BRENDA - Enzyme Database
show all sequences of 1.1.1.169

Evidence of kinetic cooperativity in dimeric ketopantoate reductase from Staphylococcus aureus

Sanchez, J.E.; Gross, P.G.; Goetze, R.W.; Walsh, R.M.; Peeples, W.B.; Wood, Z.A.; Biochemistry 54, 3360-3369 (2015)

Data extracted from this reference:

Cloned(Commentary)
Cloned (Commentary)
Organism
expressed in Escherichia coli BL21(DE3) cells
Staphylococcus aureus
recombinant expression of C-terminally His-tagged wild-type and mutant enzymes
Staphylococcus aureus
Crystallization (Commentary)
Crystallization (Commentary)
Organism
purified recombinant wild-type and mutant A181L enzymes, sitting drop vapor diffusion , for the wild-type enzyme complexed with 2-dehydropantoateand NADP+: mixing of 0.001 ml of 10 mg/mL protein in 4 mM 2-dehydropantoate, 4 mM NADP+, 50 mM NaCl, and 25 mM Tris, pH 8.0 with 0.001 ml of reservoir solution containing 300 mM magnesium acetate, 100 mM MES buffer, pH 6.6, and 15% PEG 3350, 2-3 days, 20°C, for the mutant enzyme A181L complexed with NADP+: mixing of 0.001ml of 10 mg/mL protein in 4 mM NADP+, 50 mM NaCl, and 25 mM Tris, pH 8.0, with 0.001 ml of the reservoir solution containing 6% tacsimate, 100 mM MES, pH 6, and 15% PEG 3350, 2-3 days, 20°C, X-ray diffraction structure determination and analysis at 1.81 and 2.62 A resolution, respectively
Staphylococcus aureus
sitting drop vapor diffusion method, using 300 mM magnesium acetate, 100 mM MES buffer (pH 6.6), and 15% (w/v) polyethylene glycol 3350
Staphylococcus aureus
Engineering
Protein Variants
Commentary
Organism
A181L
site-directed mutagenesis, the substitution displaces Ser239 and increases the Km for ketopantoate 844fold, without affecting kcat. The decrease in 2-dehydropantoate affinity enhances the already kinetically preferred NADPH binding path, making the random mechanism appear to be sequentially ordered and reducing the kinetic cooperativity
Staphylococcus aureus
A181L
the substitution increases the Km of ketopantoate 844fold, without affecting the kcat value
Staphylococcus aureus
Inhibitors
Inhibitors
Commentary
Organism
Structure
(R)-4-dehydropantoate
-
Staphylococcus aureus
KM Value [mM]
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
additional information
-
additional information
the enzyme shows strong positive cooperativity in kinetics. The enzyme follows a random addition mechanism in which the initial binding of NADPH is the kinetically preferred path, with a small degree of cooperativity between subunits. The mechanism of Staphylococcus aureus KPR is distinct from those of previously described members of the family of 2-hydroxyacid dehydrogenases
Staphylococcus aureus
0.0057
-
NADPH
mutant enzyme A181L, at pH 7.5 and 25°C
Staphylococcus aureus
0.0072
-
NADPH
wild type enzyme, at pH 7.5 and 25°C
Staphylococcus aureus
0.0096
-
(R)-4-dehydropantoate
wild type enzyme, at pH 7.5 and 25°C
Staphylococcus aureus
8.1
-
(R)-4-dehydropantoate
mutant enzyme A181L, at pH 7.5 and 25°C
Staphylococcus aureus
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
(R)-4-dehydropantoate + NADPH + H+
Staphylococcus aureus
-
(R)-pantoate + NADP+
-
-
?
2-dehydropantoate + NADPH + H+
Staphylococcus aureus
-
(R)-pantoate + NADP+
-
-
r
Organism
Organism
UniProt
Commentary
Textmining
Staphylococcus aureus
A0A0J9X283
-
-
Purification (Commentary)
Purification (Commentary)
Organism
recombinant C-terminally His-tagged wild-type and mutant enzymes
Staphylococcus aureus
TALON affinity resin column chromatography
Staphylococcus aureus
Reaction
Reaction
Commentary
Organism
Reaction ID
(R)-pantoate + NADP+ = 2-dehydropantoate + NADPH + H+
the enzyme follows a random addition mechanism in which the initial binding of NADPH is the kinetically preferred path, with a small degree of cooperativity between subunits. The mechanism of Staphylococcus aureus KPR is distinct from those of previously described members of the family of 2-hydroxyacid dehydrogenases
Staphylococcus aureus
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
Substrate Product ID
(R)-4-dehydropantoate + NADPH + H+
-
740065
Staphylococcus aureus
(R)-pantoate + NADP+
-
-
-
?
