Information on EC 4.1.3.36 - 1,4-dihydroxy-2-naphthoyl-CoA synthase

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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota

EC NUMBER
COMMENTARY
4.1.3.36
-
RECOMMENDED NAME
GeneOntology No.
1,4-dihydroxy-2-naphthoyl-CoA synthase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
4-(2-carboxyphenyl)-4-oxobutanoyl-CoA = 1,4-dihydroxy-2-naphthoyl-CoA + H2O
show the reaction diagram
-
-
-
-
4-(2-carboxyphenyl)-4-oxobutanoyl-CoA = 1,4-dihydroxy-2-naphthoyl-CoA + H2O
show the reaction diagram
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
-
4-(2-carboxyphenyl)-4-oxobutanoyl-CoA = 1,4-dihydroxy-2-naphthoyl-CoA + H2O
show the reaction diagram
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
-
4-(2-carboxyphenyl)-4-oxobutanoyl-CoA = 1,4-dihydroxy-2-naphthoyl-CoA + H2O
show the reaction diagram
unique induced-fit catalytic mechanism which involves intersubunit interactions, overview
-
4-(2-carboxyphenyl)-4-oxobutanoyl-CoA = 1,4-dihydroxy-2-naphthoyl-CoA + H2O
show the reaction diagram
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, unique induced-fit catalytic mechanism which involves intersubunit interactions, overview
Synechocystis sp. PCC6803
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
cleavage of 3-hydroxy acid
-
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
1,4-dihydroxy-2-naphthoate biosynthesis I
-
-
1,4-dihydroxy-2-naphthoate biosynthesis II (plants)
-
-
Biosynthesis of secondary metabolites
-
-
Metabolic pathways
-
-
Ubiquinone and other terpenoid-quinone biosynthesis
-
-
vitamin K metabolism
-
-
SYSTEMATIC NAME
IUBMB Comments
4-(2-carboxyphenyl)-4-oxobutanoyl-CoA dehydratase (cyclizing)
This enzyme is involved in the synthesis of 1,4-dihydroxy-2-naphthoate, a branch point metabolite leading to the biosynthesis of menaquinone (vitamin K2, in bacteria), phylloquinone (vitamin K1 in plants), and many plant pigments. The coenzyme A group is subsequently removed from the product by EC 3.1.2.28, 1,4-dihydroxy-2-naphthoyl-CoA hydrolase.
SYNONYMS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
DHNA synthetase
-
-
-
-
Dihydroxynaphthoic acid synthetase
-
-
-
-
synthase, 1,4-dihydroxy-2-naphthoate
-
-
-
-
CAS REGISTRY NUMBER
COMMENTARY
72506-71-9
-
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
metabolism
-
the enzyme catalyzes a carbon-carbon bond formation reaction in the biosynthesis of both vitamin K1 and K2
metabolism
-
the enzyme is involved in the menaquinone biosynthesis
physiological function
-
the enzyme is an essential enzyme in vitamin K biosynthesis
physiological function
Synechocystis sp. PCC6803
-
the enzyme is an essential enzyme in vitamin K biosynthesis
-
metabolism
Synechocystis sp. PCC6803
-
the enzyme catalyzes a carbon-carbon bond formation reaction in the biosynthesis of both vitamin K1 and K2, the enzyme is involved in the menaquinone biosynthesis
-
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
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
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
additional information
Synechocystis sp. PCC6803
-
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, 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
-
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2-(3-carboxypropyl)-benzoyl-CoA
?
show the reaction diagram
-
-
-
-
?
2-succinylbenzoyl-CoA
1,4-dihydroxy-2-naphthoyl-CoA + H2O
show the reaction diagram
-
-
-
-
?
o-succinylbenzoate
1,4-dihydroxy-2-naphthoyl-CoA + H2O
show the reaction diagram
-
-
-
-
?
o-succinylbenzoate
1,4-dihydroxy-2-naphthoyl-CoA + H2O
show the reaction diagram
P73495
-
-
-
?
o-succinylbenzoate
1,4-dihydroxy-2-naphthoyl-CoA + H2O
show the reaction diagram
-
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
-
-
?
o-succinylbenzoate
1,4-dihydroxy-2-naphthoyl-CoA + H2O
show the reaction diagram
-
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
-
-
?
