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show all sequences of 1.1.1.B35

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)
Crystallization
Organism
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]
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.038
-
NADP+
pH 7.5, 70C, determined with 10 mM D-arabinose
Saccharolobus solfataricus
0.22
-
L-fucose
pH 7.5, 70C, determined with 0.4 mM NADP+
Saccharolobus solfataricus
1.25
-
NAD+
pH 7.5, 70C, determined with 10 mM D-arabinose
Saccharolobus solfataricus
1.4
-
D-arabinose
pH 7.5, 70C, determined with 0.4 mM NADP+
Saccharolobus solfataricus
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
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
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Saccharolobus solfataricus
Q97YM2
-
-
Saccharolobus solfataricus P2
Q97YM2
-
-
Purification (Commentary)
Commentary
Organism
-
Saccharolobus solfataricus
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
D-arabinose + NAD+
-
681445
Saccharolobus solfataricus
D-arabinono-1,4-lactone + NADH + H+
-
-
-
?
D-arabinose + NAD+
-
681445
Saccharolobus solfataricus P2
D-arabinono-1,4-lactone + NADH + H+
-
-
-
?
D-arabinose + NADP+
-
681445
Saccharolobus solfataricus
D-arabinono-1,4-lactone + NADPH + H+
-
-
-
?
D-arabinose + NADP+
-
681445
Saccharolobus solfataricus P2
D-arabinono-1,4-lactone + NADPH + H+
-
-
-
?
D-ribose + NADP+
-
681445
Saccharolobus solfataricus
D-ribonolactone + NADPH
-
-
-
?
L-fucose + NADP+
-
681445
Saccharolobus solfataricus
L-fuconolactone + NADPH
-
-
-
?
L-fucose + NADP+
-
681445
Saccharolobus solfataricus P2
L-fuconolactone + NADPH
-
-
-
?
L-galactose + NADP+
-
681445
Saccharolobus solfataricus
L-galactonolactone + NADPH
-
-
-
?
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
?
-
-
-
-
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
?
-
-
-
-
Subunits
Subunits
Commentary
Organism
homotetramer
-
Saccharolobus solfataricus
Temperature Optimum [C]
Temperature Optimum [C]
Temperature Optimum Maximum [C]
Commentary
Organism
70
-
assay at
Saccharolobus solfataricus
91
-
-
Saccharolobus solfataricus
Temperature Range [C]
Temperature Minimum [C]
Temperature Maximum [C]
Commentary
Organism
70
100
70C: about 40% of maximal activity, 100C: about 90% of maximal activity
Saccharolobus solfataricus
Temperature Stability [C]
Temperature Stability Minimum [C]
Temperature Stability Maximum [C]
Commentary
Organism
85
-
half-life: 42 min
Saccharolobus solfataricus
90
-
half-life: 26 min
Saccharolobus solfataricus
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.5
-
assay at
Saccharolobus solfataricus
8.2
-
-
Saccharolobus solfataricus
pH Range
pH Minimum
pH Maximum
Commentary
Organism
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
Cofactor
Commentary
Organism
Structure
NAD+
the catalytic efficiency of NADP+ in combination with D-arabinose is 36-fold higher than that of NAD+
Saccharolobus solfataricus
NADP+
the catalytic efficiency of NADP+ in combination with D-arabinose is 36-fold higher than that of NAD+
Saccharolobus solfataricus
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
NAD+
the catalytic efficiency of NADP+ in combination with D-arabinose is 36-fold higher than that of NAD+
Saccharolobus solfataricus
NADP+
the catalytic efficiency of NADP+ in combination with D-arabinose is 36-fold higher than that of NAD+
Saccharolobus solfataricus
Crystallization (Commentary) (protein specific)
Crystallization
Organism
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)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.038
-
NADP+
pH 7.5, 70C, determined with 10 mM D-arabinose
Saccharolobus solfataricus
0.22
-
L-fucose
pH 7.5, 70C, determined with 0.4 mM NADP+
Saccharolobus solfataricus
1.25
-
NAD+
pH 7.5, 70C, determined with 10 mM D-arabinose
Saccharolobus solfataricus
1.4
-
D-arabinose
pH 7.5, 70C, determined with 0.4 mM NADP+
Saccharolobus solfataricus
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
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)
Commentary
Organism
-
Saccharolobus solfataricus
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
D-arabinose + NAD+
-
681445
Saccharolobus solfataricus
D-arabinono-1,4-lactone + NADH + H+
-
-
-
?
D-arabinose + NAD+
-
681445
Saccharolobus solfataricus P2
D-arabinono-1,4-lactone + NADH + H+
-
-
-
?
