ENTRY ko00720 Pathway NAME Other carbon fixation pathways 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 Other carbon fixation pathways 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] DBLINKS GO: 0015977 ORTHOLOGY K00024 mdh; malate dehydrogenase [EC:1.1.1.37] K00031 IDH1, IDH2, icd; isocitrate dehydrogenase [EC:1.1.1.42] K00169 porA; pyruvate ferredoxin oxidoreductase alpha subunit [EC:1.2.7.1] K00170 porB; pyruvate ferredoxin oxidoreductase beta subunit [EC:1.2.7.1] K00171 porD; pyruvate ferredoxin oxidoreductase delta subunit [EC:1.2.7.1] K00172 porC, porG; pyruvate ferredoxin oxidoreductase gamma subunit [EC:1.2.7.1] K00174 korA, oorA, oforA; 2-oxoglutarate/2-oxoacid ferredoxin oxidoreductase subunit alpha [EC:1.2.7.3 1.2.7.11] K00175 korB, oorB, oforB; 2-oxoglutarate/2-oxoacid ferredoxin oxidoreductase subunit beta [EC:1.2.7.3 1.2.7.11] K00176 korD, oorD; 2-oxoglutarate ferredoxin oxidoreductase subunit delta [EC:1.2.7.3] K00177 korC, oorC; 2-oxoglutarate ferredoxin oxidoreductase subunit gamma [EC:1.2.7.3] K00189 vorG, porG; 2-oxoisovalerate/pyruvate ferredoxin oxidoreductase gamma subunit [EC:1.2.7.7 1.2.7.1] K00194 cdhD, acsD; acetyl-CoA decarbonylase/synthase, CODH/ACS complex subunit delta [EC:2.1.1.245] K00196 cooF; anaerobic carbon-monoxide dehydrogenase iron sulfur subunit K00197 cdhE, acsC; acetyl-CoA decarbonylase/synthase, CODH/ACS complex subunit gamma [EC:2.1.1.245] K00198 cooS, acsA; anaerobic carbon-monoxide dehydrogenase catalytic subunit [EC:1.2.7.4] K00233 frdA, fdrA; succinate dehydrogenase flavoprotein subunit K00239 sdhA, frdA; succinate dehydrogenase flavoprotein subunit [EC:1.3.5.1] K00240 sdhB, frdB; succinate dehydrogenase iron-sulfur subunit [EC:1.3.5.1] K00241 sdhC, frdC; succinate dehydrogenase cytochrome b subunit K00242 sdhD, frdD; succinate dehydrogenase membrane anchor subunit K00244 frdA; succinate dehydrogenase flavoprotein subunit [EC:1.3.5.1] K00245 frdB; succinate dehydrogenase iron-sulfur subunit [EC:1.3.5.1] K00246 frdC; succinate dehydrogenase subunit C K00247 frdD; succinate dehydrogenase subunit D K00297 metF, MTHFR; methylenetetrahydrofolate reductase (NADH) [EC:1.5.1.54] K00625 pta; phosphate acetyltransferase [EC:2.3.1.8] K00626 ACAT, atoB; acetyl-CoA C-acetyltransferase [EC:2.3.1.9] K00925 ackA; acetate kinase [EC:2.7.2.1] K01006 ppdK; pyruvate, orthophosphate dikinase [EC:2.7.9.1] K01007 pps, ppsA; pyruvate, water dikinase [EC:2.7.9.2] K01491 folD; methylenetetrahydrofolate dehydrogenase (NADP+) / methenyltetrahydrofolate cyclohydrolase [EC:1.5.1.5 3.5.4.9] K01500 fchA; methenyltetrahydrofolate cyclohydrolase K01595 ppc; phosphoenolpyruvate carboxylase [EC:4.1.1.31] K01648 ACLY; ATP citrate (pro-S)-lyase [EC:2.3.3.8] K01675 fumD; fumarate hydratase D K01676 E4.2.1.2A, fumA, fumB; fumarate hydratase, class I [EC:4.2.1.2] K01677 E4.2.1.2AA, fumA; fumarate hydratase subunit alpha [EC:4.2.1.2] K01678 E4.2.1.2AB, fumB; fumarate hydratase subunit beta [EC:4.2.1.2] K01679 E4.2.1.2B, fumC, FH; fumarate hydratase, class