o-succinylbenzoate
1,4-dihydroxy-2-naphthoyl-CoA + H2O
show the reaction diagram
-
catalyzes an intramolecular Claisen condensation reaction leading to the formation of 1,4-dihydroxy-2-naphthoyl-CoA from o-succinylbenzoate, the enzyme substrate is chemically unstable
-
-
?
o-succinylbenzoate
1,4-dihydroxy-2-naphthoyl-CoA + H2O
show the reaction diagram
Synechocystis sp. PCC6803
P73495
-
-
-
?
o-succinylbenzoate
1,4-dihydroxy-2-naphthoyl-CoA + H2O
show the reaction diagram
Synechocystis sp. PCC6803
-
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
-
-
?
o-succinylbenzoate
1,4-dihydroxy-2-naphthoyl-CoA + H2O
show the reaction diagram
P9WNP5
catalyzes an intramolecular Claisen condensation reaction leading to the formation of 1,4-dihydroxy-2-naphthoyl-CoA from o-succinylbenzoate, the enzyme substrate is chemically unstable
-
-
?
O-succinylbenzoyl-CoA
1,4-dihydroxy-2-naphthoate + CoA
show the reaction diagram
Q5HH38
-
-
-
?
O-succinylbenzoyl-CoA
1,4-dihydroxy-2-naphthoate + CoA
show the reaction diagram
-
-
-
-
?
O-succinylbenzoyl-CoA
1,4-dihydroxy-2-naphthoate + CoA
show the reaction diagram
-
-
-
?
O-succinylbenzoyl-CoA
1,4-dihydroxy-2-naphthoate + CoA
show the reaction diagram
-
-
-
-
?
O-succinylbenzoyl-CoA
1,4-dihydroxy-2-naphthoate + CoA
show the reaction diagram
-
-
-
?
O-succinylbenzoyl-CoA
1,4-dihydroxy-2-naphthoate + CoA
show the reaction diagram
-
-
-
?
O-succinylbenzoyl-CoA
1,4-dihydroxy-2-naphthoate + CoA
show the reaction diagram
-
-
-
?
O-succinylbenzoyl-CoA
1,4-dihydroxy-2-naphthoate + CoA
show the reaction diagram
-
-
-
-
?
O-succinylbenzoyl-CoA
1,4-dihydroxy-2-naphthoate + CoA
show the reaction diagram
-
highly specific, no substrates are 2-(3'-carboxypropionyl)benzoyl-CoA or 4-(2'-carboxyphenyl)4-oxobutyryl-diCoA
-
?
O-succinylbenzoyl-CoA
?
show the reaction diagram
-
pathway in menaquinone biosynthesis, i.e. vitamin K2, cf. EC 6.2.1.26
-
-
-
O-succinylbenzoyl-CoA
?
show the reaction diagram
-
pathway in menaquinone biosynthesis, i.e. vitamin K2, cf. EC 6.2.1.26
-
-
-
O-succinylbenzoyl-CoA
?
show the reaction diagram
-
pathway in menaquinone biosynthesis, i.e. vitamin K2, cf. EC 6.2.1.26
-
-
-
o-succinylbenzoyl-CoA
CoA + 1,4-dihydroxy-2-naphthoate
show the reaction diagram
-
-
-
-
?
o-succinylbenzoyl-CoA
1,4-dihydroxy-2-naphthoyl-CoA + H2O
show the reaction diagram
-
-
-
-
?
o-succinylbenzoyl-CoA
1,4-dihydroxy-2-naphthoyl-CoA + H2O + H2O
show the reaction diagram
-
-
-
-
?
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
o-succinylbenzoate
1,4-dihydroxy-2-naphthoyl-CoA + H2O
show the reaction diagram
-
-
-
-
?
o-succinylbenzoate
1,4-dihydroxy-2-naphthoyl-CoA + H2O
show the reaction diagram
P73495
-
-
-
?
o-succinylbenzoate
1,4-dihydroxy-2-naphthoyl-CoA + H2O
show the reaction diagram
-
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
-
-
?
o-succinylbenzoate
1,4-dihydroxy-2-naphthoyl-CoA + H2O
show the reaction diagram
-
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
-
-
?
o-succinylbenzoate
1,4-dihydroxy-2-naphthoyl-CoA + H2O
show the reaction diagram
Synechocystis sp. PCC6803
P73495
-
-
-
?
o-succinylbenzoate
1,4-dihydroxy-2-naphthoyl-CoA + H2O
show the reaction diagram
Synechocystis sp. PCC6803
-
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
-
-
?
