BRENDA - Enzyme Database show
show all sequences of 4.1.3.36

Structural basis of the induced-fit mechanism of 1,4-dihydroxy-2-naphthoyl coenzyme A synthase from the crotonase fold superfamily

Sun, Y.; Song, H.; Li, J.; Li, Y.; Jiang, M.; Zhou, J.; Guo, Z.; PLoS ONE 8, e63095 (2013)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
expression of enzyme in Escherichia coli strain BL21(DE3)
Synechocystis sp.
expression of wild-type and mutant enzymes in Escherichia coli strain BL21(DE3). K273A mutant forms inclusion bodies
Escherichia coli
Crystallization (Commentary)
Crystallization
Organism
purified recombinant enzyme, hanging drop method, mixing of protein solution containing 10 mg/ml protein in 10 mM NaHCO3, 10 mM 1-hydroxy-2-naphthoyl-CoA, and 25 mM Tris, pH 8.0, with reservoir solution containing 200 mM (NH4)2SO4 and 23% PEG 3,350 in 100 mM Bis-Tris, pH 5.5, in a 1:1 ratio, 1 week, X-ray diffraction structure determination and analysis at 1.84 A resolution
Escherichia coli
purified recombinant enzyme, hanging drop method, mixing of protein solution containing 10 mg/ml protein in 10 mM NaHCO3, 5 mM 1-hydroxy-2-naphthoyl-CoA, 5 mM salicyloyl-CoA, 20 mM glycine, pH 9.75, 1% glycerol, and 10 mM NaHCO3 or 0.15 M ammonium acetate, 4% tacsimate, 15% PEG 3350, and 100 mM Bis-Tris, pH 6.0, with reservoir solution containing 0.15 M ammonium acetate, 0.3 M ammonium sulfate, 16% PEG 3350, 100 mM Bis-Tris, pH 5.7, and 10 mM proline or 10 mM taurine, in a 1:1 ratio, 1 week, X-ray diffraction structure determination and analysis at 2.0-2.35 A resolution
Synechocystis sp.
Engineering
Amino acid exchange
Commentary
Organism
F270A
site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
Escherichia coli
K89A
site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
Escherichia coli
K91A
site-directed mutagenesis, inactive mutant
Escherichia coli
R267A
site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
Escherichia coli
Inhibitors
Inhibitors
Commentary
Organism
Structure
1-hydroxy-2-naphthoyl-CoA
a product analogue, protein-ligand interactions, complex structure, overview
Escherichia coli
1-hydroxy-2-naphthoyl-CoA
a product analogue, protein-ligand interactions, complex structure, overview
Synechocystis sp.
salicyloyl-CoA
protein-ligand interactions, complex structure, overview
Escherichia coli
salicyloyl-CoA
protein-ligand interactions, complex structure, overview
Synechocystis sp.
KM Value [mM]
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.0028
-
o-succinylbenzoate
pH 7.0, temperature not specified in the publication, wild-type enzyme
Escherichia coli
0.0166
-
o-succinylbenzoate
pH 7.0, temperature not specified in the publication, mutant R267A
Escherichia coli
0.0197
-
o-succinylbenzoate
pH 7.0, temperature not specified in the publication, mutant F270A
Escherichia coli
0.0433
-
o-succinylbenzoate
pH 7.0, temperature not specified in the publication, mutant K89A
Escherichia coli
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
o-succinylbenzoate
Synechocystis sp.
formation of a structural motif like an oxyanion hole for orientation of the o-succinylbenzoate substrate and stabilization of the oxyanion intermediate in the intramolecular Claisen condensation, which involves a conserved tyrosine residue in the A-loop via induced fit
1,4-dihydroxy-2-naphthoyl-CoA + H2O
-
-
?
o-succinylbenzoate
Escherichia coli
formation of a structural motif like an oxyanion hole for orientation of the o-succinylbenzoate substrate and stabilization of the oxyanion intermediate in the intramolecular Claisen condensation, which involves a conserved tyrosine residue in the A-loop. via induced fit
1,4-dihydroxy-2-naphthoyl-CoA + H2O
-
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Escherichia coli
-
-
-
Synechocystis sp.
P73495
-
-
Purification (Commentary)
Commentary
Organism
recombinant enzyme from Escherichia coli strain BL21(DE3) too over 95% purity
Synechocystis sp.
recombinant wild-type and mutant enzymes from Escherichia coli strain BL21 (DE3) too over 95% purity
Escherichia coli
Reaction
Reaction
Commentary
Organism
4-(2-carboxyphenyl)-4-oxobutanoyl-CoA = 1,4-dihydroxy-2-naphthoyl-CoA + H2O
unique induced-fit catalytic mechanism which involves intersubunit interactions, overview
Escherichia coli
4-(2-carboxyphenyl)-4-oxobutanoyl-CoA = 1,4-dihydroxy-2-naphthoyl-CoA + H2O
unique induced-fit catalytic mechanism which involves intersubunit interactions, overview
Synechocystis sp.
