KEGG   PATHWAY: ko00720
Entry
ko00720                     Pathway                                

Name
Carbon fixation pathways in prokaryotes
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
ko00720  Carbon fixation pathways in prokaryotes
ko00720

Module
M00173  Reductive citrate cycle (Arnon-Buchanan cycle) [PATH:ko00720]
M00374  Dicarboxylate-hydroxybutyrate cycle [PATH:ko00720]
M00375  Hydroxypropionate-hydroxybutylate cycle [PATH:ko00720]
M00376  3-Hydroxypropionate bi-cycle [PATH:ko00720]
M00377  Reductive acetyl-CoA pathway (Wood-Ljungdahl pathway) [PATH:ko00720]
M00579  Phosphate acetyltransferase-acetate kinase pathway, acetyl-CoA => acetate [PATH:ko00720]
M00620  Incomplete reductive citrate cycle, acetyl-CoA => oxoglutarate [PATH:ko00720]
Other DBs
GO: 0015977
Orthology
K00169  pyruvate ferredoxin oxidoreductase alpha subunit [EC:1.2.7.1]
K00170  pyruvate ferredoxin oxidoreductase beta subunit [EC:1.2.7.1]
K00172  pyruvate ferredoxin oxidoreductase gamma subunit [EC:1.2.7.1]
K00189  2-oxoisovalerate/pyruvate ferredoxin oxidoreductase gamma subunit [EC:1.2.7.7 1.2.7.1]
K00171  pyruvate ferredoxin oxidoreductase delta subunit [EC:1.2.7.1]
K03737  pyruvate-ferredoxin/flavodoxin oxidoreductase [EC:1.2.7.1 1.2.7.-]
K01007  pyruvate, water dikinase [EC:2.7.9.2]
K01006  pyruvate, orthophosphate dikinase [EC:2.7.9.1]
K01595  phosphoenolpyruvate carboxylase [EC:4.1.1.31]
K01958  pyruvate carboxylase [EC:6.4.1.1]
K01959  pyruvate carboxylase subunit A [EC:6.4.1.1]
K01960  pyruvate carboxylase subunit B [EC:6.4.1.1]
K00024  malate dehydrogenase [EC:1.1.1.37]
K01676  fumarate hydratase, class I [EC:4.2.1.2]
K01677  fumarate hydratase subunit alpha [EC:4.2.1.2]
K01678  fumarate hydratase subunit beta [EC:4.2.1.2]
K01679  fumarate hydratase, class II [EC:4.2.1.2]
K01675  fumarate hydratase D [EC:4.2.1.2]
K01774  fumarate hydratase E [EC:4.2.1.2]
K00239  succinate dehydrogenase / fumarate reductase, flavoprotein subunit [EC:1.3.5.1 1.3.5.4]
K00240  succinate dehydrogenase / fumarate reductase, iron-sulfur subunit [EC:1.3.5.1 1.3.5.4]
K00241  succinate dehydrogenase / fumarate reductase, cytochrome b subunit
K00242  succinate dehydrogenase / fumarate reductase, membrane anchor subunit
K18859  succinate dehydrogenase / fumarate reductase, subunit D
K18860  putative succinate dehydrogenase / fumarate reductase, subunit D
K00244  fumarate reductase flavoprotein subunit [EC:1.3.5.4]
K00245  fumarate reductase iron-sulfur subunit [EC:1.3.5.4]
K00246  fumarate reductase subunit C
K00247  fumarate reductase subunit D
K18556  NADH-dependent fumarate reductase subunit A [EC:1.3.1.6]
K18557  NADH-dependent fumarate reductase subunit B [EC:1.3.1.6]
K18558  NADH-dependent fumarate reductase subunit C
K18559  NADH-dependent fumarate reductase subunit D
K18560  NADH-dependent fumarate reductase subunit E
K18209  fumarate reductase (CoM/CoB) subunit A [EC:1.3.4.1]
K18210  fumarate reductase (CoM/CoB) subunit B [EC:1.3.4.1]
K01902  succinyl-CoA synthetase alpha subunit [EC:6.2.1.5]
K01903  succinyl-CoA synthetase beta subunit [EC:6.2.1.5]
K15038  succinyl-CoA reductase [EC:1.2.1.76]
K14465  succinate semialdehyde reductase (NADPH) [EC:1.1.1.-]
K14466  4-hydroxybutyrate---CoA ligase (AMP-forming) [EC:6.2.1.40]
K14467  4-hydroxybutyrate---CoA ligase (AMP-forming) [EC:6.2.1.40]
K18861  4-hydroxybutyrate---CoA ligase (AMP-forming) [EC:6.2.1.40]
K18593  4-hydroxybutyrate---CoA ligase (ADP-forming) [EC:6.2.1.56]
K14534  4-hydroxybutyryl-CoA dehydratase / vinylacetyl-CoA-Delta-isomerase [EC:4.2.1.120 5.3.3.3]
K15016  enoyl-CoA hydratase / 3-hydroxyacyl-CoA dehydrogenase [EC:4.2.1.17 1.1.1.35]
K00626  acetyl-CoA C-acetyltransferase [EC:2.3.1.9]
K00174  2-oxoglutarate/2-oxoacid ferredoxin oxidoreductase subunit alpha [EC:1.2.7.3 1.2.7.11]
K00175  2-oxoglutarate/2-oxoacid ferredoxin oxidoreductase subunit beta [EC:1.2.7.3 1.2.7.11]
