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. 2014 Mar;78(1):89–175. doi: 10.1128/MMBR.00041-13

TABLE 3.

Overview of enzymes involved in gluconeogenesis in Archaea, Bacteria, and Eukarya

Enzyme EC no. Abbreviation Reaction Protein superfamily(ies) (according to the SCOP database) Protein family(ies) Distribution
Phosphoenolpyruvate carboxykinase 4.1.1.32 (GTP), 4.1.1.49 (ATP) PCK Oxaloacetate + GTP ⇆ phosphoenolpyruvate + CO2 + GDP (ADP) PEP carboxykinase N-terminal domain superfamily; PEP carboxykinase C-terminal domain superfamily PEP carboxykinase N-terminal domain family, PEP carboxykinase C-terminal domain family Eukarya, Bacteria, Euryarchaeota, Crenarchaeota
Pyruvate:phosphate dikinase 2.7.9.1 PPDK Pyruvate + ATP + Pi ⇆ phosphoenolpyruvate + AMP + PPi Glutathione synthetase ATP binding domain-like superfamily (N-terminal domain) (ATP grasp fold), phosphohistidine domain superfamily (central domain), phosphoenolpyruvate/pyruvate domain superfamily (C-terminal domain) (TIM barrel fold) Pyruvate:phosphate dikinase N-terminal, central, and C-terminal domain families, respectively (also known as the PEP-utilizing enzyme family) Eukarya, Bacteria, Archaea
Phosphoenolpyruvate synthase (pyruvate, water dikinase) 2.7.9.2 PEPS Pyruvate + ATP + H2O ⇆ phosphoenolpyruvate + AMP + Pi From sequence comparisons, domain organization likely similar to that of the glutathione synthetase ATP-binding domain-like superfamily (N-terminal domain) (ATP grasp fold); phosphohistidine domain superfamily (central domain); phosphoenolpyruvate-pyruvate domain superfamily (C-terminal domain) (TIM barrel fold) Pyruvate:phosphate dikinase N-terminal, central, and C-terminal domain families, respectively (also known as the PEP-utilizing enzyme family) Eukarya, Bacteria, Archaea
Enolase 4.2.1.11 ENO Phosphoenolpyruvate + H2O ⇆ 2-phosphoglycerate Enolase-like, N- and C-terminal domain superfamily Enolase-like, N- and C-terminal domain-like family Eukarya, Bacteria, Archaea
2,3-Bisphosphoglycerate-independent phosphoglycerate mutase 5.4.2.1 iPGAM 2-Phosphoglycerate ⇆ 3-phosphoglycerate Alkaline phosphatase superfamily, 2,3-bisphosphoglycerate-independent phosphoglycerate mutase; substrate binding domain superfamily 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, catalytic domain family; 2,3-bisphosphoglycerate-independent phosphoglycerate mutase, substrate binding domain family Plants, nematodes, Bacteria, Archaea
2,3-Bisphosphoglycerate-dependent phosphoglycerate mutase 5.4.2.1 dPGAM 2-Phosphoglycerate ⇆ 3-phosphoglycerate Phosphoglycerate mutase-like superfamily Cofactor-dependent phosphoglycerate mutase family Vertebrates, yeasts, Bacteria, mainly thermoacidophilic Archaea and Methanosarcina spp.
Phosphoglycerate kinase 2.7.3.2 PGK 3-Phosphoglycerate + ATP ⇆ 1,3-bisphosphoglycerate + ADP Phosphoglycerate kinase superfamily Phosphoglycerate kinase family Eukarya, Bacteria, Archaea
Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) 1.2.1.13 (NADP+), 1.2.1.12 (NAD+) GAPDH 1,3-Bisphosphoglycerate + NAD(P)H + H+ ⇆ glyceraldehyde 3-phosphate + NAD(P)+ + Pi N-terminal domain NAD(P) binding Rossman fold-like domain superfamily; C-terminal glyceraldehyde 3-phosphate dehydrogenase-like C-terminal domain superfamily GAPDH N- and C-terminal domain families, respectively Eukarya, Bacteria, Archaea