2-dehydropantoate + NADPH + H+
-
740065
Staphylococcus aureus
(R)-pantoate + NADP+
-
-
-
r
Subunits
Subunits
Commentary
Organism
dimer
the KPR dimer is stable in solution
Staphylococcus aureus
homodimer
x-ray crystallography
Staphylococcus aureus
More
homology modeling of structure of the ternary KPR complex using the crystal structure of Staphylococcus aureus apo-KPR as a search model, PDB ID 3G17
Staphylococcus aureus
Synonyms
Synonyms
Commentary
Organism
ketopantoate reductase
-
Staphylococcus aureus
KPR
-
Staphylococcus aureus
Temperature Optimum [°C]
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
25
-
assay at
Staphylococcus aureus
Turnover Number [1/s]
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
16.4
-
NADPH
mutant enzyme A181L, at pH 7.5 and 25°C
Staphylococcus aureus
16.6
-
(R)-4-dehydropantoate
wild type enzyme, at pH 7.5 and 25°C
Staphylococcus aureus
16.8
-
NADPH
wild type enzyme, at pH 7.5 and 25°C
Staphylococcus aureus
18.2
-
(R)-4-dehydropantoate
mutant enzyme A181L, at pH 7.5 and 25°C
Staphylococcus aureus
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.5
-
assay at
Staphylococcus aureus
Cofactor
Cofactor
Commentary
Organism
Structure
NADPH
-
Staphylococcus aureus
Ki Value [mM]
Ki Value [mM]
Ki Value maximum [mM]
Inhibitor
Commentary
Organism
Structure
0.27
-
(R)-4-dehydropantoate
wild type enzyme, at pH 7.5 and 25°C
Staphylococcus aureus
Cloned(Commentary) (protein specific)
Commentary
Organism
expressed in Escherichia coli BL21(DE3) cells
Staphylococcus aureus
recombinant expression of C-terminally His-tagged wild-type and mutant enzymes
Staphylococcus aureus
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
NADPH
-
Staphylococcus aureus
Crystallization (Commentary) (protein specific)
Crystallization
Organism
purified recombinant wild-type and mutant A181L enzymes, sitting drop vapor diffusion , for the wild-type enzyme complexed with 2-dehydropantoateand NADP+: mixing of 0.001 ml of 10 mg/mL protein in 4 mM 2-dehydropantoate, 4 mM NADP+, 50 mM NaCl, and 25 mM Tris, pH 8.0 with 0.001 ml of reservoir solution containing 300 mM magnesium acetate, 100 mM MES buffer, pH 6.6, and 15% PEG 3350, 2-3 days, 20°C, for the mutant enzyme A181L complexed with NADP+: mixing of 0.001ml of 10 mg/mL protein in 4 mM NADP+, 50 mM NaCl, and 25 mM Tris, pH 8.0, with 0.001 ml of the reservoir solution containing 6% tacsimate, 100 mM MES, pH 6, and 15% PEG 3350, 2-3 days, 20°C, X-ray diffraction structure determination and analysis at 1.81 and 2.62 A resolution, respectively
Staphylococcus aureus
sitting drop vapor diffusion method, using 300 mM magnesium acetate, 100 mM MES buffer (pH 6.6), and 15% (w/v) polyethylene glycol 3350
Staphylococcus aureus
Engineering (protein specific)
Protein Variants
Commentary
Organism
A181L
site-directed mutagenesis, the substitution displaces Ser239 and increases the Km for ketopantoate 844fold, without affecting kcat. The decrease in 2-dehydropantoate affinity enhances the already kinetically preferred NADPH binding path, making the random mechanism appear to be sequentially ordered and reducing the kinetic cooperativity
Staphylococcus aureus
A181L
the substitution increases the Km of ketopantoate 844fold, without affecting the kcat value
Staphylococcus aureus
Inhibitors (protein specific)
Inhibitors
Commentary
Organism
Structure
(R)-4-dehydropantoate
-
Staphylococcus aureus
Ki Value [mM] (protein specific)
Ki Value [mM]
Ki Value maximum [mM]
Inhibitor
Commentary
Organism
Structure
0.27
-
(R)-4-dehydropantoate
wild type enzyme, at pH 7.5 and 25°C
Staphylococcus aureus
KM Value [mM] (protein specific)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
additional information
-
additional information
the enzyme shows strong positive cooperativity in kinetics. The enzyme follows a random addition mechanism in which the initial binding of NADPH is the kinetically preferred path, with a small degree of cooperativity between subunits. The mechanism of Staphylococcus aureus KPR is distinct from those of previously described members of the family of 2-hydroxyacid dehydrogenases
Staphylococcus aureus
0.0057
-
NADPH
mutant enzyme A181L, at pH 7.5 and 25°C
Staphylococcus aureus
0.0072
-
NADPH
wild type enzyme, at pH 7.5 and 25°C
Staphylococcus aureus
0.0096
-
(R)-4-dehydropantoate
wild type enzyme, at pH 7.5 and 25°C
Staphylococcus aureus
8.1
-
(R)-4-dehydropantoate
mutant enzyme A181L, at pH 7.5 and 25°C
Staphylococcus aureus
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
(R)-4-dehydropantoate + NADPH + H+
Staphylococcus aureus
-
(R)-pantoate + NADP+
-
-
?
