KEGG   PATHWAY: chy00720
Entry
chy00720                    Pathway                                
Name
Carbon fixation pathways in prokaryotes - Carboxydothermus hydrogenoformans
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
chy00720  Carbon fixation pathways in prokaryotes
chy00720

Module
chy_M00377  Reductive acetyl-CoA pathway (Wood-Ljungdahl pathway) [PATH:chy00720]
chy_M00579  Phosphate acetyltransferase-acetate kinase pathway, acetyl-CoA => acetate [PATH:chy00720]
Other DBs
GO: 0015977
Organism
Carboxydothermus hydrogenoformans [GN:chy]
Gene
CHY_0443  ppdK; pyruvate, phosphate dikinase [KO:K01006] [EC:2.7.9.1]
CHY_0061  fumarate hydratase, alpha subunit [KO:K01677] [EC:4.2.1.2]
CHY_1375  fumarate hydratase, alpha subunit [KO:K01677] [EC:4.2.1.2]
CHY_1374  fumarate hydratase, beta subunit [KO:K01678] [EC:4.2.1.2]
CHY_0062  fumarate hydratase, beta subunit [KO:K01678] [EC:4.2.1.2]
CHY_1373  fumarate reductase, flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
CHY_1370  frdB2; fumarate reductase, iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
CHY_0064  frdB1; fumarate reductase, iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
CHY_1372  putative membrane protein [KO:K00241]
CHY_0065  putative succinate/fumarate oxidoreductase [KO:K00241]
CHY_1371  putative membrane protein [KO:K00242]
CHY_0913  sucD; succinyl-CoA synthetase, alpha subunit [KO:K01902] [EC:6.2.1.5]
CHY_0912  sucC; succinyl-CoA synthetase, beta subunit [KO:K01903] [EC:6.2.1.5]
CHY_1314  abfD; gamma-aminobutyrate metabolism dehydratase/isomerase [KO:K14534] [EC:4.2.1.120 5.3.3.3]
CHY_1730  4-hydroxyphenylacetate 3-hydroxylase family protein [KO:K14534] [EC:4.2.1.120 5.3.3.3]
CHY_1355  atoB; acetyl-CoA acetyltransferase [KO:K00626] [EC:2.3.1.9]
CHY_1288  acetyl-CoA acetyltransferase [KO:K00626] [EC:2.3.1.9]
CHY_1604  acetyl-CoA acetyltransferase [KO:K00626] [EC:2.3.1.9]
CHY_0043  putative keto/oxoacid ferredoxin oxidoreductase, alpha subunit [KO:K00174] [EC:1.2.7.3 1.2.7.11]
CHY_1972  putative keto/oxoacid ferredoxin oxidoreductase, alpha subunit [KO:K00174] [EC:1.2.7.3 1.2.7.11]
CHY_0577  putative keto/oxoacid ferredoxin oxidoreductase, alpha subunit [KO:K00174] [EC:1.2.7.3 1.2.7.11]
CHY_1311  putative keto/oxoacid ferredoxin oxidoreductase, alpha subunit [KO:K00174] [EC:1.2.7.3 1.2.7.11]
CHY_1971  putative keto/oxoacid ferredoxin oxidoreductase, beta subunit [KO:K00175] [EC:1.2.7.3 1.2.7.11]
CHY_0044  putative keto/oxoacid ferredoxin oxidoreductase, beta subunit [KO:K00175] [EC:1.2.7.3 1.2.7.11]
CHY_1312  putative keto/oxoacid ferredoxin oxidoreductase, beta subunit [KO:K00175] [EC:1.2.7.3 1.2.7.11]
CHY_0576  putative keto/oxoacid ferredoxin oxidoreductase, beta subunit [KO:K00175] [EC:1.2.7.3 1.2.7.11]
CHY_1970  putative keto/oxoacid ferredoxin oxidoreductase, gamma subunit [KO:K00177] [EC:1.2.7.3]
CHY_0575  putative keto/oxoacid ferredoxin oxidoreductase, gamma subunit [KO:K00177] [EC:1.2.7.3]
CHY_1313  putative keto/oxoacid ferredoxin oxidoreductase, gamma subunit [KO:K00177] [EC:1.2.7.3]
