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Literature summary extracted from

  • Reher, M.; Fuhrer, T.; Bott, M.; Schoenheit, P.
    The nonphosphorylative Entner-Doudoroff pathway in the thermoacidophilic euryarchaeon Picrophilus torridus involves a novel 2-keto-3-deoxygluconate-specific aldolase (2010), J. Bacteriol., 192, 964-974.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
4.1.2.20 expressed in Escherichia coli BL21 CodonPlus (DE3)-RIL cells Picrophilus torridus
4.1.2.51 expression in Escherichia coli Picrophilus torridus

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
4.1.2.20 0.3
-
 2-dehydro-3-deoxy-D-gluconate at 60°C in 50 mM sodium phosphate buffer (pH 6.2) Picrophilus torridus
4.1.2.20 8
-
 2-dehydro-3-deoxy-6-phospho-D-gluconate at 60°C in 50 mM sodium phosphate buffer (pH 6.2) Picrophilus torridus
4.1.2.51 0.3
-
 2-dehydro-3-deoxy-D-gluconate pH 6.2, 60°C, enzyme purified from Picrophilus torridus Picrophilus torridus
4.1.2.51 0.4
-
 2-dehydro-3-deoxy-D-gluconate pH 6.2, 60°C, recombinant enzyme Picrophilus torridus
4.1.2.51 2.5
-
 2-dehydro-3-deoxy-D-gluconate 6-phosphate pH 6.2, 60°C, recombinant enzyme Picrophilus torridus
4.1.2.51 2.7
-
 pyruvate pH 6.2, 60°C Picrophilus torridus
4.1.2.51 4.6
-
 D-glyceraldehyde pH 6.2, 60°C Picrophilus torridus
4.1.2.51 8
-
 2-dehydro-3-deoxy-D-gluconate 6-phosphate pH 6.2, 60°C, enzyme purified from Picrophilus torridus Picrophilus torridus
4.2.1.39 2
-
 D-galactonate
-
 Picrophilus torridus
4.2.1.39 2.5
-
 gluconate
-
 Picrophilus torridus
4.2.1.140 2
-
 D-galactonate pH 6.2, 60°C Picrophilus torridus
4.2.1.140 2.5
-
 D-gluconate pH 6.2, 60°C Picrophilus torridus

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
4.2.1.39 Mg2+ is required Picrophilus torridus
4.2.1.140 Mg2+ required, Km: 4.2 mM Picrophilus torridus

Molecular Weight [Da]

EC Number Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
4.1.2.20 32000
-
 4 * 32000, SDS-PAGE Picrophilus torridus
4.1.2.20 120000
-
 gel filtration Picrophilus torridus
4.1.2.51 32000
-
 4 * 32000, SDS-PAGE Picrophilus torridus
4.1.2.51 120000
-
 gel filtration Picrophilus torridus
4.2.1.39 44000
-
 8 * 44000, SDS-PAGE Picrophilus torridus
4.2.1.39 340000
-
 gel filtration Picrophilus torridus
4.2.1.140 44000
-
 8 * 44000, SDS-PAGE Picrophilus torridus
4.2.1.140 340000
-
 gel filtration Picrophilus torridus

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
4.1.2.51 2-dehydro-3-deoxy-D-gluconate Picrophilus torridus the enzyme from the archaeon Picrophilus torridus is involved in D-glucose and D-galactose catabolism via the nonphosphorylative variant of the Entner-Doudoroff pathway pyruvate + D-glyceraldehyde
-
 ?
4.2.1.140 D-galactonate Picrophilus torridus
-
 2-dehydro-3-deoxy-D-galactonate + H2O
-
 ?
4.2.1.140 D-gluconate Picrophilus torridus
-
 2-dehydro-3-deoxy-D-gluconate + H2O
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
4.1.2.20 Picrophilus torridus
-
-
-
4.1.2.51 Picrophilus torridus Q6KZI8
-
-
4.2.1.39 Picrophilus torridus Q6L1T2
-
-
4.2.1.140 Picrophilus torridus Q6L1T2
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
4.1.2.20 ammonium sulfate precipitation, phenyl-Sepharose column chromatography, UnoQ5 column chromatography, and Superdex 200 gel filtration Picrophilus torridus
4.1.2.51
-
 Picrophilus torridus
4.2.1.39 by centrifugation and gel filtration, 190fold to apparent homogeneity Picrophilus torridus
4.2.1.140
-
 Picrophilus torridus

Source Tissue

EC Number Source Tissue Comment Organism Textmining
4.1.2.20 culture condition:glucose-grown cell
-
 Picrophilus torridus
-

Specific Activity [micromol/min/mg]

