TABLE 1

Overview of enzymes involved in the classical EMP pathway in Bacteria and Eukarya as well as in the modified EMP pathway versions in Archaea

EnzymeEC no.AbbreviationReactionProtein superfamily(ies) (according to the SCOP database)Protein family(ies)Distribution
Hexokinase2.7.1.1HKHexose + ATP → hexose 6-phosphate + ADPActin-like ATPase superfamilyHexokinase familyEukarya
ATP-dependent glucokinase2.7.1.2ATP-GLKGlucose + ATP → glucose 6-phosphate + ADPActin-like ATPase superfamilyGlucokinase familyBacteria
ADP-dependent glucokinase2.7.1.147ADP-GLKGlucose + ADP → glucose 6-phosphate + AMPRibokinase superfamilyADP-dependent sugar kinase familyArchaea (mainly anaerobic Euryarchaeota)
ROK hexokinase2.7.1.1ROK-HKHexose + ATP → hexose 6-phosphate + ADPActin-like ATPase superfamilyROK familyArchaea (Crenarchaeota), Bacteria
Ketohexokinase2.7.1.3KHKFructose + ATP → fructose 1-phosphate + ADPProtein sequence in Archaea unknown; eukaryote ribokinase superfamilyPFK-BHalophilic Euryarchaeota, Eukarya
Hexokinase2.7.1.1HKHexose + ATP → hexose 6-phosphate + ADPActin-like ATPase superfamilyProbably BadF/BadG/BcrA/BcrD ATPase familyCrenarchaeota (Sulfolobus)
Phosphoglucose isomerase5.3.1.9PGIGlucose 6-phosphate ⇆ fructose 6-phosphatePGI superfamily (SIS domain superfamily)PGI familyEukarya, Bacteria, halophilic Euryarchaeota, methanogenic Euryarchaeota (Methanococcus)
Phosphoglucose/phosphomannose isomerase5.3.1.9/5.3.1.8PGI/PMIGlucose 6-phosphate/mannose 6-phosphate ⇆ fructose 6-phosphatePGI superfamily (SIS domain superfamily)PGI/PMI familyCrenarchaeota, Euryarchaeota (Thermoplasma)
Cupin-type phosphoglucose isomerase5.3.1.9cPGIGlucose 6-phosphate ⇆ fructose 6-phosphateCupin superfamilycPGI familyAnaerobic Euryarchaeota (including Methanosarcina mazei), some Bacteria (Ensifer meliloti, Salmonella Typhimurium, horizontal gene transfer)
ATP-dependent phosphofructokinase2.7.1.11ATP-PFKFructose 6-phosphate + ATP → fructose 1,6-bisphosphate + ADPPhosphofructokinase superfamilyPhosphofructokinase family (known as PFK-A)Eukarya, Bacteria
ADP-dependent phosphofructokinase2.7.1.146ADP-PFKFructose 6-phosphate + ADP → fructose 1,6-bisphosphate + AMPRibokinase superfamilyADP-dependent sugar kinase familyArchaea, (mainly anaerobic Euryarchaeota), glycogen-forming methanogens
ATP-dependent phosphofructokinase2.7.1.11PFK-BFructose 6-phosphate + ATP → fructose 1,6-bisphosphate + ADPRibokinase superfamilyPFK-B familyCrenarchaeota (Aeropyrum pernix, Desulfurococcus amylolyticus)
PPi-dependent phosphofructokinase2.7.1.90PPi-PFKFructose 6-phosphate + PPi ⇆ fructose 1,6-bisphosphate + PiPhosphofructokinase superfamilyPhosphofructokinase family (known as PFK-A), forming a distinct subfamilyCrenarchaeota (Thermoproteus tenax), some Bacteria, Eukarya (protists, plants)
Fructose-1,6-bisphosphate aldolase class I4.1.2.13FBPA IFructose 1,6-bisphosphate ⇆ dihydroxyacetone phosphate + glyceraldehyde 3-phosphateAldolase superfamily [(βα)8 barrel fold]Class I aldolase familyEukarya
Archaeal type class I fructose-1,6-bisphosphate aldolase4.1.2.13FBPA IAFructose 1,6-bisphosphate ⇆ dihydroxyacetone phosphate + glyceraldehyde 3-phosphateAldolase superfamily [(βα)8 barrel fold]Class I aldolase familyArchaea, Bacteria
