Literature summary for 4.1.3.36 extracted from

Sun, Y.; Song, H.; Li, J.; Li, Y.; Jiang, M.; Zhou, J.; Guo, Z.
Structural basis of the induced-fit mechanism of 1,4-dihydroxy-2-naphthoyl coenzyme A synthase from the crotonase fold superfamily (2013), PLoS ONE, 8, e63095.

Cloned(Commentary)

Cloned (Comment)	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 (Comment)	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.

Crystallization (Comment)

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.

Protein Variants

Protein Variants	Comment	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	Comment	Organism
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	Comment	Organism
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	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
o-succinylbenzoate + CoA	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 + CoA	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	UniProt	Comment	Textmining
Escherichia coli	-	-	-
Synechocystis sp.	P73495	-	-

Purification (Commentary)

Purification (Comment)	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	Comment	Organism	Reaction ID
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	a
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.	a

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
o-succinylbenzoate + CoA	-	Escherichia coli	1,4-dihydroxy-2-naphthoyl-CoA + H2O	-	?
o-succinylbenzoate + CoA	-	Synechocystis sp.	1,4-dihydroxy-2-naphthoyl-CoA + H2O	-	?
o-succinylbenzoate + CoA	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	Synechocystis sp.	1,4-dihydroxy-2-naphthoyl-CoA + H2O	-	?
o-succinylbenzoate + CoA	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	Escherichia coli	1,4-dihydroxy-2-naphthoyl-CoA + H2O	-	?

Synonyms

Synonyms	Comment	Organism
1,4-dihydroxy-2-naphthoyl coenzyme A synthase	-	Escherichia coli
1,4-dihydroxy-2-naphthoyl coenzyme A synthase	-	Synechocystis sp.
DHNA-CoA synthase	-	Escherichia coli
DHNA-CoA synthase	-	Synechocystis sp.
MenB	-	Escherichia coli
MenB	-	Synechocystis sp.

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism
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	Comment	Organism
7	-	assay at	Escherichia coli
7	-	assay at	Synechocystis sp.

General Information

General Information	Comment	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	Comment	Organism
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