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Literature summary extracted from

  • Pick, A.; Beer, B.; Hemmi, R.; Momma, R.; Schmid, J.; Miyamoto, K.; Sieber, V.
    Identification and characterization of two new 5-keto-4-deoxy-D-glucarate dehydratases/decarboxylases (2016), BMC Biotechnol., 16, 80 .
    View publication on PubMedView publication on EuropePMC

Application

EC Number Application Comment Organism
4.2.1.41 analysis by establishing a pH-shift assay, an easy measurement method for 5-dehydro-4-deoxy-D-glucarate dehydratases/decarboxylase is developed. It can be used for measurements of the purified enzymes or using crude extracts. It is especially suitable as the method of choice within an engineering approach for further optimization of the enzyme Comamonas testosteroni
4.2.1.41 analysis by establishing a pH-shift assay, an easy measurement method for 5-keto-4-deoxy-D-glucarate dehydratases/decarboxylase is developed. It can be used for measurements of the purified enzymes or using crude extracts. It is especially suitable as the method of choice within an engineering approach for further optimization of the enzyme Acinetobacter baylyi
4.2.1.41 analysis by establishing a pH-shift assay, an easy measurement method for 5-keto-4-deoxy-D-glucarate dehydratases/decarboxylase is developed. It can be used for measurements of the purified enzymes or using crude extracts. It is especially suitable as the method of choice within an engineering approach for further optimization of the enzyme Polaromonas naphthalenivorans CJ2

Cloned(Commentary)

EC Number Cloned (Comment) Organism
4.2.1.41 Escherichia coli ArcticExpress(DE3) Acinetobacter baylyi
4.2.1.41 Escherichia coli ArcticExpress(DE3) Comamonas testosteroni
4.2.1.41 Escherichia coli ArcticExpress(DE3) Polaromonas naphthalenivorans CJ2
4.2.1.41 expressed in Escherichia coli ArcticExpress(DE3) cells Polaromonas naphthalenivorans
4.2.1.41 expressed in Escherichia coli ArcticExpress(DE3) cells Comamonas testosteroni

General Stability

EC Number General Stability Organism
4.2.1.41 NH4HCO3 at a concentration of 0.5 mM, maintains stability of the enzyme Acinetobacter baylyi

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
4.2.1.41 1
-
 5-dehydro-4-deoxy-D-glucarate pH 7.0, 37°C Acinetobacter baylyi
4.2.1.41 1.1
-
 5-dehydro-4-deoxy-D-glucarate pH 7.0, 37°C Comamonas testosteroni
4.2.1.41 1.1
-
 5-dehydro-4-deoxy-D-glucarate pH 7.0, 37°C Polaromonas naphthalenivorans CJ2
4.2.1.41 1.1
-
 5-dehydro-4-deoxy-D-glucarate in 25 mM potassium phosphate buffer, at pH 7.0 and 37°C Polaromonas naphthalenivorans
4.2.1.41 1.1
-
 5-dehydro-4-deoxy-D-glucarate in 25 mM potassium phosphate buffer, at pH 7.0 and 37°C Comamonas testosteroni

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
4.2.1.41 5-dehydro-4-deoxy-D-glucarate Polaromonas naphthalenivorans
-
 2,5-dioxopentanoate + H2O + CO2
-
 ?
4.2.1.41 5-dehydro-4-deoxy-D-glucarate Comamonas testosteroni
-
 2,5-dioxopentanoate + H2O + CO2
-
 ?
4.2.1.41 5-dehydro-4-deoxy-D-glucarate Comamonas testosteroni KF-1
-
 2,5-dioxopentanoate + H2O + CO2
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
4.2.1.41 Acinetobacter baylyi Q6FFQ1
-
-
4.2.1.41 Comamonas testosteroni B7WZA5
-
-
4.2.1.41 Comamonas testosteroni KF-1 B7WZA5
-
-
4.2.1.41 Polaromonas naphthalenivorans A1VMN2
-
-
4.2.1.41 Polaromonas naphthalenivorans CJ2 A1VMN2
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
4.2.1.41 HisTrap column chromatography Polaromonas naphthalenivorans
4.2.1.41 HisTrap column chromatography Comamonas testosteroni

Storage Stability

EC Number Storage Stability Organism
4.2.1.41 -20°C, 50 mM Tris-HCl, pH 7.5, 4 months, the enzyme remains stable Polaromonas naphthalenivorans
4.2.1.41 -20°C, 50 mM Tris-HCl, pH 7.5, 4 months, the enzyme remains stable Comamonas testosteroni
4.2.1.41 -80°C, 50 mM Tris-HCl, pH 7.5, 4 months, the enzyme remains stable Polaromonas naphthalenivorans
4.2.1.41 -80°C, 50 mM Tris-HCl, pH 7.5, 4 months, the enzyme remains stable Comamonas testosteroni
4.2.1.41 8°C, 50 mM Tris-HCl, pH 7.5, 14 days, the enzyme remains stable Polaromonas naphthalenivorans
4.2.1.41 8°C, 50 mM Tris-HCl, pH 7.5, 14 days, the enzyme remains stable Comamonas testosteroni

