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Literature summary for 4.1.3.36 extracted from

  • Sun, Y.; Song, H.; Li, J.; Jiang, M.; Li, Y.; Zhou, J.; Guo, Z.
    Active site binding and catalytic role of bicarbonate in 1,4-dihydroxy-2-naphthoyl coenzyme a synthases from vitamin K biosynthetic pathways (2012), Biochemistry, 51, 4580-4589.
    View publication on PubMed

Cloned(Commentary)

Cloned (Comment) Organism
recombinant expression Escherichia coli
recombinant expression Synechocystis sp.

Crystallization (Commentary)

Crystallization (Comment) Organism
purified recombinant enzyme free or in complex with bicarbonate or nitrate, hanging drop vapor diffusion method, 0.01 ml of protein solution containing 10 mg/mL purified ecMenB, 25 mM Tris, pH 8.0, and 10% glycerol, including 10 mM NaHCO3 or NaNO3 for the complexed enzyme, is mixed with 0.001 ml of reservoir solution containing reservoir solution containing 300 mM NaCl, 100 mM Tris, pH 7.5, 2% Tacsimate, and 20% PEG 335, equilibration against 0.5 ml of reservoir solution, 22°C, X-ray diffraction structure determination and analysis at 2.30 A resolution Escherichia coli
purified recombinant enzyme, hanging drop vapor diffusion method, 0.01 ml of protein solution containing 10 mg/mL purified scMenB, 20 mM glycine, pH 9.75, and 1% glycerol, with or without 10 mM NaHCO3, is mixed with 0.001 ml of reservoir solution containing of 0.15 M ammonium acetate, 0.02 M L-proline, 0.1 M Bis-Tris, pH 6.1, and 45% MPD, equilibration against 0.5 ml of reservoir solution, 22°C, X-ray diffraction structure determination and analysis at 2.04 A resolution Synechocystis sp.

Metals/Ions

Metals/Ions Comment Organism Structure
bicarbonate the enzyme from Escherichia coli is a type I enzyme, which is dependent on exogenous bicarbonate for catalytic activity. The bicarbonate cofactor is bound to the enzyme active site at a position equivalent to that of the side chain carboxylate of an aspartate residue conserved among bicarbonate-insensitive DHNA-CoA synthases, binding site structure, overview Escherichia coli
bicarbonate the enzyme from Synechocystis is a type I enzyme, type I enzymes are dependent on exogenous bicarbonate for catalytic activity. The bicarbonate cofactor is bound to the enzyme active site at a position equivalent to that of the side chain carboxylate of an aspartate residue conserved among bicarbonate-insensitive DHNA-CoA synthases, binding site structure, overview Synechocystis sp.

Natural Substrates/ Products (Substrates)

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

Organism

Organism UniProt Comment Textmining
Escherichia coli
-
-
-
Synechocystis sp. P73495
-
-

Purification (Commentary)

Purification (Comment) Organism
recombinant enzyme Escherichia coli
recombinant enzyme Synechocystis sp.

Reaction

Reaction Comment Organism Reaction ID
4-(2-carboxyphenyl)-4-oxobutanoyl-CoA = 1,4-dihydroxy-2-naphthoyl-CoA + H2O the enzyme is an essential enzyme in vitamin K biosynthesis, which is responsible for conversion of o-succinylbenzoyl-CoA to 1,4-dihydroxy-2-naphthoyl-CoA via catalysis of a multiple-step intramolecular Claisen condensation reaction, proposed reaction mechanism, overview Synechocystis sp.
4-(2-carboxyphenyl)-4-oxobutanoyl-CoA = 1,4-dihydroxy-2-naphthoyl-CoA + H2O the enzyme is an essential enzyme in vitamin K biosynthesis, which is responsible for conversion of o-succinylbenzoyl-CoA to DHNACoA via catalysis of a multiple-step intramolecular Claisen condensation reaction, proposed reaction mechanism, overview Escherichia coli

Substrates and Products (Substrate)

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

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 catalyzes a carbon-carbon bond formation reaction in the biosynthesis of both vitamin K1 and K2 Escherichia coli
metabolism the enzyme catalyzes a carbon-carbon bond formation reaction in the biosynthesis of both vitamin K1 and K2 Synechocystis sp.
additional information active site structure, catalytically essential is Asp185 in the active site, residues Gly77 and Gly123 form an oxyanion hole for stabilization of the enolate intermediate, a hydrophobic patch consisting of Leu96, Val98, and Leu99 for recognition and interaction with the nonpolar aromatic ring of the substrate, and other catalytically essential motifs consisting of Ser151, Asp153, and Tyr248 from a different subunit, detailed overview and modeling Synechocystis sp.
additional information active site structure, catalytically essential is Gly156 in the active site, residues Gly86 and Gly133 form an oxyanion hole for stabilization of the enolate intermediate, a hydrophobic patch consisting of Leu106, Val108, and Leu109 for recognition and interaction with the nonpolar aromatic ring of the substrate, and other catalytically essential motifs consisting of Ser161, Asp163, and Tyr258 from a different subunit, detailed overview and modeling Escherichia coli
physiological function the enzyme is an essential enzyme in vitamin K biosynthesis Escherichia coli
physiological function the enzyme is an essential enzyme in vitamin K biosynthesis Synechocystis sp.