BRENDA - Enzyme Database

Structural determinants in bacterial 2-keto-3-deoxy-D-gluconate dehydrogenase KduD for dual-coenzyme specificity

Takase, R.; Maruyama, Y.; Oiki, S.; Mikami, B.; Murata, K.; Hashimoto, W.; Proteins 84, 934-947 (2016)

Data extracted from this reference:

Cloned(Commentary)
EC Number
Commentary
Organism
1.1.1.127
expressed in Escherichia coli BL21(DE3) cells
Pectobacterium carotovorum subsp. carotovorum
Crystallization (Commentary)
EC Number
Crystallization
Organism
1.1.1.127
in complex with NAD+, hanging drop vapor diffusion method, using 5% (w/v) polyethylene glycol 4000, and 10% (v/v) isopropanol
Pectobacterium carotovorum subsp. carotovorum
KM Value [mM]
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
1.1.1.127
0.0021
-
NADH
at pH 7.2 and 45°C
Pectobacterium carotovorum subsp. carotovorum
1.1.1.127
0.005
-
NADPH
at pH 7.2 and 45°C
Pectobacterium carotovorum subsp. carotovorum
Molecular Weight [Da]
EC Number
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
1.1.1.127
25000
-
4 * 25000, SDS-PAGE
Pectobacterium carotovorum subsp. carotovorum
1.1.1.127
90000
-
gel filtration
Pectobacterium carotovorum subsp. carotovorum
Natural Substrates/ Products (Substrates)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
1.1.1.127
2,5-didehydro-3-deoxy-D-gluconate + NADH + H+
Pectobacterium carotovorum subsp. carotovorum
-
2-dehydro-3-deoxy-D-gluconate + NAD+
-
-
?
1.1.1.127
2,5-didehydro-3-deoxy-D-gluconate + NADPH + H+
Pectobacterium carotovorum subsp. carotovorum
-
2-dehydro-3-deoxy-D-gluconate + NADP+
-
-
?
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
1.1.1.127
Pectobacterium carotovorum subsp. carotovorum
A0A093RP61
-
-
Purification (Commentary)
EC Number
Commentary
Organism
1.1.1.127
Toyopearl DEAE-650 M column chromatography, Toyopearl butyl-650 M column chromatography, Q-Sepharose column chromatography, and Superdex 200 pg gel filtration
Pectobacterium carotovorum subsp. carotovorum
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
1.1.1.127
2,5-didehydro-3-deoxy-D-gluconate + NADH + H+
-
741387
Pectobacterium carotovorum subsp. carotovorum
2-dehydro-3-deoxy-D-gluconate + NAD+
-
-
-
?
1.1.1.127
2,5-didehydro-3-deoxy-D-gluconate + NADPH + H+
-
741387
Pectobacterium carotovorum subsp. carotovorum
2-dehydro-3-deoxy-D-gluconate + NADP+
-
-
-
?
Subunits
EC Number
Subunits
Commentary
Organism
1.1.1.127
homotetramer
4 * 25000, SDS-PAGE
Pectobacterium carotovorum subsp. carotovorum
Temperature Optimum [°C]
EC Number
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
1.1.1.127
45
-
-
Pectobacterium carotovorum subsp. carotovorum
Temperature Stability [°C]
EC Number
Temperature Stability Minimum [°C]
Temperature Stability Maximum [°C]
Commentary
Organism
1.1.1.127
40
-
the enzyme shows more than 70% activity at 40°C for 5 min
Pectobacterium carotovorum subsp. carotovorum
Turnover Number [1/s]
EC Number
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
1.1.1.127
0.021
-
NADPH
at pH 7.2 and 45°C
Pectobacterium carotovorum subsp. carotovorum
1.1.1.127
0.024
-
NADH
at pH 7.2 and 45°C
Pectobacterium carotovorum subsp. carotovorum
pH Optimum
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
1.1.1.127
7.2
-
-
Pectobacterium carotovorum subsp. carotovorum
Cofactor
EC Number
Cofactor
Commentary
Organism
Structure
1.1.1.127
NADH
the enzyme utilizes both NADH and NADPH
Pectobacterium carotovorum subsp. carotovorum
1.1.1.127