Fructose-1,6-bisphosphate aldolase class II4.1.2.13FBPA IIFructose 1,6-bisphosphate ⇆ dihydroxyacetone phosphate + glyceraldehyde 3-phosphateAldolase superfamily [(βα)8 barrel fold]Class II FBP aldolase familyHalophilic Euryarchaeota, Bacteria, fungi
Triosephosphate isomerase5.3.1.1TIMDihydroxyacetone phosphate ⇆ glyceraldehyde 3-phosphateTriosephosphate isomerase superfamily [(βα)8 barrel fold]Triosephosphate isomerase familyEukarya, Bacteria, Archaea
Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)1.2.1.13 (NADP+), 1.2.1.12 (NAD+)GAPDHGlyceraldehyde 3-phosphate + NAD(P)+ + Pi ⇆ 1,3-bisphosphoglycerate + NAD(P)H + H+N-terminal domain NAD(P) binding Rossman fold-like domain superfamily; C-terminal glyceraldehyde 3-phosphate dehydrogenase-like, C-terminal domain superfamilyGAPDH N- and C-terminal domain families, respectivelyEukarya, Bacteria, halophilic Euryarchaeota, glycogen-degrading methanogens (catabolic and anabolic), all other Archaea (only anabolic)
Phosphoglycerate kinase2.7.3.2PGK1,3-Bisphosphoglycerate + ADP ⇆ 3-phosphoglycerate + ATPPhosphoglycerate kinase superfamilyPhosphoglycerate kinase familyEukarya, Bacteria, halophilic Euryarchaeota, glycogen-degrading methanogens (catabolic and anabolic), all other Archaea (only anabolic)
Glyceraldehyde-3-phosphate dehydrogenase (nonphosphorylating)1.2.1.9GAPNGlyceraldehyde 3-phosphate + NAD(P)+ → 3-phosphoglycerate + NAD(P)H + H+ALDH-like superfamilyALDH-like family(Hyper)thermophilic Archaea
Glyceraldehyde-3-phosphate:ferredoxin oxidoreductase1.2.7.6GAPORGlyceraldehyde 3-phosphate + Fdox → 3-phosphoglycerate + FdredaAldehyde:ferredoxin oxidoreductase, N- and C-terminal domain superfamilyAldehyde:ferredoxin oxidoreductase, N- and C-terminal domain familyAnaerobic Archaea, some anaerobic (hyper)thermophiles in addition to GAPN
2,3-Bisphosphoglycerate-dependent phosphoglycerate mutase5.4.2.1dPGAM3-Phosphoglycerate ⇆ 2-phosphoglyceratePhosphoglycerate mutase-like superfamilyCofactor-dependent phosphoglycerate mutase familyVertebrates, yeasts, Bacteria, mainly thermoacidophilic Archaea and Methanosarcina spp.
2,3-Bisphosphoglycerate-independent phosphoglycerate mutase5.4.2.1iPGAM3-Phosphoglycerate ⇆ 2-phosphoglycerateAlkaline phosphatase superfamily; 2,3-bisphosphoglycerate-independent phosphoglycerate mutase, substrate binding domain superfamily2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, catalytic domain family; 2,3-bisphosphoglycerate-independent phosphoglycerate mutase, substrate binding domain familyPlants, nematodes, Bacteria, Archaea
Enolase4.2.1.11ENO2-Phosphoglycerate ⇆ phosphoenolpyruvateEnolase-like, N- and C-terminal domain superfamilyEnolase-like, N- and C-terminal domain-like familyEukarya, Bacteria, Archaea
Pyruvate kinase2.7.1.40PKPhosphoenolpyruvate + ADP → pyruvate + ATPPEP-pyruvate domain superfamily; pyruvate kinase beta-barrel domain-like superfamilyPyruvate kinase family (N-terminal domain); pyruvate kinase beta barrel domain family (C terminal)Eukarya, Bacteria, Archaea
Pyruvate:phosphate dikinase2.7.9.1PPDKPyruvate + ATP + Pi ⇆ phosphoenolpyruvate + AMP + PPiGlutathione 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 PEP-utilizing enzyme family)Eukarya, Bacteria, Archaea
  • a Fdox, oxidized ferredoxin; Fdred, reduced ferredoxin.