II [EC:4.2.1.2] K01681 ACO; aconitate hydratase [EC:4.2.1.3] K01682 acnB; aconitate hydratase 2 / 2-methylisocitrate dehydratase [EC:4.2.1.3 4.2.1.99] K01774 fumE; fumarate hydratase E K01847 MUT; methylmalonyl-CoA mutase [EC:5.4.99.2] K01848 E5.4.99.2A, mcmA1; methylmalonyl-CoA mutase, N-terminal domain [EC:5.4.99.2] K01849 E5.4.99.2B, mcmA2; methylmalonyl-CoA mutase, C-terminal domain [EC:5.4.99.2] K01895 ACSS1_2, acs; acetyl-CoA synthetase [EC:6.2.1.1] K01902 sucD; succinyl-CoA synthetase alpha subunit [EC:6.2.1.5] K01903 sucC; succinyl-CoA synthetase beta subunit [EC:6.2.1.5] K01938 fhs; formate--tetrahydrofolate ligase [EC:6.3.4.3] K01958 PC, pyc; pyruvate carboxylase [EC:6.4.1.1] K01959 pycA; pyruvate carboxylase subunit A [EC:6.4.1.1] K01960 pycB; pyruvate carboxylase subunit B [EC:6.4.1.1] K01961 accC; acetyl-CoA carboxylase, biotin carboxylase subunit [EC:6.4.1.2 6.3.4.14] K01962 accA; acetyl-CoA carboxylase carboxyl transferase subunit alpha [EC:6.4.1.2 2.1.3.15] K01963 accD; acetyl-CoA carboxylase carboxyl transferase subunit beta [EC:6.4.1.2 2.1.3.15] K01964 K01964; acetyl-CoA/propionyl-CoA carboxylase [EC:6.4.1.2 6.4.1.3] K02160 accB, bccP; acetyl-CoA carboxylase biotin carboxyl carrier protein K03737 por, nifJ; pyruvate-ferredoxin/flavodoxin oxidoreductase [EC:1.2.7.1 1.2.7.-] K05299 fdhA; formate dehydrogenase (NADP+) alpha subunit [EC:1.17.1.10] K05606 MCEE, epi; methylmalonyl-CoA/ethylmalonyl-CoA epimerase [EC:5.1.99.1] K08691 mcl; malyl-CoA/(S)-citramalyl-CoA lyase [EC:4.1.3.24 4.1.3.25] K09709 meh; 3-methylfumaryl-CoA hydratase [EC:4.2.1.153] K13788 pta; phosphate acetyltransferase [EC:2.3.1.8] K14138 acsB; acetyl-CoA synthase [EC:2.3.1.169] K14449 mch, mcd; 2-methylfumaryl-CoA hydratase [EC:4.2.1.148] K14465 K14465; succinate semialdehyde reductase (NADPH) [EC:1.1.1.-] K14466 K14466; 4-hydroxybutyrate---CoA ligase (AMP-forming) [EC:6.2.1.40] K14467 4hbl; 4-hydroxybutyrate---CoA ligase (AMP-forming) [EC:6.2.1.40] K14468 mcr; malonyl-CoA reductase / 3-hydroxypropionate dehydrogenase (NADP+) [EC:1.2.1.75 1.1.1.298] K14469 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] K14470 mct; 2-methylfumaryl-CoA isomerase [EC:5.4.1.3] K14471 smtA1; succinyl-CoA:(S)-malate CoA-transferase subunit A [EC:2.8.3.22] K14472 smtB; succinyl-CoA:(S)-malate CoA-transferase subunit B [EC:2.8.3.22] K14534 abfD; 4-hydroxybutyryl-CoA dehydratase / vinylacetyl-CoA-Delta-isomerase [EC:4.2.1.120 5.3.3.3] K15016 K15016; enoyl-CoA hydratase / 3-hydroxyacyl-CoA dehydrogenase [EC:4.2.1.17 1.1.1.35] K15017 K15017; malonyl-CoA/succinyl-CoA reductase (NADPH) [EC:1.2.1.75 1.2.1.76] K15018 K15018; 3-hydroxypropionyl-coenzyme A synthetase [EC:6.2.1.36] K15019 K15019; 3-hydroxypropionyl-coenzyme A dehydratase [EC:4.2.1.116] K15020 K15020; acryloyl-coenzyme A reductase [EC:1.3.1.84] K15022 fdhB; formate dehydrogenase (NADP+) beta subunit [EC:1.17.1.10] K15023 acsE; 5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase [EC:2.1.1.258] K15024 K15024; putative phosphotransacetylase [EC:2.3.1.8] K15036 K15036; acetyl-CoA/propionyl-CoA carboxylase [EC:6.4.1.2 6.4.1.3 2.1.3.15] K15037 K15037; biotin carboxyl carrier protein K15038 K15038; succinyl-CoA reductase [EC:1.2.1.76] K15039 K15039; 3-hydroxypropionate dehydrogenase (NADP+) [EC:1.1.1.298] K15052 K15052; propionyl-CoA carboxylase [EC:6.4.1.3 2.1.3.15] K15230 aclA; ATP-citrate lyase alpha-subunit [EC:2.3.3.8] K15231 aclB; ATP-citrate lyase beta-subunit [EC:2.3.3.8] K15232 ccsA; citryl-CoA synthetase large subunit [EC:6.2.1.18] K15233 ccsB; citryl-CoA synthetase small subunit K15234 ccl; citryl-CoA lyase [EC:4.1.3.34] K18209 tfrA; fumarate reductase (CoM/CoB) subunit A [EC:1.3.4.1] K18210 tfrB; fumarate reductase (CoM/CoB) subunit B [EC:1.3.4.1] K18556 frdA; NADH-dependent fumarate reductase subunit A [EC:1.3.1.6] K18557 frdB; NADH-dependent fumarate reductase subunit B [EC:1.3.1.6] K18558 frdC; NADH-dependent fumarate reductase subunit C K18559 frdD; NADH-dependent fumarate reductase subunit D K18560 frdE; NADH-dependent fumarate reductase subunit E K18593 E6.2.1.56; 4-hydroxybutyrate---CoA ligase (ADP-forming) [EC:6.2.1.56] K18594 K18594; 3-hydroxypropionyl-CoA synthetase (ADP-forming) [EC:6.2.1.-] K18602 K18602; malonic semialdehyde reductase [EC:1.1.1.-] K18603 K18603; acetyl-CoA/propionyl-CoA carboxylase [EC:6.4.1.2 6.4.1.3] K18604 K18604; acetyl-CoA/propionyl-CoA carboxylase [EC:6.4.1.2 6.4.1.3 2.1.3.15] K18605 K18605; biotin carboxyl carrier protein K18859 sdhD, frdD; succinate dehydrogenase subunit D K18860 sdhD, frdD; succinate dehydrogenase subunit D K18861 K18861; 4-hydroxybutyrate---CoA ligase (AMP-forming) [EC:6.2.1.40] K22015 fdhF; formate dehydrogenase (hydrogenase) [EC:1.17.98.4 1.17.98.-] K25007 metV; methylenetetrahydrofolate reductase (NADH) small subunit K25008 rnfC2; ion-translocating oxidoreductase complex subunit C K25123 hydA2; iron hydrogenase HydA2 K25124 hycB; FeS-containing electron transfer protein K25221 mtgA; [methyl-Co(III) glycine betaine-specific corrinoid protein]---tetrahydrofolate methyltransferase K25774 K25774; 4-hydroxybutyrate---CoA ligase (AMP-forming) K25915 mtvA; [methyl-Co(III) methoxylated-aromatic-compound-specific corrinoid protein]---tetrahydrofolate methyltransferase K25995 frdB, fdrB; succinate dehydrogenase iron-sulfur subunit K25996 frdC, fdrC; succinate dehydrogenase subunit C K26318 fccA, fcc3; fumarate reductase (cytochrome) K26930 mtqA; [methyl-Co(III) quaternary-amine-specific corrinoid protein]---tetrahydrofolate methyltransferase K27802 acnA; aconitate hydratase A / 2-methylisocitrate dehydratase 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 PMID:19955419 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 PMID:19429610 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 PMID:18511565 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 PMID:15838028 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 PMID:11827525 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 REL_PATHWAY ko00710 Carbon fixation by Calvin cycle ///