CHY_0045  putative keto/oxoacid ferredoxin oxidoreductase, gamma subunit [KO:K00177] [EC:1.2.7.3]
CHY_0046  putative keto/oxoacid ferredoxin oxidoreductase, delta subunit [KO:K00176] [EC:1.2.7.3]
CHY_1973  putative keto/oxoacid ferredoxin oxidoreductase, delta subunit [KO:K00176] [EC:1.2.7.3]
CHY_1310  putative keto/oxoacid ferredoxin oxidoreductase, delta subunit [KO:K00176] [EC:1.2.7.3]
CHY_0578  putative keto/oxoacid ferredoxin oxidoreductase, delta subunit [KO:K00176] [EC:1.2.7.3]
CHY_1142  accA; acetyl-CoA carboxylase, carboxyl transferase, alpha subunit [KO:K01962] [EC:6.4.1.2 2.1.3.15]
CHY_0918  accC1; acetyl-CoA carboxylase, biotin carboxylase [KO:K01961] [EC:6.4.1.2 6.3.4.14]
CHY_1998  accC2; acetyl-CoA carboxylase, biotin carboxylase [KO:K01961] [EC:6.4.1.2 6.3.4.14]
CHY_1141  accD; acetyl-CoA carboxylase, carboxyl transferase, beta subunit [KO:K01963] [EC:6.4.1.2 2.1.3.15]
CHY_0916  glyoxalase family protein [KO:K05606] [EC:5.1.99.1]
CHY_0733  fdhA; NAD-dependent formate dehydrogenase, alpha subunit, selenocysteine-containing [KO:K05299] [EC:1.17.1.10]
CHY_2385  fhs; formate--tetrahydrofolate ligase [KO:K01938] [EC:6.3.4.3]
CHY_1878  folD; methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase [KO:K01491] [EC:1.5.1.5 3.5.4.9]
CHY_0696  fchA1; methenyltetrahydrofolate cyclohydrolase [KO:K01500] [EC:3.5.4.9]
CHY_1879  fchA2; methenyltetrahydrofolate cyclohydrolase [KO:K01500] [EC:3.5.4.9]
CHY_1233  methylenetetrahydrofolate reductase family protein [KO:K00297] [EC:1.5.1.54]
CHY_1227  acsE; 5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase [KO:K15023] [EC:2.1.1.258]
CHY_0736  cooSIV; carbon-monoxide dehydrogenase, catalytic subunit [KO:K00198] [EC:1.2.7.4]
CHY_0034  cooSV; carbon-monoxide dehydrogenase, catalytic subunit [KO:K00198] [EC:1.2.7.4]
CHY_0085  cooSII; carbon-monoxide dehydrogenase, catalytic subunit [KO:K00198] [EC:1.2.7.4]
CHY_1824  cooSI; carbon-monoxide dehydrogenase, catalytic subunit [KO:K00198] [EC:1.2.7.4]
CHY_0735  cooF2; iron-sulfur cluster-binding protein CooF [KO:K00196]
CHY_1825  cooF3; iron-sulfur cluster-binding protein CooF [KO:K00196]
CHY_1713  iron-sulfur cluster-binding protein [KO:K00196]
CHY_0086  cooF1; iron-sulfur cluster-binding protein CooF [KO:K00196]
CHY_1222  acsB; CO dehydrogenase/acetyl-CoA synthase complex, beta subunit [KO:K14138] [EC:2.3.1.169]
CHY_1223  acsC; carbon monoxide dehydrogenase corrinoid/iron-sulfur protein, gamma subunit [KO:K00197] [EC:2.1.1.245]
CHY_1226  acsD; CO dehydrogenase/acetyl-CoA synthase, iron-sulfur protein [KO:K00194] [EC:2.1.1.245]
CHY_1456  pta; phosphate acetyltransferase [KO:K00625] [EC:2.3.1.8]
CHY_1455  ackA; acetate kinase [KO:K00925] [EC:2.7.2.1]
CHY_0572  acetyl-coenzyme A synthetase family protein [KO:K01895] [EC:6.2.1.1]
CHY_0249  acsA; acetyl-coenzyme A synthetase [KO:K01895] [EC:6.2.1.1]
CHY_0659  acoE; acetyl-CoA synthetase [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
Related
pathway
chy00710  Carbon fixation in photosynthetic organisms
KO pathway
ko00720   
LinkDB

DBGET integrated database retrieval system