2-dehydropantoate + NADPH + H+
Staphylococcus aureus
-
(R)-pantoate + NADP+
-
-
r
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant C-terminally His-tagged wild-type and mutant enzymes
Staphylococcus aureus
TALON affinity resin column chromatography
Staphylococcus aureus
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
ID
(R)-4-dehydropantoate + NADPH + H+
-
740065
Staphylococcus aureus
(R)-pantoate + NADP+
-
-
-
?
2-dehydropantoate + NADPH + H+
-
740065
Staphylococcus aureus
(R)-pantoate + NADP+
-
-
-
r
Subunits (protein specific)
Subunits
Commentary
Organism
dimer
the KPR dimer is stable in solution
Staphylococcus aureus
homodimer
x-ray crystallography
Staphylococcus aureus
More
homology modeling of structure of the ternary KPR complex using the crystal structure of Staphylococcus aureus apo-KPR as a search model, PDB ID 3G17
Staphylococcus aureus
Temperature Optimum [°C] (protein specific)
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
25
-
assay at
Staphylococcus aureus
Turnover Number [1/s] (protein specific)
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
16.4
-
NADPH
mutant enzyme A181L, at pH 7.5 and 25°C
Staphylococcus aureus
16.6
-
(R)-4-dehydropantoate
wild type enzyme, at pH 7.5 and 25°C
Staphylococcus aureus
16.8
-
NADPH
wild type enzyme, at pH 7.5 and 25°C
Staphylococcus aureus
18.2
-
(R)-4-dehydropantoate
mutant enzyme A181L, at pH 7.5 and 25°C
Staphylococcus aureus
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.5
-
assay at
Staphylococcus aureus
General Information
General Information
Commentary
Organism
evolution
the enzyme is a member of the family of 2-hydroxyacid dehydrogenases
Staphylococcus aureus
malfunction
enzyme mutation A181L causes substitution of Ser239 and increases the Km for ketopantoate 844fold, without affecting kcat. The decrease in 2-dehydropantoate affinity enhances the already kinetically preferred NADPH binding path, making the random mechanism appear to be sequentially ordered and reducing the kinetic cooperativity
Staphylococcus aureus
additional information
residue Ser239 is known to be important for the binding affinity of 2-dehydropantoate
Staphylococcus aureus
physiological function
ketopantoate reductase (KPR) catalyzes the NADPH-dependent production of pantoate, an essential precursor in the biosynthesis of coenzyme A
Staphylococcus aureus
General Information (protein specific)
General Information
Commentary
Organism
evolution
the enzyme is a member of the family of 2-hydroxyacid dehydrogenases
Staphylococcus aureus
malfunction
enzyme mutation A181L causes substitution of Ser239 and increases the Km for ketopantoate 844fold, without affecting kcat. The decrease in 2-dehydropantoate affinity enhances the already kinetically preferred NADPH binding path, making the random mechanism appear to be sequentially ordered and reducing the kinetic cooperativity
Staphylococcus aureus
additional information
residue Ser239 is known to be important for the binding affinity of 2-dehydropantoate
Staphylococcus aureus
physiological function
ketopantoate reductase (KPR) catalyzes the NADPH-dependent production of pantoate, an essential precursor in the biosynthesis of coenzyme A
Staphylococcus aureus
Other publictions for EC 1.1.1.169
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
Synonyms
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)
739822
Aikawa
Crystal structure of ketopanto ...
Thermococcus kodakarensis, Thermococcus kodakarensis ATCC BAA-918
Acta crystallogr. Sect. F
72
369-375
2016
-
-
1
1
3
-
1
-
-
-
-
2
-
9
-
-
1
-
-
-
-
-
2
1
4
1
-
-
-
1
-
-
1
-
-
-
-
-
1
1
1
3
-
-
1
-
-
-
-
-
2
-
-
-
1
-
-
-
-
2
1
1
-
-
-
1
-
-
-
-
1
1
-
-
-
741385
Aikawa
Crystal structure of archaeal ...
