evidence supporting the catalytic intermediacy of a paramagnetic NiFeC species in the autotrophic Wood-Ljungdahl pathway.
  Journal
Biochemistry 41:1807-19 (2002)
DOI:10.1021/bi011687i
Reference
PMID:3096193
  Authors
Ljungdahl LG
  Title
The autotrophic pathway of acetate synthesis in acetogenic bacteria.
  Journal
Annu Rev Microbiol 40:415-50 (1986)
DOI:10.1146/annurev.mi.40.100186.002215
KO pathway
ko00720   
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