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Literature summary 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.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
4.1.3.36 expression of enzyme in Escherichia coli strain BL21(DE3) Synechocystis sp.
4.1.3.36 expression of wild-type and mutant enzymes in Escherichia coli strain BL21(DE3). K273A mutant forms inclusion bodies Escherichia coli

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
4.1.3.36 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
4.1.3.36 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

EC Number Protein Variants Comment Organism
4.1.3.36 F270A site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme Escherichia coli
4.1.3.36 K89A site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme Escherichia coli
4.1.3.36 K91A site-directed mutagenesis, inactive mutant Escherichia coli
4.1.3.36 R267A site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme Escherichia coli

Inhibitors

EC Number Inhibitors Comment Organism Structure
4.1.3.36 1-hydroxy-2-naphthoyl-CoA a product analogue, protein-ligand interactions, complex structure, overview Escherichia coli
4.1.3.36 1-hydroxy-2-naphthoyl-CoA a product analogue, protein-ligand interactions, complex structure, overview Synechocystis sp.
4.1.3.36 salicyloyl-CoA protein-ligand interactions, complex structure, overview Escherichia coli
4.1.3.36 salicyloyl-CoA protein-ligand interactions, complex structure, overview Synechocystis sp.

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
4.1.3.36 0.0028
-
o-succinylbenzoate pH 7.0, temperature not specified in the publication, wild-type enzyme Escherichia coli
4.1.3.36 0.0166
-
o-succinylbenzoate pH 7.0, temperature not specified in the publication, mutant R267A Escherichia coli
4.1.3.36 0.0197
-
o-succinylbenzoate pH 7.0, temperature not specified in the publication, mutant F270A Escherichia coli
4.1.3.36 0.0433
-
o-succinylbenzoate pH 7.0, temperature not specified in the publication, mutant K89A Escherichia coli

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
4.1.3.36 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
-
?
4.1.3.36 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

EC Number Organism UniProt Comment Textmining
4.1.3.36 Escherichia coli
-
-
-
4.1.3.36 Synechocystis sp. P73495
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
4.1.3.36 recombinant enzyme from Escherichia coli strain BL21(DE3) too over 95% purity Synechocystis sp.
4.1.3.36 recombinant wild-type and mutant enzymes from Escherichia coli strain BL21 (DE3) too over 95% purity Escherichia coli

Reaction

EC Number Reaction Comment Organism Reaction ID
4.1.3.36 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
4.1.3.36 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)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
4.1.3.36 o-succinylbenzoate + CoA
-
Escherichia coli 1,4-dihydroxy-2-naphthoyl-CoA + H2O
-
?
4.1.3.36 o-succinylbenzoate + CoA
-
Synechocystis sp. 1,4-dihydroxy-2-naphthoyl-CoA + H2O
-
?
4.1.3.36 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
-
?
4.1.3.36 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

EC Number Synonyms Comment Organism
4.1.3.36 1,4-dihydroxy-2-naphthoyl coenzyme A synthase
-
Escherichia coli
4.1.3.36 1,4-dihydroxy-2-naphthoyl coenzyme A synthase
-
Synechocystis sp.
4.1.3.36 DHNA-CoA synthase
-
Escherichia coli
4.1.3.36 DHNA-CoA synthase
-
Synechocystis sp.
4.1.3.36 MenB
-
Escherichia coli
4.1.3.36 MenB
-
Synechocystis sp.

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
4.1.3.36 0.0027
-
o-succinylbenzoate pH 7.0, temperature not specified in the publication, mutant R267A Escherichia coli
4.1.3.36 0.0035
-
o-succinylbenzoate pH 7.0, temperature not specified in the publication, mutant F270A Escherichia coli
4.1.3.36 0.021
-
o-succinylbenzoate pH 7.0, temperature not specified in the publication, wild-type enzyme Escherichia coli
4.1.3.36 0.038
-
o-succinylbenzoate pH 7.0, temperature not specified in the publication, mutant K89A Escherichia coli

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
4.1.3.36 7
-
assay at Escherichia coli
4.1.3.36 7
-
assay at Synechocystis sp.

General Information

EC Number General Information Comment Organism
4.1.3.36 metabolism the enzyme is involved in the menaquinone biosynthesis Escherichia coli
4.1.3.36 metabolism the enzyme is involved in the menaquinone biosynthesis Synechocystis sp.
4.1.3.36 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]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
4.1.3.36 0.16
-
o-succinylbenzoate pH 7.0, temperature not specified in the publication, mutant R267A Escherichia coli
4.1.3.36 0.18
-
o-succinylbenzoate pH 7.0, temperature not specified in the publication, mutant F270A Escherichia coli
4.1.3.36 0.89
-
o-succinylbenzoate pH 7.0, temperature not specified in the publication, mutant K89A Escherichia coli
4.1.3.36 7.4
-
o-succinylbenzoate pH 7.0, temperature not specified in the publication, wild-type enzyme Escherichia coli