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Literature summary for 4.2.1.41 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
Search for more literature for 4.2.1.41

Application

Application Comment Organism
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
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
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)

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

General Stability

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

KM Value [mM]

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

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

Organism

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

Purification (Commentary)

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

Storage Stability

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

Substrates and Products (Substrate)

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

Synonyms

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

Temperature Optimum [°C]

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

Temperature Stability [°C]

Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
37
-
 activity is stable over 150 h. NH4HCO3 (0.5 mM) shows no effect on stability Comamonas testosteroni
37
-
 activity is stable over 150 h. NH4HCO3 (0.5 mM) shows no effect on stability Polaromonas naphthalenivorans CJ2
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
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
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
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
65
-
 t1/2: 2.71 h in presence of 0.5 mM NH4HCO3 Acinetobacter baylyi

Turnover Number [1/s]

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

pH Optimum

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

kcat/KM [mM/s]

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