K00177  2-oxoglutarate ferredoxin oxidoreductase subunit gamma [EC:1.2.7.3]
K00176  2-oxoglutarate ferredoxin oxidoreductase subunit delta [EC:1.2.7.3]
K00031  isocitrate dehydrogenase [EC:1.1.1.42]
K01681  aconitate hydratase [EC:4.2.1.3]
K01682  aconitate hydratase 2 / 2-methylisocitrate dehydratase [EC:4.2.1.3 4.2.1.99]
K01648  ATP citrate (pro-S)-lyase [EC:2.3.3.8]
K15230  ATP-citrate lyase alpha-subunit [EC:2.3.3.8]
K15231  ATP-citrate lyase beta-subunit [EC:2.3.3.8]
K15232  citryl-CoA synthetase large subunit [EC:6.2.1.18]
K15233  citryl-CoA synthetase small subunit
K15234  citryl-CoA lyase [EC:4.1.3.34]
K01962  acetyl-CoA carboxylase carboxyl transferase subunit alpha [EC:6.4.1.2 2.1.3.15]
K02160  acetyl-CoA carboxylase biotin carboxyl carrier protein
K01961  acetyl-CoA carboxylase, biotin carboxylase subunit [EC:6.4.1.2 6.3.4.14]
K01963  acetyl-CoA carboxylase carboxyl transferase subunit beta [EC:6.4.1.2 2.1.3.15]
K01964  acetyl-CoA/propionyl-CoA carboxylase [EC:6.4.1.2 6.4.1.3]
K18603  acetyl-CoA/propionyl-CoA carboxylase [EC:6.4.1.2 6.4.1.3]
K15036  acetyl-CoA/propionyl-CoA carboxylase [EC:6.4.1.2 6.4.1.3 2.1.3.15]
K18604  acetyl-CoA/propionyl-CoA carboxylase [EC:6.4.1.2 6.4.1.3 2.1.3.15]
K15037  biotin carboxyl carrier protein
K18605  biotin carboxyl carrier protein
K14468  malonyl-CoA reductase / 3-hydroxypropionate dehydrogenase (NADP+) [EC:1.2.1.75 1.1.1.298]
K15017  malonyl-CoA/succinyl-CoA reductase (NADPH) [EC:1.2.1.75 1.2.1.76]
K15039  3-hydroxypropionate dehydrogenase (NADP+) [EC:1.1.1.298]
K18602  malonic semialdehyde reductase [EC:1.1.1.-]
K14469  acrylyl-CoA reductase (NADPH) / 3-hydroxypropionyl-CoA dehydratase / 3-hydroxypropionyl-CoA synthetase [EC:1.3.1.84 4.2.1.116 6.2.1.36]
K15018  3-hydroxypropionyl-coenzyme A synthetase [EC:6.2.1.36]
K18594  3-hydroxypropionyl-CoA synthetase (ADP-forming) [EC:6.2.1.-]
K15019  3-hydroxypropionyl-coenzyme A dehydratase [EC:4.2.1.116]
K15020  acryloyl-coenzyme A reductase [EC:1.3.1.84]
K08691  malyl-CoA/(S)-citramalyl-CoA lyase [EC:4.1.3.24 4.1.3.25]
K14449  2-methylfumaryl-CoA hydratase [EC:4.2.1.148]
K14470  2-methylfumaryl-CoA isomerase [EC:5.4.1.3]
K09709  3-methylfumaryl-CoA hydratase [EC:4.2.1.153]
K15052  propionyl-CoA carboxylase [EC:6.4.1.3 2.1.3.15]
K05606  methylmalonyl-CoA/ethylmalonyl-CoA epimerase [EC:5.1.99.1]
K01847  methylmalonyl-CoA mutase [EC:5.4.99.2]
K01848  methylmalonyl-CoA mutase, N-terminal domain [EC:5.4.99.2]
K01849  methylmalonyl-CoA mutase, C-terminal domain [EC:5.4.99.2]
K14471  succinyl-CoA:(S)-malate CoA-transferase subunit A [EC:2.8.3.22]
K14472  succinyl-CoA:(S)-malate CoA-transferase subunit B [EC:2.8.3.22]
K05299  formate dehydrogenase (NADP+) alpha subunit [EC:1.17.1.10]
K15022  formate dehydrogenase (NADP+) beta subunit [EC:1.17.1.10]
K01938  formate--tetrahydrofolate ligase [EC:6.3.4.3]
K01491  methylenetetrahydrofolate dehydrogenase (NADP+) / methenyltetrahydrofolate cyclohydrolase [EC:1.5.1.5 3.5.4.9]
K00297  methylenetetrahydrofolate reductase (NADPH) [EC:1.5.1.20]
K15023  5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase [EC:2.1.1.258]
K00198  anaerobic carbon-monoxide dehydrogenase catalytic subunit [EC:1.2.7.4]
K00196  anaerobic carbon-monoxide dehydrogenase iron sulfur subunit
K14138  acetyl-CoA synthase [EC:2.3.1.169]
K00197  acetyl-CoA decarbonylase/synthase, CODH/ACS complex subunit gamma [EC:2.1.1.245]
K00194  acetyl-CoA decarbonylase/synthase, CODH/ACS complex subunit delta [EC:2.1.1.245]
K00625  phosphate acetyltransferase [EC:2.3.1.8]
K13788  phosphate acetyltransferase [EC:2.3.1.8]
K15024  putative phosphotransacetylase [EC:2.3.1.8]
K00925  acetate kinase [EC:2.7.2.1]
K01895  acetyl-CoA synthetase [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
Related
pathway
ko00710  Carbon fixation in photosynthetic organisms
LinkDB

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