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
4.2.1.41 5-dehydro-4-deoxy-D-glucarate
-
 Acinetobacter baylyi 2,5-dioxopentanoate + H2O + CO2
-
 ?
4.2.1.41 5-dehydro-4-deoxy-D-glucarate
-
 Polaromonas naphthalenivorans 2,5-dioxopentanoate + H2O + CO2
-
 ?
4.2.1.41 5-dehydro-4-deoxy-D-glucarate
-
 Comamonas testosteroni 2,5-dioxopentanoate + H2O + CO2
-
 ?
4.2.1.41 5-dehydro-4-deoxy-D-glucarate
-
 Polaromonas naphthalenivorans CJ2 2,5-dioxopentanoate + H2O + CO2
-
 ?
4.2.1.41 5-dehydro-4-deoxy-D-glucarate
-
 Comamonas testosteroni KF-1 2,5-dioxopentanoate + H2O + CO2
-
 ?

Synonyms

EC Number Synonyms Comment Organism
4.2.1.41 5-keto-4-deoxy-D-glucarate dehydratase/decarboxylase
-
 Polaromonas naphthalenivorans
4.2.1.41 5-keto-4-deoxy-D-glucarate dehydratase/decarboxylase
-
 Comamonas testosteroni
4.2.1.41 5-keto-4-deoxy-D-glucarate dehydratases/decarboxylase
-
 Acinetobacter baylyi
4.2.1.41 5-keto-4-deoxy-D-glucarate dehydratases/decarboxylase
-
 Comamonas testosteroni
4.2.1.41 5-keto-4-deoxy-D-glucarate dehydratases/decarboxylase
-
 Polaromonas naphthalenivorans CJ2
4.2.1.41 KdgD
-
 Acinetobacter baylyi
4.2.1.41 KdgD
-
 Polaromonas naphthalenivorans
4.2.1.41 KdgD
-
 Comamonas testosteroni
4.2.1.41 KdgD
-
 Polaromonas naphthalenivorans CJ2

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
4.2.1.41 37
-
 assay at Acinetobacter baylyi
4.2.1.41 37
-
 assay at Comamonas testosteroni
4.2.1.41 37
-
 assay at Polaromonas naphthalenivorans CJ2

Temperature Stability [°C]

EC Number Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
4.2.1.41 37
-
 activity is stable over 150 h. NH4HCO3 (0.5 mM) shows no effect on stability Comamonas testosteroni
4.2.1.41 37
-
 activity is stable over 150 h. NH4HCO3 (0.5 mM) shows no effect on stability Polaromonas naphthalenivorans CJ2
4.2.1.41 37 65 the enzyme is stable over 150 h at 37°C, whereas after 4 h at 65°C the initial activity decreases below 50% Polaromonas naphthalenivorans
4.2.1.41 37 65 the enzyme is stable over 150 h at 37°C, whereas after 4 h at 65°C the initial activity decreases below 50% Comamonas testosteroni
4.2.1.41 65
-
 after 4 h the initial activity decreases below 50%. T1/2: 2.79 h. NH4HCO3 (0.5 mM) shows no effect on stability Comamonas testosteroni
4.2.1.41 65
-
 after 4 h the initial activity decreases below 50%. T1/2: 3.83 h. NH4HCO3 (0.5 mM) shows no effect on stability Polaromonas naphthalenivorans CJ2
4.2.1.41 65
-
 t1/2: 2.71 h in presence of 0.5 mM NH4HCO3 Acinetobacter baylyi

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
4.2.1.41 1.7
-
 5-dehydro-4-deoxy-D-glucarate pH 7.0, 37°C Polaromonas naphthalenivorans CJ2
4.2.1.41 1.7
-
 5-dehydro-4-deoxy-D-glucarate in 25 mM potassium phosphate buffer, at pH 7.0 and 37°C Polaromonas naphthalenivorans
4.2.1.41 3.1
-
 5-dehydro-4-deoxy-D-glucarate pH 7.0, 37°C Comamonas testosteroni
4.2.1.41 3.1
-
 5-dehydro-4-deoxy-D-glucarate in 25 mM potassium phosphate buffer, at pH 7.0 and 37°C Comamonas testosteroni
4.2.1.41 4.5
-
 5-dehydro-4-deoxy-D-glucarate pH 7.0, 37°C Acinetobacter baylyi

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
4.2.1.41 7
-
 assay at Acinetobacter baylyi
4.2.1.41 7
-
 assay at Comamonas testosteroni
4.2.1.41 7
-
 assay at Polaromonas naphthalenivorans CJ2

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
4.2.1.41 1.5
-
 5-dehydro-4-deoxy-D-glucarate pH 7.0, 37°C Polaromonas naphthalenivorans CJ2
4.2.1.41 1.5
-
 5-dehydro-4-deoxy-D-glucarate in 25 mM potassium phosphate buffer, at pH 7.0 and 37°C Polaromonas naphthalenivorans
4.2.1.41 2.8
-
 5-dehydro-4-deoxy-D-glucarate pH 7.0, 37°C Comamonas testosteroni
4.2.1.41 2.8
-
 5-dehydro-4-deoxy-D-glucarate in 25 mM potassium phosphate buffer, at pH 7.0 and 37°C Comamonas testosteroni
4.2.1.41 4.5
-
 5-dehydro-4-deoxy-D-glucarate pH 7.0, 37°C Acinetobacter baylyi