O-succinylbenzoyl-CoA
1,4-dihydroxy-2-naphthoate + CoA
show the reaction diagram
-
-
-
-
?
O-succinylbenzoyl-CoA
?
show the reaction diagram
-
pathway in menaquinone biosynthesis, i.e. vitamin K2, cf. EC 6.2.1.26
-
-
-
O-succinylbenzoyl-CoA
?
show the reaction diagram
-
pathway in menaquinone biosynthesis, i.e. vitamin K2, cf. EC 6.2.1.26
-
-
-
O-succinylbenzoyl-CoA
?
show the reaction diagram
-
pathway in menaquinone biosynthesis, i.e. vitamin K2, cf. EC 6.2.1.26
-
-
-
o-succinylbenzoyl-CoA
CoA + 1,4-dihydroxy-2-naphthoate
show the reaction diagram
-
-
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
-
no cofactor required
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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
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
additional information
-
no metal ion required
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
(3Z)-3-(3,3-dimethyl-2-oxobutylidene)-3,4-dihydro-2H-1,4-benzoxazin-2-one
-
68.4% inhibition at 0.125 mg/ml, 0.00015 mM o-succinylbenzoate , pH not specified in the publication, temperature not specified in the publication
(3Z)-3-(3,3-dimethyl-2-oxobutylidene)-6-(ethylsulfonyl)-3,4-dihydro-2H-1,4-benzoxazin-2-one
-
60.3% inhibition at 0.125 mg/ml, 0.00015 mM o-succinylbenzoate, pH not specified in the publication, temperature not specified in the publication
(3Z)-6-chloro-3-(4-methyl-2-oxopentylidene)-3,4-dihydro-2H-1,4-benzoxazin-2-one
-
98% inhibition at 0.125 mg/ml, 0.00015 mM o-succinylbenzoate, pH not specified in the publication, temperature not specified in the publication
(3Z)-6-methyl-3-(4-methyl-2-oxopentylidene)-3,4-dihydro-2H-1,4-benzoxazin-2-one
-
77.3% inhibition at 0.125 mg/ml, 0.00015 mM o-succinylbenzoate, pH not specified in the publication, temperature not specified in the publication
1-hydroxy-2-naphthoyl-CoA
-
-
1-hydroxy-2-naphthoyl-CoA
-
a product analogue, protein-ligand interactions, complex structure, overview
2,3-dihydroxybenzoyl-CoA
-
-
2,4-dihydroxybenzoyl-CoA
-
-
2-CoA-4-(2,4-dichlorophenyl)-4-oxobutanoic acid
-
-
2-CoA-4-(2-bromophenyl)-4-oxobutanoic acid
-
-
2-CoA-4-(2-chlorophenyl)-4-oxobutanoic acid
-
-
2-CoA-4-(2-fluorophenyl)-4-oxobutanoic acid
-
-
2-CoA-4-(2-iodophenyl)-4-oxobutanoic acid
-
-
2-CoA-4-(2-methoxyphenyl)-4-oxobutanoic acid
-
-
2-CoA-4-(2-nitrophenyl)-4-oxobutanoic acid
-
-
2-CoA-4-(3-chlorophenyl)-4-oxobutanoic acid
-
-
2-CoA-4-(4-dichlorophenyl)-4-oxobutanoic acid
-
-
2-CoA-4-(4-methoxyphenyl)-4-oxobutanoic acid
-
-
3-(2,4-dichlorophenyl)-3-oxopropyl-CoA
-
weak inhibition
4-(2,4-dichlorophenyl)-4-oxobutanoyl-CoA
-
-
4-(2-chlorophenyl)-4-oxo-2-[[(1S)-1-phenylethyl]amino]butanoic acid
-
half-life at 25C, pH 7.4, is 0.4 h
4-(2-methoxyphenyl)-4-oxo-2-[[(1S)-1-phenylethyl]amino]butanoic acid
-
half-life at 25C, pH 7.4, is 11.6 h
4-(4-chlorophenyl)-4-oxo-2-[[(1S)-1-phenylethyl]amino]butanoic acid
-
half-life at 25C, pH 7.4, is 6.8 h