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
o-succinylbenzoate
-
728604
Escherichia coli
1,4-dihydroxy-2-naphthoyl-CoA + H2O
-
-
-
?
o-succinylbenzoate
-
728604
Synechocystis sp.
1,4-dihydroxy-2-naphthoyl-CoA + H2O
-
-
-
?
o-succinylbenzoate
formation of a structural motif like an oxyanion hole for orientation of the o-succinylbenzoate substrate and stabilization of the oxyanion intermediate in the intramolecular Claisen condensation, which involves a conserved tyrosine residue in the A-loop via induced fit
728604
Synechocystis sp.
1,4-dihydroxy-2-naphthoyl-CoA + H2O
-
-
-
?
o-succinylbenzoate
formation of a structural motif like an oxyanion hole for orientation of the o-succinylbenzoate substrate and stabilization of the oxyanion intermediate in the intramolecular Claisen condensation, which involves a conserved tyrosine residue in the A-loop. via induced fit
728604
Escherichia coli
1,4-dihydroxy-2-naphthoyl-CoA + H2O
-
-
-
?
Turnover Number [1/s]
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
0.0027
-
o-succinylbenzoate
pH 7.0, temperature not specified in the publication, mutant R267A
Escherichia coli
0.0035
-
o-succinylbenzoate
pH 7.0, temperature not specified in the publication, mutant F270A
Escherichia coli
0.021
-
o-succinylbenzoate
pH 7.0, temperature not specified in the publication, wild-type enzyme
Escherichia coli
0.038
-
o-succinylbenzoate
pH 7.0, temperature not specified in the publication, mutant K89A
Escherichia coli
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7
-
assay at
Escherichia coli
7
-
assay at
Synechocystis sp.
Cloned(Commentary) (protein specific)
Commentary
Organism
expression of enzyme in Escherichia coli strain BL21(DE3)
Synechocystis sp.
expression of wild-type and mutant enzymes in Escherichia coli strain BL21(DE3). K273A mutant forms inclusion bodies
Escherichia coli
Crystallization (Commentary) (protein specific)
Crystallization
Organism
purified recombinant enzyme, hanging drop method, mixing of protein solution containing 10 mg/ml protein in 10 mM NaHCO3, 10 mM 1-hydroxy-2-naphthoyl-CoA, and 25 mM Tris, pH 8.0, with reservoir solution containing 200 mM (NH4)2SO4 and 23% PEG 3,350 in 100 mM Bis-Tris, pH 5.5, in a 1:1 ratio, 1 week, X-ray diffraction structure determination and analysis at 1.84 A resolution
Escherichia coli
purified recombinant enzyme, hanging drop method, mixing of protein solution containing 10 mg/ml protein in 10 mM NaHCO3, 5 mM 1-hydroxy-2-naphthoyl-CoA, 5 mM salicyloyl-CoA, 20 mM glycine, pH 9.75, 1% glycerol, and 10 mM NaHCO3 or 0.15 M ammonium acetate, 4% tacsimate, 15% PEG 3350, and 100 mM Bis-Tris, pH 6.0, with reservoir solution containing 0.15 M ammonium acetate, 0.3 M ammonium sulfate, 16% PEG 3350, 100 mM Bis-Tris, pH 5.7, and 10 mM proline or 10 mM taurine, in a 1:1 ratio, 1 week, X-ray diffraction structure determination and analysis at 2.0-2.35 A resolution
Synechocystis sp.
Engineering (protein specific)
Amino acid exchange
Commentary
Organism
F270A
site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
Escherichia coli
K89A
site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
Escherichia coli
K91A
site-directed mutagenesis, inactive mutant
Escherichia coli
R267A
site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
Escherichia coli
Inhibitors (protein specific)
Inhibitors
Commentary
Organism
Structure
1-hydroxy-2-naphthoyl-CoA
a product analogue, protein-ligand interactions, complex structure, overview
Escherichia coli
1-hydroxy-2-naphthoyl-CoA
a product analogue, protein-ligand interactions, complex structure, overview
Synechocystis sp.
salicyloyl-CoA
protein-ligand interactions, complex structure, overview
Escherichia coli
salicyloyl-CoA
protein-ligand interactions, complex structure, overview
Synechocystis sp.
