BRENDA - Enzyme Database

Crystal structure and biochemical properties of the D-arabinose dehydrogenase from Sulfolobus solfataricus

Brouns, S.J.; Turnbull, A.P.; Willemen, H.L.; Akerboom, J.; van der Oost, J.; J. Mol. Biol. 371, 1249-1260 (2007)

Data extracted from this reference:

Crystallization (Commentary)
EC Number
Crystallization
Organism
1.1.1.B35
the structure is solved to a resolution of 1.80 A by single-wavelength anomalous diffraction and phased using the two endogenous zinc ions per subunit. The structure reveals a catalytic and cofactor binding domain
Saccharolobus solfataricus
1.1.1.122
the structure is solved to a resolution of 1.80 A by single-wavelength anomalous diffraction and phased using the two endogenous zinc ions per subunit. The structure reveals a catalytic and cofactor binding domain
Saccharolobus solfataricus
KM Value [mM]
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
1.1.1.B35
0.038
-
NADP+
pH 7.5, 70°C, determined with 10 mM D-arabinose
Saccharolobus solfataricus
1.1.1.B35
0.22
-
L-fucose
pH 7.5, 70°C, determined with 0.4 mM NADP+
Saccharolobus solfataricus
1.1.1.B35
1.25
-
NAD+
pH 7.5, 70°C, determined with 10 mM D-arabinose
Saccharolobus solfataricus
1.1.1.B35
1.4
-
D-arabinose
pH 7.5, 70°C, determined with 0.4 mM NADP+
Saccharolobus solfataricus
Metals/Ions
EC Number
Metals/Ions
Commentary
Organism
Structure
1.1.1.B35
Zn2+
contains two endogenous zinc ions per subunit.A zinc ion is bound in the loop that protrudes from the catalytic domain. This zinc is tetrahedrally coordinated by residues D94, C97, C100 and C108
Saccharolobus solfataricus
1.1.1.122
Zn2+
contains two endogenous zinc ions per subunit.A zinc ion is bound in the loop that protrudes from the catalytic domain. This zinc is tetrahedrally coordinated by residues D94, C97, C100 and C108
Saccharolobus solfataricus
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
1.1.1.B35
Saccharolobus solfataricus
Q97YM2
-
-
1.1.1.B35
Saccharolobus solfataricus P2
Q97YM2
-
-
1.1.1.122
Saccharolobus solfataricus
Q97YM2
-
-
1.1.1.122
Saccharolobus solfataricus P2
Q97YM2
-
-
Purification (Commentary)
EC Number
Commentary
Organism
1.1.1.B35
-
Saccharolobus solfataricus
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
1.1.1.B35
D-arabinose + NAD+
-
681445
Saccharolobus solfataricus
D-arabinono-1,4-lactone + NADH + H+
-
-
-
?
1.1.1.B35
D-arabinose + NAD+
-
681445
Saccharolobus solfataricus P2
D-arabinono-1,4-lactone + NADH + H+
-
-
-
?
1.1.1.B35
D-arabinose + NADP+
-
681445
Saccharolobus solfataricus
D-arabinono-1,4-lactone + NADPH + H+
-
-
-
?
1.1.1.B35
D-arabinose + NADP+
-
681445
Saccharolobus solfataricus P2
D-arabinono-1,4-lactone + NADPH + H+
-
-
-
?
1.1.1.B35
D-ribose + NADP+
-
681445
Saccharolobus solfataricus
D-ribonolactone + NADPH
-
-
-
?
1.1.1.B35
L-fucose + NADP+
-
681445
Saccharolobus solfataricus
L-fuconolactone + NADPH
-
-
-
?
1.1.1.B35
L-fucose + NADP+
-
681445
Saccharolobus solfataricus P2
L-fuconolactone + NADPH
-
-
-
?
1.1.1.B35
L-galactose + NADP+
-
681445
Saccharolobus solfataricus
L-galactonolactone + NADPH
-
-
-
?
1.1.1.B35
additional information
the enzyme is specific for sugars with D-arabinose-type hydroxyl group stereo-configurations at C3 and C4. Negligible activity with D-glucose, D-galactose, D-fucose, L-arabinose and D-xylose
681445
Saccharolobus solfataricus
?