4-(4-fluorophenyl)-4-oxo-2-[[(1S)-1-phenylethyl]amino]butanoic acid
-
half-life at 25C, pH 7.4, is 12.2 h
4-oxo-2-[[(1S)-1-phenylethyl]amino]-4-[2-(trifluoromethyl)phenyl]butanoic acid
-
half-life at 25C, pH 7.4, is 0.2 h
4-oxo-4-chlorophenylbutenoyl methyl ester
-
penetrates the cell where it is hydrolyzed and reacts with CoA to generate the active antibacterial compound, mechanism, overview
-
4-oxo-4-phenyl-2-[[(1S)-1-phenylethyl]amino]butanoic acid
-
half-life at 25C, pH 7.4, is 11.6 h
methyl (2Z)-(2-oxo-2H-1,4-benzoxazin-3(4H)-ylidene)ethanoate
-
-
methyl (2Z)-(5-methyl-2-oxo-2H-1,4-benzoxazin-3(4H)-ylidene)ethanoate
-
-
methyl (2Z)-(6-chloro-2-oxo-2H-1,4-benzoxazin-3(4H)-ylidene)ethanoate
-
-
methyl (2Z)-(6-fluoro-2-oxo-2H-1,4-benzoxazin-3(4H)-ylidene)ethanoate
-
-
methyl (2Z)-(6-methyl-2-oxo-2H-1,4-benzoxazin-3(4H)-ylidene)ethanoate
-
-
methyl (2Z)-(6-nitro-2-oxo-2H-1,4-benzoxazin-3(4H)-ylidene)ethanoate
-
-
methyl (2Z)-(7-chloro-2-oxo-2H-1,4-benzoxazin-3(4H)-ylidene)ethanoate
-
-
methyl (2Z)-(7-fluoro-2-oxo-2H-1,4-benzoxazin-3(4H)-ylidene)ethanoate
-
-
methyl (2Z)-(7-methyl-2-oxo-2H-1,4-benzoxazin-3(4H)-ylidene)ethanoate
-
-
methyl (2Z)-(7-nitro-2-oxo-2H-1,4-benzoxazin-3(4H)-ylidene)ethanoate
-
-
salicyloyl-CoA
-
protein-ligand interactions, complex structure, overview
salicylyl-CoA
-
-
methyl (2Z)-[6-(ethylsulfonyl)-2-oxo-2H-1,4-benzoxazin-3(4H)-ylidene]ethanoate
-
-
additional information
-
2-amino-4-oxo-4-phenylbutanoate inhibitors are unstable in solution and eliminate to form the corresponding 4-oxo-4-phenylbut-2-enoates that then react with CoA in situ to form nanomolar inhibitors of MenB. The potency of these compounds results from interaction of the CoA adduct carboxylate with the MenB oxyanion hole, a conserved structural motif in the crotonase superfamily. No inhibition by 1548L21 at 0.3 mM
-
additional information
-
little or no inhibition by dimethylamide
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.106
2-(3-carboxypropyl)-benzoyl-CoA
-
wild type protein protein, pH 7.0, 25C
0.0031
2-succinylbenzoyl-CoA
-
D185N mutant protein, pH 7.0, 25C
0.0048
2-succinylbenzoyl-CoA
-
D185E mutant protein, pH 7.0, 25C
0.0224
2-succinylbenzoyl-CoA
-
wild type protein, pH 7.0, 25C
0.0402
2-succinylbenzoyl-CoA
-
S190A mutant protein, pH 7.0, 25C
0.0028
o-succinylbenzoate
-
pH 7.0, temperature not specified in the publication, wild-type enzyme
0.0166
o-succinylbenzoate
-
pH 7.0, temperature not specified in the publication, mutant R267A
0.0197
o-succinylbenzoate
-
pH 7.0, temperature not specified in the publication, mutant F270A
0.0433
o-succinylbenzoate
-
pH 7.0, temperature not specified in the publication, mutant K89A
0.0259
o-succinylbenzoyl-CoA
-
pH 7.0, 25C
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.00025
2-(3-carboxypropyl)-benzoyl-CoA
-
wild type protein protein, pH 7.0, 25C
0.00022
2-succinylbenzoyl-CoA
-
D185N mutant protein, pH 7.0, 25C