KM Value [mM] (protein specific)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.0028
-
o-succinylbenzoate
pH 7.0, temperature not specified in the publication, wild-type enzyme
Escherichia coli
0.0166
-
o-succinylbenzoate
pH 7.0, temperature not specified in the publication, mutant R267A
Escherichia coli
0.0197
-
o-succinylbenzoate
pH 7.0, temperature not specified in the publication, mutant F270A
Escherichia coli
0.0433
-
o-succinylbenzoate
pH 7.0, temperature not specified in the publication, mutant K89A
Escherichia coli
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
o-succinylbenzoate
Synechocystis sp.
formation of a structural motif like an oxyanion hole for orientation of the o-succinylbenzoate substrate and stabilization of the oxyanion intermediate in the intramolecular Claisen condensation, which involves a conserved tyrosine residue in the A-loop via induced fit
1,4-dihydroxy-2-naphthoyl-CoA + H2O
-
-
?
o-succinylbenzoate
Escherichia coli
formation of a structural motif like an oxyanion hole for orientation of the o-succinylbenzoate substrate and stabilization of the oxyanion intermediate in the intramolecular Claisen condensation, which involves a conserved tyrosine residue in the A-loop. via induced fit
1,4-dihydroxy-2-naphthoyl-CoA + H2O
-
-
?
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant enzyme from Escherichia coli strain BL21(DE3) too over 95% purity
Synechocystis sp.
recombinant wild-type and mutant enzymes from Escherichia coli strain BL21 (DE3) too over 95% purity
Escherichia coli
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
o-succinylbenzoate
-
728604
Escherichia coli
1,4-dihydroxy-2-naphthoyl-CoA + H2O
-
-
-
?
o-succinylbenzoate
-
728604
Synechocystis sp.
1,4-dihydroxy-2-naphthoyl-CoA + H2O
-
-
-
?
o-succinylbenzoate
formation of a structural motif like an oxyanion hole for orientation of the o-succinylbenzoate substrate and stabilization of the oxyanion intermediate in the intramolecular Claisen condensation, which involves a conserved tyrosine residue in the A-loop via induced fit
728604
Synechocystis sp.
1,4-dihydroxy-2-naphthoyl-CoA + H2O
-
-
-
?
o-succinylbenzoate
formation of a structural motif like an oxyanion hole for orientation of the o-succinylbenzoate substrate and stabilization of the oxyanion intermediate in the intramolecular Claisen condensation, which involves a conserved tyrosine residue in the A-loop. via induced fit
728604
Escherichia coli
1,4-dihydroxy-2-naphthoyl-CoA + H2O
-
-
-
?
Turnover Number [1/s] (protein specific)
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
0.0027
-
o-succinylbenzoate
pH 7.0, temperature not specified in the publication, mutant R267A
Escherichia coli
0.0035
-
o-succinylbenzoate
pH 7.0, temperature not specified in the publication, mutant F270A
Escherichia coli
0.021
-
o-succinylbenzoate
pH 7.0, temperature not specified in the publication, wild-type enzyme
Escherichia coli
0.038
-
o-succinylbenzoate
pH 7.0, temperature not specified in the publication, mutant K89A
Escherichia coli
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7
-
assay at
Escherichia coli
7
-
assay at
Synechocystis sp.
General Information
General Information
Commentary
Organism
metabolism
the enzyme is involved in the menaquinone biosynthesis
Escherichia coli
metabolism
the enzyme is involved in the menaquinone biosynthesis
Synechocystis sp.
additional information
enzyme structure in complex with a product analogue, the structural changes include the folding of an active-site loop into a beta-hairpin and significant reorientation of a helix at the carboxy terminus. A new interface is formed between the ordered loop and the reoriented helix, both of which also form additional interactions with the coenzyme A moiety of the ligand
Synechocystis sp.
General Information (protein specific)
General Information
Commentary
Organism
metabolism
the enzyme is involved in the menaquinone biosynthesis
Escherichia coli
metabolism
the enzyme is involved in the menaquinone biosynthesis
Synechocystis sp.
additional information
enzyme structure in complex with a product analogue, the structural changes include the folding of an active-site loop into a beta-hairpin and significant reorientation of a helix at the carboxy terminus. A new interface is formed between the ordered loop and the reoriented helix, both of which also form additional interactions with the coenzyme A moiety of the ligand
Synechocystis sp.