EC Number Specific Activity Minimum [µmol/min/mg] Specific Activity Maximum [µmol/min/mg] Comment Organism
4.1.2.20 0.14
-
 crude extract, at 60°C in 50 mM sodium phosphate buffer (pH 6.2) Picrophilus torridus
4.1.2.20 48
-
 after 343fold purification, at 60°C in 50 mM sodium phosphate buffer (pH 6.2) Picrophilus torridus
4.1.2.51 48
-
 pH 6.2, 60°C, substrate: 2-dehydro-3-deoxy-D-gluconate Picrophilus torridus
4.2.1.140 5.1
-
 substrate: D-gluconate, pH 6.2, 60°C Picrophilus torridus

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
4.1.2.20 2-dehydro-3-deoxy-6-phospho-D-gluconate
-
 Picrophilus torridus pyruvate + glyceraldehyde-3-phosphate
-
 ?
4.1.2.20 2-dehydro-3-deoxy-D-gluconate the enzyme is highly specific for 2-dehydro-3-deoxy-D-gluconate with up to 2000fold higher catalytic efficiency compared to 2-dehydro-3-deoxy-6-phosphogluconate Picrophilus torridus pyruvate + glyceraldehyde
-
 ?
4.1.2.51 2-dehydro-3-deoxy-D-galactonate
-
 Picrophilus torridus pyruvate + D-glyceraldehyde
-
 ?
4.1.2.51 2-dehydro-3-deoxy-D-galactonate the enzyme shows substrate promiscuity, as measured in the direction of aldol synthesis. The enzyme catalyzes the formation of both 2-dehydro-3-deoxy-D-gluconate and its C-4 epimer 2-keto-3-deoxygalactonate from D- or L-glyceraldehyde and pyruvate at a similar ratio, indicating lack of stereospecific control in formation and cleavage of 2-dehydro-3-deoxy-D-gluconate and 2-dehydro-3-deoxy-D-galactonate Picrophilus torridus pyruvate + D-glyceraldehyde
-
 r
4.1.2.51 2-dehydro-3-deoxy-D-gluconate the enzyme from the archaeon Picrophilus torridus is involved in D-glucose and D-galactose catabolism via the nonphosphorylative variant of the Entner-Doudoroff pathway Picrophilus torridus pyruvate + D-glyceraldehyde
-
 ?
4.1.2.51 2-dehydro-3-deoxy-D-gluconate highly specific for 2-dehydro-3-deoxy-D-gluconate with up to 2000fold-higher catalytic efficiency compared to 2-dehydro-3-deoxy-6-phosphogluconate Picrophilus torridus pyruvate + D-glyceraldehyde
-
 ?
4.1.2.51 2-dehydro-3-deoxy-D-gluconate 6-phosphate highly specific for 2-dehydro-3-deoxy-D-gluconate with up to 2000fold-higher catalytic efficiency compared to 2-dehydro-3-deoxy-6-phosphogluconate Picrophilus torridus pyruvate + D-glyceraldehyde 3-phosphate
-
 ?
4.2.1.39 D-galactonate
-
 Picrophilus torridus 2-dehydro-3-deoxy-D-galactonate + H2O
-
 ?
4.2.1.39 gluconate
-
 Picrophilus torridus 2-dehydro-3-deoxy-D-gluconate + H2O
-
 ?
4.2.1.39 additional information xylonate (10 mM) is not utilized Picrophilus torridus ?
-
 ?
4.2.1.140 D-galactonate
-
 Picrophilus torridus 2-dehydro-3-deoxy-D-galactonate + H2O
-
 ?
4.2.1.140 D-galactonate the ratio of catalytic efficiency for gluconate and galactonate utilization is about 10 to 1 Picrophilus torridus 2-dehydro-3-deoxy-D-galactonate + H2O
-
 ?
4.2.1.140 D-gluconate
-
 Picrophilus torridus 2-dehydro-3-deoxy-D-gluconate + H2O
-
 ?
4.2.1.140 D-gluconate the ratio of catalytic efficiency for gluconate and galactonate utilization is about 10 to 1 Picrophilus torridus 2-dehydro-3-deoxy-D-gluconate + H2O
-
 ?
4.2.1.140 additional information no activity with xylonate Picrophilus torridus ?
-
 ?

Subunits

EC Number Subunits Comment Organism
4.1.2.20 homotetramer 4 * 32000, SDS-PAGE Picrophilus torridus
4.1.2.51 homotetramer 4 * 32000, SDS-PAGE Picrophilus torridus
4.2.1.39 homooctamer 8 * 44000, SDS-PAGE Picrophilus torridus
4.2.1.140 homooctamer 8 * 44000, SDS-PAGE Picrophilus torridus

Synonyms

EC Number Synonyms Comment Organism
4.1.2.20 2-keto-3-deoxygluconate-specific aldolase
-
 Picrophilus torridus
4.1.2.20 KDG-specific aldolase
-
 Picrophilus torridus
4.1.2.20 KDGA
-
 Picrophilus torridus
4.1.2.51 KDG-specific aldolase
-
 Picrophilus torridus
4.1.2.51 KDGA
-
 Picrophilus torridus
4.1.2.51 Pto1279
-
 Picrophilus torridus
4.2.1.39 GAD
-
 Picrophilus torridus
4.2.1.39 gluconate dehydratase
-
 Picrophilus torridus
4.2.1.140 Pto0485
-
 Picrophilus torridus