NADPH
the enzyme utilizes both NADH and NADPH
Pectobacterium carotovorum subsp. carotovorum
Cloned(Commentary) (protein specific)
EC Number
Commentary
Organism
1.1.1.127
expressed in Escherichia coli BL21(DE3) cells
Pectobacterium carotovorum subsp. carotovorum
Cofactor (protein specific)
EC Number
Cofactor
Commentary
Organism
Structure
1.1.1.127
NADH
the enzyme utilizes both NADH and NADPH
Pectobacterium carotovorum subsp. carotovorum
1.1.1.127
NADPH
the enzyme utilizes both NADH and NADPH
Pectobacterium carotovorum subsp. carotovorum
Crystallization (Commentary) (protein specific)
EC Number
Crystallization
Organism
1.1.1.127
in complex with NAD+, hanging drop vapor diffusion method, using 5% (w/v) polyethylene glycol 4000, and 10% (v/v) isopropanol
Pectobacterium carotovorum subsp. carotovorum
KM Value [mM] (protein specific)
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
1.1.1.127
0.0021
-
NADH
at pH 7.2 and 45°C
Pectobacterium carotovorum subsp. carotovorum
1.1.1.127
0.005
-
NADPH
at pH 7.2 and 45°C
Pectobacterium carotovorum subsp. carotovorum
Molecular Weight [Da] (protein specific)
EC Number
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
1.1.1.127
25000
-
4 * 25000, SDS-PAGE
Pectobacterium carotovorum subsp. carotovorum
1.1.1.127
90000
-
gel filtration
Pectobacterium carotovorum subsp. carotovorum
Natural Substrates/ Products (Substrates) (protein specific)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
1.1.1.127
2,5-didehydro-3-deoxy-D-gluconate + NADH + H+
Pectobacterium carotovorum subsp. carotovorum
-
2-dehydro-3-deoxy-D-gluconate + NAD+
-
-
?
1.1.1.127
2,5-didehydro-3-deoxy-D-gluconate + NADPH + H+
Pectobacterium carotovorum subsp. carotovorum
-
2-dehydro-3-deoxy-D-gluconate + NADP+
-
-
?
Purification (Commentary) (protein specific)
EC Number
Commentary
Organism
1.1.1.127
Toyopearl DEAE-650 M column chromatography, Toyopearl butyl-650 M column chromatography, Q-Sepharose column chromatography, and Superdex 200 pg gel filtration
Pectobacterium carotovorum subsp. carotovorum
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
1.1.1.127
2,5-didehydro-3-deoxy-D-gluconate + NADH + H+
-
741387
Pectobacterium carotovorum subsp. carotovorum
2-dehydro-3-deoxy-D-gluconate + NAD+
-
-
-
?
1.1.1.127
2,5-didehydro-3-deoxy-D-gluconate + NADPH + H+
-
741387
Pectobacterium carotovorum subsp. carotovorum
2-dehydro-3-deoxy-D-gluconate + NADP+
-
-
-
?
Subunits (protein specific)
EC Number
Subunits
Commentary
Organism
1.1.1.127
homotetramer
4 * 25000, SDS-PAGE
Pectobacterium carotovorum subsp. carotovorum
Temperature Optimum [°C] (protein specific)
EC Number
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
1.1.1.127
45
-
-
Pectobacterium carotovorum subsp. carotovorum
Temperature Stability [°C] (protein specific)
EC Number
Temperature Stability Minimum [°C]
Temperature Stability Maximum [°C]
Commentary
Organism
1.1.1.127
40
-
the enzyme shows more than 70% activity at 40°C for 5 min
Pectobacterium carotovorum subsp. carotovorum
Turnover Number [1/s] (protein specific)
EC Number
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
1.1.1.127
0.021
-
NADPH
at pH 7.2 and 45°C
Pectobacterium carotovorum subsp. carotovorum
1.1.1.127
0.024
-
NADH
at pH 7.2 and 45°C
Pectobacterium carotovorum subsp. carotovorum
pH Optimum (protein specific)
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
1.1.1.127
7.2
-
-
Pectobacterium carotovorum subsp. carotovorum