-
-
-
-
1.1.1.B35
additional information
the enzyme is specific for sugars with D-arabinose-type hydroxyl group stereo-configurations at C3 and C4. Negligible activity with D-glucose, D-galactose, D-fucose, L-arabinose and D-xylose
681445
Saccharolobus solfataricus P2
?
-
-
-
-
1.1.1.122
6-deoxy-L-galactose + NAD+
i.e. L-fucose. The enzyme is specific for sugars with D-arabinose-type hydroxyl group stereo-configurations at C3 and C4. This configuration is shared among the hexoses L-fucose (6-deoxy-L-galactose) and L-galactose, and the pentose D-ribose. Although the highest activity is observed with L-fucose in combination with NAD+, the remaining sugars are oxidized at higher rates using NADP+
681445
Saccharolobus solfataricus
6-deoxy-L-galactono-1,5-lactone + NADH
-
-
-
?
1.1.1.122
6-deoxy-L-galactose + NAD+
i.e. L-fucose. The enzyme is specific for sugars with D-arabinose-type hydroxyl group stereo-configurations at C3 and C4. This configuration is shared among the hexoses L-fucose (6-deoxy-L-galactose) and L-galactose, and the pentose D-ribose. Although the highest activity is observed with L-fucose in combination with NAD+, the remaining sugars are oxidized at higher rates using NADP+
681445
Saccharolobus solfataricus P2
6-deoxy-L-galactono-1,5-lactone + NADH
-
-
-
?
Subunits
EC Number
Subunits
Commentary
Organism
1.1.1.B35
homotetramer
-
Saccharolobus solfataricus
1.1.1.122
homotetramer
-
Saccharolobus solfataricus
Temperature Optimum [°C]
EC Number
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
1.1.1.B35
70
-
assay at
Saccharolobus solfataricus
1.1.1.B35
91
-
-
Saccharolobus solfataricus
Temperature Range [°C]
EC Number
Temperature Minimum [°C]
Temperature Maximum [°C]
Commentary
Organism
1.1.1.B35
70
100
70°C: about 40% of maximal activity, 100°C: about 90% of maximal activity
Saccharolobus solfataricus
Temperature Stability [°C]
EC Number
Temperature Stability Minimum [°C]
Temperature Stability Maximum [°C]
Commentary
Organism
1.1.1.B35
85
-
half-life: 42 min
Saccharolobus solfataricus
1.1.1.B35
90
-
half-life: 26 min
Saccharolobus solfataricus
pH Optimum
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
1.1.1.B35
7.5
-
assay at
Saccharolobus solfataricus
1.1.1.B35
8.2
-
-
Saccharolobus solfataricus
pH Range
EC Number
pH Minimum
pH Maximum
Commentary
Organism
1.1.1.B35
7.1
9.1
pH 7.1: about 40% of maximal activity, pH 9.1: about 60% of maximal activity, pH 9.5: about 30% of maximal activity
Saccharolobus solfataricus
Cofactor
EC Number
Cofactor
Commentary
Organism
Structure
1.1.1.B35
NAD+
the catalytic efficiency of NADP+ in combination with D-arabinose is 36-fold higher than that of NAD+
Saccharolobus solfataricus
1.1.1.B35
NADP+
the catalytic efficiency of NADP+ in combination with D-arabinose is 36-fold higher than that of NAD+
Saccharolobus solfataricus
1.1.1.122
NAD+
the enzyme is specific for sugars with D-arabinose-type hydroxyl group stereo-configurations at C3 and C4. This configuration is shared among the hexoses L-fucose (6-deoxy-L-galactose) and L-galactose, and the pentose D-ribose. Although the highest activity is observed with L-fucose in combination with NAD+, the remaining sugars are oxidized at higher rates using NADP+
Saccharolobus solfataricus
Cofactor (protein specific)
EC Number
Cofactor
Commentary
Organism
Structure
1.1.1.B35
NAD+
the catalytic efficiency of NADP+ in combination with D-arabinose is 36-fold higher than that of NAD+
Saccharolobus solfataricus
1.1.1.B35
NADP+
the catalytic efficiency of NADP+ in combination with D-arabinose is 36-fold higher than that of NAD+
