TABLE 4.
Overview of enzymes involved in pentose degradation in Archaea and some Bacteria
| Enzyme | EC no. | Abbreviation | Reaction(s) | Protein superfamily(ies) (according to the SCOP database) | Protein family(ies) | Distribution |
|---|---|---|---|---|---|---|
| d-Glucose dehydrogenase | 1.1.1.47 | GDH | d-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 dehydrogenase | 1.1.1.175 | XDH | d-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 dehydrogenase | 1.1.1.46 | l-AraDH | l-Arabinose + NAD(P)+ → l-arabinolactone + NAD(P)H + H+ | Short-chain dehydrogenase/reductase family (SDRe family) | Halophilic Euryarchaeota | |
| d-Arabinose dehydrogenase | 1.1.1.116 | AraDH | d-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 dehydratase | 4.2.1.82 | XAD | d-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 superfamily | Halophilic Euryarchaeota, Archaea, thermoacidophilic Crenarchaeota (Sulfolobus spp.) | |
| d-Arabinonate dehydratase | 4.2.1.5 | AraD | d-Arabinonate → 2-keto-3-deoxy-d-arabinonate + H2O | Enolase-like N-terminal and C-terminal domain superfamily | Thermoacidophilic Crenarchaeota (Sulfolobus spp.) | |
| 2-Keto-3-deoxy-d-arabinonate/xylonate dehydratase | 4.2.1.43 | KDAD/KDXD | 2-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 family | Bacteria, ED pathway-utilizing Archaea |
| 2-Keto-3-deoxy-(6-phospho)-d-gluconate aldolase | 4.1.2.14/4.1.2.18/4.1.2.21 | KD(P)GA | 2-Keto-3-deoxy-(6-phospho)-d-gluconate/d-galactonate ⇆ glyceraldehyde (3-phosphate) + pyruvate, 2-keto-3-deoxy-d-arabinonate/d-xylonate ⇆ glycolaldehyde + pyruvate | Aldolase 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 dehydrogenase | 1.2.1.26 | α-KGSADH | α-Ketoglutarate semialdehyde + NAD(P)+ + H2O → α-ketoglutarate + NAD(P)H + H+ | ALDH-like superfamily | Thermoacidophilic Crenarchaeota, halophilic Euryarchaeota | |
| Glyceraldehyde:ferredoxin oxidoreductase | 1.2.99.B1 | GAOR | Glyceraldehyde + Fdox + H2O → glycerate + Fdred + H+; likely with side activity toward glycolaldehyde yielding glycolate | Aldehyde oxidase/xanthine dehydrogenase superfamily | Sulfolobus spp. | |
| Glyoxylate reductase | 1.1.1.26 | Glycolate +NAD+ ⇆ glyoxylate + NADH + H+ | Formate/glycerate dehydrogenase-like superfamily (NCBI) | Formate/glycerate dehydrogenase-like family (NCBI) | Thermoacidophilic Crenarchaeota (Sulfolobus spp.) | |
| Malate synthase | 2.3.3.9 | MS | Glyoxylate + acetyl-CoA + H2O → malate + HS-CoAa | Malate synthase superfamily (NCBI) | Halophilic Euryarchaeota, thermoacidophilic Crenarchaeota (Sulfolobus spp.), Bacteria, Eukarya (plants, fungi) |
a
HS-CoA, free unbound coenzyme A.