Thermococcus kodakarensis, Thermococcus kodakarensis ATCC BAA-918
Proteins
84
374-382
2016
-
-
1
1
1
-
1
-
-
-
-
2
-
13
-
-
1
-
-
-
-
-
4
1
4
1
-
-
-
1
-
-
1
-
-
-
-
-
1
1
1
1
-
-
1
-
-
-
-
-
2
-
-
-
1
-
-
-
-
4
1
1
-
-
-
1
-
-
-
-
2
2
-
-
-
740065
Sanchez
Evidence of kinetic cooperativ ...
Staphylococcus aureus
Biochemistry
54
3360-3369
2015
-
-
2
2
2
-
1
5
-
-
-
2
-
6
-
-
2
1
-
-
-
-
2
3
2
1
-
-
4
1
-
-
1
1
-
-
-
-
2
1
2
2
-
-
1
1
5
-
-
-
2
-
-
-
2
-
-
-
-
2
3
1
-
-
4
1
-
-
-
-
4
4
-
-
-
725293
Miller
PanG, a new ketopantoate reduc ...
Francisella tularensis subsp. novicida
J. Bacteriol.
195
965-976
2013
-
-
-
-
-
-
-
-
-
-
-
-
-
25
-
-
-
-
-
-
-
-
-
-
3
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
1
-
-
-
729136
Miyanaga
The crystal structure of D-man ...
Enterococcus faecalis, Enterococcus faecalis IAM10071
Biochem. Biophys. Res. Commun.
439
109-114
2013
-
-
-
-
-
-
-
-
-
-
-
2
-
4
-
-
-
-
-
-
-
-
2
-
2
-
-
-
-
-
-
-
1
-
-
-
-
-
-
1
-
-
-
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-
-
2
-
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-
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-
-
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
736827
Tomita
Identification and characteriz ...
Thermococcus kodakarensis, Thermococcus kodakarensis ATCC BAA-918
Mol. Microbiol.
90
307-321
2013
-
-
1
-
1
-
1
7
-
-
2
4
-
19
-
-
1
-
-
-
-
-
13
1
5
1
1
1
6
1
-
-
4
1
-
-
-
-
1
4
-
1
-
-
1
1
7
-
-
2
4
-
-
-
1
-
-
-
-
13
1
1
1
1
6
1
-
-
-
-
2
2
-
6
6
696603
Headey
Backbone assignments of the 34 ...
Escherichia coli
Biomol. NMR Assign.
2
93-96
2008
-
-
1
-
-
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-
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1
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1
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1
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1
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1
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1
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1
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1
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-
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684140
Ciulli
pH-tuneable binding of 2-phosp ...
Escherichia coli
Acta Crystallogr. Sect. D
63
171-178
2007
-
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1
-
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1
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4
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3
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3
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1
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1
1
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1
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3
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687675
Ciulli
Crystal structure of Escherich ...
Escherichia coli
J. Biol. Chem.
282
8487-8497
2007
-
-
1
1
6
-
-
3
-
-
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1
-
4
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-
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-
-
-
2
-
2
1
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2
1
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2
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1
2
1
6
-
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3
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1
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-
-
2
-
1
-
-
2
1
-
-
-
-
-
-
-
-
-
669806
Ciulli
Probing hot spots at protein-l ...
Escherichia coli
J. Med. Chem.
49
4992-5000
2006
-
-
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-
7
1
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1
-
4
-
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-
1
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2
-
2
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-
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1
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3
6
-
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3
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7
6
1
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-
-
1
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-
2
-
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-
-
1
-
-
-
-
-
-
-
-
-
667561
Ciulli
Biophysical tools to monitor e ...
Escherichia coli
Biochem. Soc. Trans.
33
767-771
2005
-
-
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1
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1
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1
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2
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2
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2
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2
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1
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1
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2
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667687
Lobley
The crystal structure of Esche ...
Escherichia coli
Biochemistry
44
8930-8939
2005
-
-
1
1
7
-
-
1
-
-
-
1
-
4
-
-
1
1
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2
-
2
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2
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1
2
1
7
-
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1
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1
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1
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2
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654677
Zheng
Substrate specificity and kine ...
Escherichia coli
Biochemistry
42
11289-11296
2003
-
-
1
-
-
-
-
8
-
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4
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1
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2
1
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286109
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Identification of active site ...
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286107
Frodyma
ApbA, the ketopantoate reducta ...
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3
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6
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1
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1
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Novel enzymic production of D- ...
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2
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1
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1
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10
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4
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4
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1
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2
1
6
1
1
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Ketopantoic acid and ketopanto ...
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Separation and preliminary stu ...
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1
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1
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