D-arabinose + NADP+
-
681445
Saccharolobus solfataricus
D-arabinono-1,4-lactone + NADPH + H+
-
-
-
?
D-arabinose + NADP+
-
681445
Saccharolobus solfataricus P2
D-arabinono-1,4-lactone + NADPH + H+
-
-
-
?
D-ribose + NADP+
-
681445
Saccharolobus solfataricus
D-ribonolactone + NADPH
-
-
-
?
L-fucose + NADP+
-
681445
Saccharolobus solfataricus
L-fuconolactone + NADPH
-
-
-
?
L-fucose + NADP+
-
681445
Saccharolobus solfataricus P2
L-fuconolactone + NADPH
-
-
-
?
L-galactose + NADP+
-
681445
Saccharolobus solfataricus
L-galactonolactone + NADPH
-
-
-
?
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
?
-
-
-
-
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
?
-
-
-
-
Subunits (protein specific)
Subunits
Commentary
Organism
homotetramer
-
Saccharolobus solfataricus
Temperature Optimum [C] (protein specific)
Temperature Optimum [C]
Temperature Optimum Maximum [C]
Commentary
Organism
70
-
assay at
Saccharolobus solfataricus
91
-
-
Saccharolobus solfataricus
Temperature Range [C] (protein specific)
Temperature Minimum [C]
Temperature Maximum [C]
Commentary
Organism
70
100
70C: about 40% of maximal activity, 100C: about 90% of maximal activity
Saccharolobus solfataricus
Temperature Stability [C] (protein specific)
Temperature Stability Minimum [C]
Temperature Stability Maximum [C]
Commentary
Organism
85
-
half-life: 42 min
Saccharolobus solfataricus
90
-
half-life: 26 min
Saccharolobus solfataricus
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.5
-
assay at
Saccharolobus solfataricus
8.2
-
-
Saccharolobus solfataricus
pH Range (protein specific)
pH Minimum
pH Maximum
Commentary
Organism
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]
kcat/KM Value [1/mMs-1]
kcat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
10.6
-
D-arabinose
pH 7.5, 70C, determined with 0.4 mM NADP+
Saccharolobus solfataricus
14.5
-
NAD+
pH 7.5, 70C, determined with 10 mM D-arabinose
Saccharolobus solfataricus
67
-
L-fucose
pH 7.5, 70C, determined with 0.4 mM NADP+
Saccharolobus solfataricus
525
-
NADP+
pH 7.5, 70C, determined with 10 mM D-arabinose
Saccharolobus solfataricus
KCat/KM [mM/s] (protein specific)
KCat/KM Value [1/mMs-1]
KCat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
10.6
-
D-arabinose
pH 7.5, 70C, determined with 0.4 mM NADP+
Saccharolobus solfataricus
14.5
-
NAD+
pH 7.5, 70C, determined with 10 mM D-arabinose
Saccharolobus solfataricus
67
-
L-fucose
pH 7.5, 70C, determined with 0.4 mM NADP+
Saccharolobus solfataricus
525
-
NADP+
pH 7.5, 70C, determined with 10 mM D-arabinose
Saccharolobus solfataricus
Other publictions for EC 1.1.1.B35
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [C]
Temperature Range [C]
Temperature Stability [C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [C] (protein specific)
Temperature Range [C] (protein specific)
Temperature Stability [C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
741519
Hu
Structures of Saccharomyces c ...
Saccharomyces cerevisiae
Acta Crystallogr. Sect. F
69
1190-1195
2013
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710944
Gonzalez
Role of Saccharomyces cerevisi ...
Saccharomyces cerevisiae
Appl. Environ. Microbiol.
76
670-679
2010
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681445
Brouns
Crystal structure and biochemi ...
Saccharolobus solfataricus, Saccharolobus solfataricus P2
J. Mol. Biol.
371
1249-1260
2007
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-
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1
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4
-
1
-
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3
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1
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10
1
2
1
2
-
2
1
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2
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2
1
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4
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1
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1
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10
1
2
1
2
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2
1
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4
4
719837
Brouns
Identification of the missing ...
Saccharolobus solfataricus, Saccharolobus solfataricus P2
J. Biol. Chem.
281
27378-27388
2006
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1
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1
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1
2
2
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3
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1
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9
1
1
1
2
4
2
1
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1
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1
1
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2
2
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9
1
1
1
2
4
2
1
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285774
Kim
D-Arabinose dehydrogenase and ...
Saccharomyces cerevisiae
Biochim. Biophys. Acta
1429
29-39
1998
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4
1
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3
1
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1
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1
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10
2
1
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1
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1
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1
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4
1
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3
1
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10
2
1
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1
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