KCat/KM [mM/s]
kcat/KM Value [1/mMs-1]
kcat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
0.16
-
o-succinylbenzoate
pH 7.0, temperature not specified in the publication, mutant R267A
Escherichia coli
0.18
-
o-succinylbenzoate
pH 7.0, temperature not specified in the publication, mutant F270A
Escherichia coli
0.89
-
o-succinylbenzoate
pH 7.0, temperature not specified in the publication, mutant K89A
Escherichia coli
7.4
-
o-succinylbenzoate
pH 7.0, temperature not specified in the publication, wild-type enzyme
Escherichia coli
KCat/KM [mM/s] (protein specific)
KCat/KM Value [1/mMs-1]
KCat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
0.16
-
o-succinylbenzoate
pH 7.0, temperature not specified in the publication, mutant R267A
Escherichia coli
0.18
-
o-succinylbenzoate
pH 7.0, temperature not specified in the publication, mutant F270A
Escherichia coli
0.89
-
o-succinylbenzoate
pH 7.0, temperature not specified in the publication, mutant K89A
Escherichia coli
7.4
-
o-succinylbenzoate
pH 7.0, temperature not specified in the publication, wild-type enzyme
Escherichia coli
Other publictions for EC 4.1.3.36
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)
748290
Passi
RepTB a gene ontology based d ...
Mycobacterium tuberculosis
J. Cheminform.
10
24
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-
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12
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1
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1
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-
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1
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12
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1
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-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
746618
Song
Ligand-dependent active-site ...
Mycobacterium tuberculosis, Mycobacterium tuberculosis H37Rv
Acta Crystallogr. Sect. D
70
2959-2969
2014
-
-
1
1
-
-
-
-
-
-
-
2
-
4
-
-
1
-
-
-
-
-
2
1
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1
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1
1
1
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-
-
2
-
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-
1
-
-
-
-
2
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
728604
Sun
Structural basis of the induce ...
Escherichia coli, Synechocystis sp.
PLoS ONE
8
e63095
2013
-
-
2
2
4
-
4
4
-
-
-
2
-
4
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2
2
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4
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4
2
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2
-
2
4
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4
-
4
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2
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-
2
-
-
-
-
4
-
-
-
-
4
2
-
-
-
-
3
3
-
4
4
726985
Sun
Active site binding and cataly ...
Escherichia coli, Synechocystis sp.
Biochemistry
51
4580-4589
2012
-
-
2
2
-
-
-
-
-
2
-
2
-
2
-
-
2
2
-
-
-
-
2
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-
2
-
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2
-
2
-
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-
-
2
-
2
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-
2
-
-
-
-
2
-
-
-
-
-
2
-
-
-
-
6
6
-
-
-
714260
Chen
Stabilization of the second ox ...
Escherichia coli
Biochemistry
50
5893-5904
2011
-
-
1
-
8
-
4
-
-
-
-
-
-
3
-
-
1
-
-
-
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1
-
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4
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1
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8
-
-
4
4
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1
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-
1
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-
-
-
-
-
714273
Li
Mechanism of the intramolecula ...
Escherichia coli, Mycobacterium tuberculosis
Biochemistry
50
9532-9544
2011
-
-
2
2
8
-
-
6
-
-
1
-
-
4
-
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2
-
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-
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3
2
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6
-
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2
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2
8
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6
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1
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2
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-
3
2
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-
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6
-
-
-
-
-
-
-
-
6
6
726554
Li
CoA adducts of 4-oxo-4-phenylb ...
Mycobacterium tuberculosis, Mycobacterium tuberculosis H37Rv
ACS Med. Chem. Lett.
2
818-823
2011
-
1
-
-
-
-
20
-
-
-
-
-
-
4
-
-
-
-
-
-
-
-
2
-
1
-
-
-
1
-
-
-
3
-
18
-
1
-
-
-
-
-
18
20
3
-
-
-
-
-
-
-
-
-
-
-
-
-
2
-
1
-
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-
1
-
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-
-
-
-
-
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-
704888
Babujee
The proteome map of spinach le ...
Spinacia oleracea
J. Exp. Bot.
61
1441-1453
2010
-
-
-
-
-
-
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1
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1
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6
-
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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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714417
Li
Synthesis and SAR studies of 1 ...
Mycobacterium tuberculosis
Bioorg. Med. Chem. Lett.
20
6306-6309
2010
-
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1
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15
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3
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1
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1
1
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3
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11
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1
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11
15
3
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1
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1
1
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690466
Lannergard
Identification of the genetic ...
Staphylococcus aureus
Antimicrob. Agents Chemother.
52
4017-4022
2008
-
1
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4
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1
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1
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1
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1
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Structure of naphthoate syntha ...
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Heide
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Heide
Enzymatic synthesis of the coe ...
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Meganathan
Menaquinone (vitamin K2) biosy ...
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