0.0017
2-succinylbenzoyl-CoA
-
S190A mutant protein, pH 7.0, 25C
0.0023
2-succinylbenzoyl-CoA
-
D185E mutant protein, pH 7.0, 25C
0.462
2-succinylbenzoyl-CoA
-
wild type protein, pH 7.0, 25C
0.0027
o-succinylbenzoate
-
pH 7.0, temperature not specified in the publication, mutant R267A
0.0035
o-succinylbenzoate
-
pH 7.0, temperature not specified in the publication, mutant F270A
0.021
o-succinylbenzoate
-
pH 7.0, temperature not specified in the publication, wild-type enzyme
0.038
o-succinylbenzoate
-
pH 7.0, temperature not specified in the publication, mutant K89A
0.062
o-succinylbenzoyl-CoA
-
pH 7.0, 25C
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0024
2-(3-carboxypropyl)-benzoyl-CoA
-
wild type protein protein, pH 7.0, 25C
41715
0.04
2-succinylbenzoyl-CoA
-
S190A mutant protein, pH 7.0, 25C
5683
0.07
2-succinylbenzoyl-CoA
-
D185N mutant protein, pH 7.0, 25C
5683
0.48
2-succinylbenzoyl-CoA
-
D185E mutant protein, pH 7.0, 25C
5683
21
2-succinylbenzoyl-CoA
-
wild type protein, pH 7.0, 25C
5683
0.16
o-succinylbenzoate
-
pH 7.0, temperature not specified in the publication, mutant R267A
7261
0.18
o-succinylbenzoate
-
pH 7.0, temperature not specified in the publication, mutant F270A
7261
0.89
o-succinylbenzoate
-
pH 7.0, temperature not specified in the publication, mutant K89A
7261
7.4
o-succinylbenzoate
-
pH 7.0, temperature not specified in the publication, wild-type enzyme
7261
2.4
o-succinylbenzoyl-CoA
-
pH 7.0, 25C
6009
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0013
1-hydroxy-2-naphthoyl-CoA
-
pH 7,0, 23C
0.0031
2,3-dihydroxybenzoyl-CoA
-
pH 7,0, 23C
0.0022
2,4-dihydroxybenzoyl-CoA
-
pH 7,0, 23C
0.000049
2-CoA-4-(2,4-dichlorophenyl)-4-oxobutanoic acid
-
pH 7.4, 25C
0.000097
2-CoA-4-(2-chlorophenyl)-4-oxobutanoic acid
-
pH 7.4, 25C
0.00035
2-CoA-4-(4-dichlorophenyl)-4-oxobutanoic acid
-
pH 7.4, 25C
0.0091
methyl (2Z)-(2-oxo-2H-1,4-benzoxazin-3(4H)-ylidene)ethanoate
-
non-competitive inhibitor, pH not specified in the publication, temperature not specified in the publication
0.0225
methyl (2Z)-(6-chloro-2-oxo-2H-1,4-benzoxazin-3(4H)-ylidene)ethanoate
-
non-competitive inhibitor, pH not specified in the publication, temperature not specified in the publication
0.0115
methyl (2Z)-(6-fluoro-2-oxo-2H-1,4-benzoxazin-3(4H)-ylidene)ethanoate
-
non-competitive inhibitor , pH not specified in the publication, temperature not specified in the publication
0.006
salicylyl-CoA
-
pH 7,0, 23C
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.000106
2-CoA-4-(2,4-dichlorophenyl)-4-oxobutanoic acid
-
pH 7.4, 25C
0.000135
2-CoA-4-(2-bromophenyl)-4-oxobutanoic acid
-
pH 7.4, 25C
0.000103
2-CoA-4-(2-chlorophenyl)-4-oxobutanoic acid
-
pH 7.4, 25C
0.000204
2-CoA-4-(2-fluorophenyl)-4-oxobutanoic acid
-
pH 7.4, 25C
0.000421
2-CoA-4-(2-iodophenyl)-4-oxobutanoic acid
-
pH 7.4, 25C
0.0121
2-CoA-4-(2-methoxyphenyl)-4-oxobutanoic acid
-
pH 7.4, 25C
0.000154