Saccharolobus solfataricus
1.1.1.122
NAD+
the enzyme is specific for sugars with D-arabinose-type hydroxyl group stereo-configurations at C3 and C4. This configuration is shared among the hexoses L-fucose (6-deoxy-L-galactose) and L-galactose, and the pentose D-ribose. Although the highest activity is observed with L-fucose in combination with NAD+, the remaining sugars are oxidized at higher rates using NADP+
Saccharolobus solfataricus
Crystallization (Commentary) (protein specific)
EC Number
Crystallization
Organism
1.1.1.B35
the structure is solved to a resolution of 1.80 A by single-wavelength anomalous diffraction and phased using the two endogenous zinc ions per subunit. The structure reveals a catalytic and cofactor binding domain
Saccharolobus solfataricus
1.1.1.122
the structure is solved to a resolution of 1.80 A by single-wavelength anomalous diffraction and phased using the two endogenous zinc ions per subunit. The structure reveals a catalytic and cofactor binding domain
Saccharolobus solfataricus
KM Value [mM] (protein specific)
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
1.1.1.B35
0.038
-
NADP+
pH 7.5, 70°C, determined with 10 mM D-arabinose
Saccharolobus solfataricus
1.1.1.B35
0.22
-
L-fucose
pH 7.5, 70°C, determined with 0.4 mM NADP+
Saccharolobus solfataricus
1.1.1.B35
1.25
-
NAD+
pH 7.5, 70°C, determined with 10 mM D-arabinose
Saccharolobus solfataricus
1.1.1.B35
1.4
-
D-arabinose
pH 7.5, 70°C, determined with 0.4 mM NADP+
Saccharolobus solfataricus
Metals/Ions (protein specific)
EC Number
Metals/Ions
Commentary
Organism
Structure
1.1.1.B35
Zn2+
contains two endogenous zinc ions per subunit.A zinc ion is bound in the loop that protrudes from the catalytic domain. This zinc is tetrahedrally coordinated by residues D94, C97, C100 and C108
Saccharolobus solfataricus
1.1.1.122
Zn2+
contains two endogenous zinc ions per subunit.A zinc ion is bound in the loop that protrudes from the catalytic domain. This zinc is tetrahedrally coordinated by residues D94, C97, C100 and C108
Saccharolobus solfataricus
Purification (Commentary) (protein specific)
EC Number
Commentary
Organism
1.1.1.B35
-
Saccharolobus solfataricus
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.B35
D-arabinose + NAD+
-
681445
Saccharolobus solfataricus
D-arabinono-1,4-lactone + NADH + H+
-
-
-
?
1.1.1.B35
D-arabinose + NAD+
-
681445
Saccharolobus solfataricus P2
D-arabinono-1,4-lactone + NADH + H+
-
-
-
?
1.1.1.B35
D-arabinose + NADP+
-
681445
Saccharolobus solfataricus
D-arabinono-1,4-lactone + NADPH + H+
-
-
-
?
1.1.1.B35
D-arabinose + NADP+
-
681445
Saccharolobus solfataricus P2
D-arabinono-1,4-lactone + NADPH + H+
-
-
-
?
1.1.1.B35
D-ribose + NADP+
-
681445
Saccharolobus solfataricus
D-ribonolactone + NADPH
-
-
-
?
1.1.1.B35
L-fucose + NADP+
-
681445
Saccharolobus solfataricus
L-fuconolactone + NADPH
-
-
-
?
1.1.1.B35
L-fucose + NADP+
-
681445
Saccharolobus solfataricus P2
L-fuconolactone + NADPH
-
-
-
?
1.1.1.B35
L-galactose + NADP+
-
681445
Saccharolobus solfataricus
L-galactonolactone + NADPH
-
-
-
?
1.1.1.B35
additional information
the enzyme is specific for sugars with D-arabinose-type hydroxyl group stereo-configurations at C3 and C4. Negligible activity with D-glucose, D-galactose, D-fucose, L-arabinose and D-xylose
681445
Saccharolobus solfataricus
?
-
-
-
-
1.1.1.B35
additional information
the enzyme is specific for sugars with D-arabinose-type hydroxyl group stereo-configurations at C3 and C4. Negligible activity with D-glucose, D-galactose, D-fucose, L-arabinose and D-xylose
681445
Saccharolobus solfataricus P2
?
