BRENDA - Enzyme Database show
show all sequences of 4.1.3.36

Active site binding and catalytic role of bicarbonate in 1,4-dihydroxy-2-naphthoyl coenzyme a synthases from vitamin K biosynthetic pathways

Sun, Y.; Song, H.; Li, J.; Jiang, M.; Li, Y.; Zhou, J.; Guo, Z.; Biochemistry 51, 4580-4589 (2012)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
recombinant expression
Escherichia coli
recombinant expression
Synechocystis sp.
Crystallization (Commentary)
Crystallization
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
Commentary
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
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
o-succinylbenzoate
Escherichia coli
-
1,4-dihydroxy-2-naphthoyl-CoA + H2O
-
-
?
o-succinylbenzoate
Synechocystis sp.
-
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
Escherichia coli
recombinant enzyme
Synechocystis sp.
Reaction
Reaction
Commentary
Organism
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
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.
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
o-succinylbenzoate
-
726985
Escherichia coli
1,4-dihydroxy-2-naphthoyl-CoA + H2O
-
-
-
?
o-succinylbenzoate
-
726985
Synechocystis sp.
1,4-dihydroxy-2-naphthoyl-CoA + H2O
-
-
-
?
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
recombinant expression
Escherichia coli
recombinant expression
Synechocystis sp.
Crystallization (Commentary) (protein specific)
Crystallization
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 (protein specific)
Metals/Ions
Commentary
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) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
o-succinylbenzoate
Escherichia coli
-
1,4-dihydroxy-2-naphthoyl-CoA + H2O
-
-
?
o-succinylbenzoate
Synechocystis sp.
-
1,4-dihydroxy-2-naphthoyl-CoA + H2O
-
-
?
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant enzyme
Escherichia coli
recombinant enzyme
Synechocystis sp.
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
o-succinylbenzoate
-
726985
Escherichia coli
1,4-dihydroxy-2-naphthoyl-CoA + H2O
-
-
-
?
o-succinylbenzoate
-
726985
Synechocystis sp.
1,4-dihydroxy-2-naphthoyl-CoA + H2O
-
-
-
?
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 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 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
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.
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.
General Information (protein specific)
General Information
Commentary
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 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
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.
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.
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
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2
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4
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3
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4
4
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Sun
Active site binding and cataly ...
Escherichia coli, Synechocystis sp.
Biochemistry
51
4580-4589
2012
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2
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2
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6
6
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714260
Chen
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5893-5904
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8
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4
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714273
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50
9532-9544
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2
2
8
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6
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1
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4
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2
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2
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8
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6
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3
2
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6
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6
6
726554
Li
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Mycobacterium tuberculosis, Mycobacterium tuberculosis H37Rv
ACS Med. Chem. Lett.
2
818-823
2011
-
1
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20
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4
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1
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3
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1
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704888
Babujee
The proteome map of spinach le ...
Spinacia oleracea
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61
1441-1453
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15
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15
3
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690466
Lannergard
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Antimicrob. Agents Chemother.
52
4017-4022
2008
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1
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677366
Kanaujia
Cloning, expression, purificat ...
Geobacillus kaustophilus
Acta Crystallogr. Sect. F
63
103-105
2007
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1
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677390
Ulaganathan
Structure of Staphylococcus au ...
Staphylococcus aureus
Acta Crystallogr. Sect. F
63
908-913
2007
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1
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663500
Johnston
Structure of naphthoate syntha ...
Mycobacterium tuberculosis
Acta Crystallogr. Sect. D
61
1199-1206
2005
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1
1
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93959
Kolkmann
4-(2'-Carboxyphenyl)-4-oxobuty ...
Escherichia coli, Galium mollugo, Mycolicibacterium phlei
Z. Naturforsch. C
42
1207-1214
1987
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3
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93961
Shaw
-
Recombinent plasmids containin ...
Escherichia coli
FEMS Microbiol. Lett.
17
63-67
1983
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93962
Heide
Enzymatic synthesis, character ...
Escherichia coli, Mycolicibacterium phlei
J. Biol. Chem.
257
7396-7400
1982
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2
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2
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93960
Heide
Enzymatic synthesis of the coe ...
Mycolicibacterium phlei
FEBS Lett.
128
201-204
1981
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93958
Meganathan
Menaquinone (vitamin K2) biosy ...
Mycolicibacterium phlei
J. Bacteriol.
140
92-98
1979
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