Triosephosphate isomerase 5.3.1.1 TIM Glyceraldehyde 3-phosphate ⇆ dihydroxyacetone phosphate Triosephosphate isomerase superfamily [(βα)8 barrel fold] Triosephosphate isomerase family Eukarya, Bacteria, Archaea
Fructose-1,6-bisphosphatase 3.1.3.11 FBPase Fructose 1,6-bisphosphate → fructose 6-phosphate + Pi Carbohydrate phosphatase superfamily Inositol monophosphatase/fructose-1,6-bisphosphatase-like family (classes I and IV); GlpX-like bacterial fructose-1,6-bisphosphatase family (class II) Type I, Eukarya, Bacteria, and a few haloarchaea and methanogens; type II, Bacteria and a few methanogens; type III, Bacteria; type IV, Euryarchaeota, Crenarchaeota, and a few Bacteria (Thermotoga)
Fructose-1,6-bisphosphate aldolase class II 4.1.2.13 FBPA II Dihydroxyacetone phosphate + glyceraldehyde 3-phosphate ⇆ fructose 1,6-bisphosphate Aldolase superfamily [(βα)8 barrel fold] Class II FBP aldolase family A few halophilic Euryarchaeota, Bacteria, fungi
Archaeal-type class I fructose-1,6-bisphosphate aldolase 4.1.2.13 FBPA IA Dihydroxyacetone phosphate + glyceraldehyde 3-phosphate ⇆ fructose 1,6-bisphosphate Aldolase superfamily [(βα)8 barrel fold] Class I aldolase family Archaea, Bacteria
Fructose-1,6-bisphosphate aldolase class I 4.1.2.13 FBPA I Dihydroxyacetone phosphate + glyceraldehyde 3-phosphate ⇆ fructose 1,6-bisphosphate Aldolase superfamily [(βα)8 barrel fold] Class I aldolase family Eukarya
PPi-dependent phosphofructokinase 2.7.1.90 PPi-PFK Fructose 1,6-bisphosphate + Pi ⇆ glucose 6-phosphate + PPi Phosphofructokinase superfamily Phosphofructokinase family (known as PFK-A), forming a distinct subfamily Crenarchaeota (Thermoproteus tenax), some Bacteria, Eukarya (protists, plants)
Fructose-1,6-bisphosphate aldolase/phosphatase (type V fructose-1,6-bisphosphatase) 3.1.3.11 FBPA/ase Dihydroxyacetone phosphate + glyceraldehyde 3-phosphate → fructose 6-phosphate + Pi Sulfolobus fructose-1,6-bisphosphatase-like protein superfamily (SCOP database) (similarity to the ferredoxin fold in their N-terminal part and to bacterial S-adenosylmethionine decarboxylase in their C-terminal part) Sulfolobus fructose-1,6-bisphosphatase-like protein superfamily (SCOP database) Archaea, deeply branching Bacteria
Cupin-type phosphoglucose isomerase 5.3.1.9 cPGI Fructose 6-phosphate ⇆ glucose 6-phosphate Cupin superfamily cPGI family Anaerobic Euryarchaeota (including Methanosarcina mazei), some Bacteria (Ensifer meliloti, Salmonella Typhimurium, horizontal gene transfer)
Phosphoglucose isomerase/phosphomannose isomerase 5.3.1.9/5.3.1.8 PGI/PMI Fructose 6-phosphate ⇆ glucose 6-phosphate/mannose 6-phosphate PGI superfamily (SIS domain superfamily) PGI/PMI family Crenarchaeota, Euryarchaeota (Thermoplasma)
Phosphoglucose isomerase 5.3.1.9 PGI Fructose 6-phosphate ⇆ glucose 6-phosphate PGI superfamily (SIS domain superfamily) PGI family Eukarya, Bacteria, halophilic Euryarchaeota, methanogenic Euryarchaeota (Methanococcus)