TABLE 4

Overview of enzymes involved in pentose degradation in Archaea and some Bacteria

EnzymeEC no.AbbreviationReaction(s)Protein superfamily(ies) (according to the SCOP database)Protein family(ies)Distribution
d-Glucose dehydrogenase1.1.1.47GDHd-Glucose + NAD(P)+d-glucono-1,5-lactone + NAD(P)H + H+ (also converts d-xylose, d-galactose, and l-arabinose in Sulfolobus spp.)N-terminal GroES-like superfamily; C-terminal NAD(P) binding Rossman fold domain superfamily (also known as the MDR superfamily)Alcohol dehydrogenase N-terminal domain-like and C-terminal domain-like (classical Rossman fold)Thermoacidophilic Crenarchaeota (Sulfolobus spp.)
d-Xylose dehydrogenase1.1.1.175XDHd-Xylose + NADP+d-xylonolactone + NADPH + H+N-terminal domain NAD(P) binding Rossman fold-like domain superfamily; C-terminal glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain superfamily (also known as the GFO/IDH/MocA superfamily)Halophilic Euryarchaeota, Archaea, some Bacteria (e.g., Caulobacter crescentus)
l-Arabinose dehydrogenase1.1.1.46l-AraDHl-Arabinose + NAD(P)+l-arabinolactone + NAD(P)H + H+Short-chain dehydrogenase/reductase family (SDRe family)Halophilic Euryarchaeota
d-Arabinose dehydrogenase1.1.1.116AraDHd-Arabinose + NADP+d-arabinolactone + NADPH + H+ (also converts l-fucose, l-galactose, and d-ribose in Sulfolobus spp.)N-terminal GroES-like superfamily; C-terminal NAD(P) binding Rossman fold domain superfamily (also known as the MDR superfamily)Alcohol dehydrogenase N-terminal domain-like and C-terminal domain-like (classical Rossman fold)Thermoacidophilic Crenarchaeota (Sulfolobus spp.)
d-Xylonate dehydratase4.2.1.82XADd-Xylonate → 2-keto-3-deoxy-d-xylonate + H2O (also converts l-arabinonate in Sulfolobus spp. and Hfx. volcanii)Enolase-like N-terminal and C-terminal domain superfamilyHalophilic Euryarchaeota, Archaea, thermoacidophilic Crenarchaeota (Sulfolobus spp.)
d-Arabinonate dehydratase4.2.1.5AraDd-Arabinonate → 2-keto-3-deoxy-d-arabinonate + H2OEnolase-like N-terminal and C-terminal domain superfamilyThermoacidophilic Crenarchaeota (Sulfolobus spp.)
2-Keto-3-deoxy-d-arabinonate/xylonate dehydratase4.2.1.43KDAD/KDXD2-Keto-3-deoxy-d-arabinonate → α-ketoglutarate semialdehyde + H2O (2-keto-3-deoxy-d-arabinonate and 2-keto-3-deoxy-d-xylonate are identical; in Hfx. volcanii, the enzyme also converts 2-keto-3-deoxy-l-arabinonate)FAH superfamily (C-terminal domain)FAH familyBacteria, ED pathway-utilizing Archaea
2-Keto-3-deoxy-(6-phospho)-d-gluconate aldolase4.1.2.14/4.1.2.18/4.1.2.21KD(P)GA2-Keto-3-deoxy-(6-phospho)-d-gluconate/d-galactonate ⇆ glyceraldehyde (3-phosphate) + pyruvate, 2-keto-3-deoxy-d-arabinonate/d-xylonate ⇆ glycolaldehyde + pyruvateAldolase superfamily [(βα)8 barrel fold]Class I aldolase family (KDG aldolase subfamily distinct from bacterial KDPG aldolases and also from class I F1,6BP aldolases and archaeal-type class IA F1,6BP aldolases)Bacteria, halophilic Euryarchaeota, thermoacidophilic Crenarchaeota (Sulfolobus spp.)
α-Ketoglutarate semialdehyde dehydrogenase1.2.1.26α-KGSADHα-Ketoglutarate semialdehyde + NAD(P)+ + H2O → α-ketoglutarate + NAD(P)H + H+ALDH-like superfamilyThermoacidophilic Crenarchaeota, halophilic Euryarchaeota
Glyceraldehyde:ferredoxin oxidoreductase1.2.99.B1GAORGlyceraldehyde + Fdox + H2O → glycerate + Fdred + H+; likely with side activity toward glycolaldehyde yielding glycolateAldehyde oxidase/xanthine dehydrogenase superfamilySulfolobus spp.
Glyoxylate reductase1.1.1.26Glycolate +NAD+ ⇆ glyoxylate + NADH + H+Formate/glycerate dehydrogenase-like superfamily (NCBI)Formate/glycerate dehydrogenase-like family (NCBI)Thermoacidophilic Crenarchaeota (Sulfolobus spp.)
Malate synthase2.3.3.9MSGlyoxylate + acetyl-CoA + H2O → malate + HS-CoAaMalate synthase superfamily (NCBI)Halophilic Euryarchaeota, thermoacidophilic Crenarchaeota (Sulfolobus spp.), Bacteria, Eukarya (plants, fungi)
  • a HS-CoA, free unbound coenzyme A.