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
4.1.2.20 65
-
-
 Picrophilus torridus
4.1.2.51 60
-
 assay at Picrophilus torridus
4.1.2.51 65
-
-
 Picrophilus torridus
4.2.1.39 70
-
 half-life is about 15 min Picrophilus torridus
4.2.1.140 60
-
 assay at Picrophilus torridus
4.2.1.140 70
-
-
 Picrophilus torridus

Temperature Stability [°C]

EC Number Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
4.1.2.20 70 90 at 70°C, the enzyme does not lose activity upon incubation for 2 h. The half-lives of the enzyme at 80°C and 90°C are 20 min and 15 min, respectively Picrophilus torridus
4.1.2.51 70
-
 2 h, stable Picrophilus torridus
4.1.2.51 80
-
 half-life: 20 min Picrophilus torridus
4.1.2.51 90
-
 half-life: 15 min Picrophilus torridus
4.2.1.39 60
-
 no loss of activity upon incubation for 2 h Picrophilus torridus
4.2.1.140 60
-
 2 h, stable Picrophilus torridus
4.2.1.140 70
-
 half-life: 15 min Picrophilus torridus

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
4.1.2.20 0.34
-
 2-dehydro-3-deoxy-6-phospho-D-gluconate at 60°C in 50 mM sodium phosphate buffer (pH 6.2) Picrophilus torridus
4.1.2.20 26.7
-
 2-dehydro-3-deoxy-D-gluconate at 60°C in 50 mM sodium phosphate buffer (pH 6.2) Picrophilus torridus
4.1.2.51 0.34
-
 2-dehydro-3-deoxy-D-gluconate 6-phosphate pH 6.2, 60°C, enzyme purified from Picrophilus torridus Picrophilus torridus
4.1.2.51 0.36
-
 2-dehydro-3-deoxy-D-gluconate 6-phosphate pH 6.2, 60°C, recombinant enzyme Picrophilus torridus
4.1.2.51 24.2
-
 2-dehydro-3-deoxy-D-gluconate pH 6.2, 60°C, recombinant enzyme Picrophilus torridus
4.1.2.51 26.7
-
 2-dehydro-3-deoxy-D-gluconate pH 6.2, 60°C, enzyme purified from Picrophilus torridus Picrophilus torridus

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
4.1.2.20 5.5
-
-
 Picrophilus torridus
4.1.2.51 5.5
-
-
 Picrophilus torridus
4.1.2.51 6.2
-
 assay at Picrophilus torridus
4.2.1.39 6
-
-
 Picrophilus torridus
4.2.1.140 6
-
-
 Picrophilus torridus
4.2.1.140 6.2
-
 assay at Picrophilus torridus

pH Range

EC Number pH Minimum pH Maximum Comment Organism
4.1.2.20 4.5 7.5
-
 Picrophilus torridus
4.1.2.51 4.5 7.5 pH 4.5: 50% of maximal activity, pH 7.5: about 50% of maximal activity Picrophilus torridus
4.2.1.39 4.5 8.1 50% of activity at pH 8.1 and at pH 4.5 Picrophilus torridus
4.2.1.140 4.5 8.1 pH 4.5: 50% of maximal activity, pH 8.1: about 50% of maximal activity Picrophilus torridus

General Information

EC Number General Information Comment Organism
4.1.2.20 metabolism Picrophilus torridus degrades glucose via a strictly nonphosphorylative Entner-Doudoroff pathway with a 2-keto-3-deoxygluconate-specific aldolase Picrophilus torridus
4.1.2.51 physiological function the enzyme is involved in the nonphosphorylative variant of the Entner–Doudoroff pathway Picrophilus torridus

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
4.1.2.20 0.04
-
 2-dehydro-3-deoxy-6-phospho-D-gluconate at 60°C in 50 mM sodium phosphate buffer (pH 6.2) Picrophilus torridus
4.1.2.20 89
-
 2-dehydro-3-deoxy-D-gluconate at 60°C in 50 mM sodium phosphate buffer (pH 6.2) Picrophilus torridus
4.1.2.51 0.04
-
 2-dehydro-3-deoxy-D-gluconate 6-phosphate pH 6.2, 60°C, enzyme purified from Picrophilus torridus Picrophilus torridus
4.1.2.51 0.14
-
 2-dehydro-3-deoxy-D-gluconate 6-phosphate pH 6.2, 60°C, recombinant enzyme Picrophilus torridus
4.1.2.51 52
-
 2-dehydro-3-deoxy-D-gluconate pH 6.2, 60°C, recombinant enzyme Picrophilus torridus
4.1.2.51 89
-
 2-dehydro-3-deoxy-D-gluconate pH 6.2, 60°C, enzyme purified from Picrophilus torridus Picrophilus torridus