-
-
-
-
1.1.1.122
6-deoxy-L-galactose + NAD+
i.e. L-fucose. The enzyme is specific for sugars with D-arabinose-type hydroxyl group stereo-configurations at C3 and C4. This configuration is shared among the hexoses L-fucose (6-deoxy-L-galactose) and L-galactose, and the pentose D-ribose. Although the highest activity is observed with L-fucose in combination with NAD+, the remaining sugars are oxidized at higher rates using NADP+
681445
Saccharolobus solfataricus
6-deoxy-L-galactono-1,5-lactone + NADH
-
-
-
?
1.1.1.122
6-deoxy-L-galactose + NAD+
i.e. L-fucose. The enzyme is specific for sugars with D-arabinose-type hydroxyl group stereo-configurations at C3 and C4. This configuration is shared among the hexoses L-fucose (6-deoxy-L-galactose) and L-galactose, and the pentose D-ribose. Although the highest activity is observed with L-fucose in combination with NAD+, the remaining sugars are oxidized at higher rates using NADP+
681445
Saccharolobus solfataricus P2
6-deoxy-L-galactono-1,5-lactone + NADH
-
-
-
?
Subunits (protein specific)
EC Number
Subunits
Commentary
Organism
1.1.1.B35
homotetramer
-
Saccharolobus solfataricus
1.1.1.122
homotetramer
-
Saccharolobus solfataricus
Temperature Optimum [°C] (protein specific)
EC Number
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
1.1.1.B35
70
-
assay at
Saccharolobus solfataricus
1.1.1.B35
91
-
-
Saccharolobus solfataricus
Temperature Range [°C] (protein specific)
EC Number
Temperature Minimum [°C]
Temperature Maximum [°C]
Commentary
Organism
1.1.1.B35
70
100
70°C: about 40% of maximal activity, 100°C: about 90% of maximal activity
Saccharolobus solfataricus
Temperature Stability [°C] (protein specific)
EC Number
Temperature Stability Minimum [°C]
Temperature Stability Maximum [°C]
Commentary
Organism
1.1.1.B35
85
-
half-life: 42 min
Saccharolobus solfataricus
1.1.1.B35
90
-
half-life: 26 min
Saccharolobus solfataricus
pH Optimum (protein specific)
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
1.1.1.B35
7.5
-
assay at
Saccharolobus solfataricus
1.1.1.B35
8.2
-
-
Saccharolobus solfataricus
pH Range (protein specific)
EC Number
pH Minimum
pH Maximum
Commentary
Organism
1.1.1.B35
7.1
9.1
pH 7.1: about 40% of maximal activity, pH 9.1: about 60% of maximal activity, pH 9.5: about 30% of maximal activity
Saccharolobus solfataricus
KCat/KM [mM/s]
EC Number
kcat/KM Value [1/mMs-1]
kcat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
1.1.1.B35
10.6
-
D-arabinose
pH 7.5, 70°C, determined with 0.4 mM NADP+
Saccharolobus solfataricus
1.1.1.B35
14.5
-
NAD+
pH 7.5, 70°C, determined with 10 mM D-arabinose
Saccharolobus solfataricus
1.1.1.B35
67
-
L-fucose
pH 7.5, 70°C, determined with 0.4 mM NADP+
Saccharolobus solfataricus
1.1.1.B35
525
-
NADP+
pH 7.5, 70°C, determined with 10 mM D-arabinose
Saccharolobus solfataricus
KCat/KM [mM/s] (protein specific)
EC Number
KCat/KM Value [1/mMs-1]
KCat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
1.1.1.B35
10.6
-
D-arabinose
pH 7.5, 70°C, determined with 0.4 mM NADP+
Saccharolobus solfataricus
1.1.1.B35
14.5
-
NAD+
pH 7.5, 70°C, determined with 10 mM D-arabinose
Saccharolobus solfataricus
1.1.1.B35
67
-
L-fucose
pH 7.5, 70°C, determined with 0.4 mM NADP+
Saccharolobus solfataricus
1.1.1.B35
525
-
NADP+
pH 7.5, 70°C, determined with 10 mM D-arabinose
Saccharolobus solfataricus