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Literature summary extracted from

  • Rashid, N.; Imanaka, H.; Fukui, T.; Atomi, H.; Imanaka, T.
    Presence of a novel phosphopentomutase and a 2-deoxyribose 5-phosphate aldolase reveals a metabolic link between pentoses and central carbon metabolism in the hyperthermophilic archaeon Thermococcus kodakaraensis (2004), J. Bacteriol., 186, 4185-4191.
    View publication on PubMedView publication on EuropePMC

Activating Compound

EC Number Activating Compound Comment Organism Structure
4.1.2.4 citrate enhances activity Thermococcus kodakarensis

Cloned(Commentary)

EC Number Cloned (Comment) Organism
4.1.2.4 expression in Escherichia coli Thermococcus kodakarensis
5.4.2.7 expression in Escherichia coli Thermococcus kodakarensis

Inhibitors

EC Number Inhibitors Comment Organism Structure
4.1.2.4 Zn2+ 1 mM, 35% decrease in activity Thermococcus kodakarensis

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
4.1.2.4 0.81
-
 2-deoxy-D-ribose 5-phosphate 95°C Thermococcus kodakarensis
5.4.2.7 2.5
-
 2-deoxy-D-ribose 1-phosphate 90°C Thermococcus kodakarensis

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
5.4.2.7 Mg2+ 1 mM, high activation Thermococcus kodakarensis
5.4.2.7 Mn2+ 1 mM, 50% of the activation with Mg2+ Thermococcus kodakarensis
5.4.2.7 Ni2+ 1 mM, 70% of the activation with Mg2+ Thermococcus kodakarensis
5.4.2.7 Zn2+ 1 mM, 45% of the activation with Mg2+ Thermococcus kodakarensis

Molecular Weight [Da]

EC Number Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
4.1.2.4 24500
-
 2 * 24500, SDS-PAGE Thermococcus kodakarensis
4.1.2.4 53000
-
 gel filtration Thermococcus kodakarensis
5.4.2.7 210000
-
 gel filtration Thermococcus kodakarensis

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
4.1.2.4 2-deoxy-D-ribose 5-phosphate Thermococcus kodakarensis presence of a novel phosphopentomutase and a 2-deoxyribose 5-phosphate aldolase reveals a metabolic link between pentoses and central carbon metabolism. Alternative route for pentose biosynthesis trough the function of the novel phosphopentomutase and a 2-deoxyribose 5-phosphate aldolase D-glyceraldehyde 3-phosphate + acetaldehyde
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
4.1.2.4 Thermococcus kodakarensis Q877I0 KOD1
-
5.4.2.7 Thermococcus kodakarensis Q6I7B6 KOD1
-

Purification (Commentary)

EC Number Purification (Comment) Organism
4.1.2.4
-
 Thermococcus kodakarensis
5.4.2.7 partial Thermococcus kodakarensis

Specific Activity [micromol/min/mg]

EC Number Specific Activity Minimum [µmol/min/mg] Specific Activity Maximum [µmol/min/mg] Comment Organism
4.1.2.4 285
-
 pH 4.0, 95°C Thermococcus kodakarensis
5.4.2.7 210
-
-
 Thermococcus kodakarensis

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
4.1.2.4 2-deoxy-D-ribose 5-phosphate
-
 Thermococcus kodakarensis D-glyceraldehyde 3-phosphate + acetaldehyde
-
 ?
4.1.2.4 2-deoxy-D-ribose 5-phosphate presence of a novel phosphopentomutase and a 2-deoxyribose 5-phosphate aldolase reveals a metabolic link between pentoses and central carbon metabolism. Alternative route for pentose biosynthesis trough the function of the novel phosphopentomutase and a 2-deoxyribose 5-phosphate aldolase Thermococcus kodakarensis D-glyceraldehyde 3-phosphate + acetaldehyde
-
 ?
5.4.2.7 2-deoxy-D-ribose 1-phosphate
-
 Thermococcus kodakarensis 2-deoxy-D-ribose 5-phosphate
-
 ?
5.4.2.7 additional information trace levels of activity with glucose 1-phosphate and mannose 1-phosphate. No activity with fructose 1-phosphate, N-acetylglucosamine 1-phosphate and 3-phosphoglycerate Thermococcus kodakarensis ?
-
 ?

Subunits

EC Number Subunits Comment Organism
4.1.2.4 dimer 2 * 24500, SDS-PAGE Thermococcus kodakarensis
5.4.2.7 tetramer
-
 Thermococcus kodakarensis

Synonyms

EC Number Synonyms Comment Organism
4.1.2.4 DERA
-
 Thermococcus kodakarensis
4.1.2.4 TK2104
-
 Thermococcus kodakarensis
5.4.2.7 PPM
-
 Thermococcus kodakarensis

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
4.1.2.4 95
-
-
 Thermococcus kodakarensis
5.4.2.7 90
-
-
 Thermococcus kodakarensis

Temperature Range [°C]

EC Number Temperature Minimum [°C] Temperature Maximum [°C] Comment Organism
4.1.2.4 85 100 85°C: about 35% of maximal activity, 100°C: about 95% of maximal activity Thermococcus kodakarensis
5.4.2.7 70 100 70°C: about 55% of maximal activity, 100°C: about 90% of maximal activity Thermococcus kodakarensis

Temperature Stability [°C]

EC Number Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
5.4.2.7 100
-
 half-life: 90 min Thermococcus kodakarensis

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
4.1.2.4 116
-
 2-deoxy-D-ribose 5-phosphate 95°C Thermococcus kodakarensis
5.4.2.7 173
-
 2-deoxy-D-ribose 1-phosphate 90°C Thermococcus kodakarensis

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
4.1.2.4 4
-
-
 Thermococcus kodakarensis