2-CoA-4-(2-nitrophenyl)-4-oxobutanoic acid
-
pH 7.4, 25C
0.0141
2-CoA-4-(3-chlorophenyl)-4-oxobutanoic acid
-
pH 7.4, 25C
0.00047
2-CoA-4-(4-dichlorophenyl)-4-oxobutanoic acid
-
pH 7.4, 25C
0.0335
2-CoA-4-(4-methoxyphenyl)-4-oxobutanoic acid
-
pH 7.4, 25C
0.4
3-(2,4-dichlorophenyl)-3-oxopropyl-CoA
-
above, pH 7.4, 25C
0.0022
4-(2,4-dichlorophenyl)-4-oxobutanoyl-CoA
-
pH 7.4, 25C
0.0084
4-(2-chlorophenyl)-4-oxo-2-[[(1S)-1-phenylethyl]amino]butanoic acid
-
pH 7.4, 25C
0.12
4-(2-methoxyphenyl)-4-oxo-2-[[(1S)-1-phenylethyl]amino]butanoic acid
-
pH 7.4, 25C
117
4-(4-chlorophenyl)-4-oxo-2-[[(1S)-1-phenylethyl]amino]butanoic acid
-
pH 7.4, 25C
0.0144
4-(4-fluorophenyl)-4-oxo-2-[[(1S)-1-phenylethyl]amino]butanoic acid
-
pH 7.4, 25C
0.0032
4-oxo-2-[[(1S)-1-phenylethyl]amino]-4-[2-(trifluoromethyl)phenyl]butanoic acid
-
pH 7.4, 25C
0.0527
4-oxo-4-phenyl-2-[[(1S)-1-phenylethyl]amino]butanoic acid
-
pH 7.4, 25C
0.01
methyl (2Z)-(2-oxo-2H-1,4-benzoxazin-3(4H)-ylidene)ethanoate
-
non-competitive inhibitor Ki' = 0.067 mM, pH not specified in the publication, temperature not specified in the publication
0.0241
methyl (2Z)-(5-methyl-2-oxo-2H-1,4-benzoxazin-3(4H)-ylidene)ethanoate
-
pH not specified in the publication, temperature not specified in the publication
0.0463
methyl (2Z)-(6-chloro-2-oxo-2H-1,4-benzoxazin-3(4H)-ylidene)ethanoate
-
non-competitive inhibitor Ki' = 0.0185 mM, pH not specified in the publication, temperature not specified in the publication
0.027
methyl (2Z)-(6-fluoro-2-oxo-2H-1,4-benzoxazin-3(4H)-ylidene)ethanoate
-
non-competitive inhibitor Ki' = 0.0101 mM, pH not specified in the publication, temperature not specified in the publication
0.0231
methyl (2Z)-(6-methyl-2-oxo-2H-1,4-benzoxazin-3(4H)-ylidene)ethanoate
-
pH not specified in the publication, temperature not specified in the publication
0.0282
methyl (2Z)-(6-nitro-2-oxo-2H-1,4-benzoxazin-3(4H)-ylidene)ethanoate
-
pH not specified in the publication, temperature not specified in the publication
0.0357
methyl (2Z)-(7-chloro-2-oxo-2H-1,4-benzoxazin-3(4H)-ylidene)ethanoate
-
pH not specified in the publication, temperature not specified in the publication
0.03
methyl (2Z)-(7-fluoro-2-oxo-2H-1,4-benzoxazin-3(4H)-ylidene)ethanoate
-
pH not specified in the publication, temperature not specified in the publication
0.0182
methyl (2Z)-(7-methyl-2-oxo-2H-1,4-benzoxazin-3(4H)-ylidene)ethanoate
-
pH not specified in the publication, temperature not specified in the publication
0.0203
methyl (2Z)-(7-nitro-2-oxo-2H-1,4-benzoxazin-3(4H)-ylidene)ethanoate
-
pH not specified in the publication, temperature not specified in the publication
0.0179
methyl (2Z)-[6-(ethylsulfonyl)-2-oxo-2H-1,4-benzoxazin-3(4H)-ylidene]ethanoate
-
pH not specified in the publication, temperature not specified in the publication
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
-
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30
-
assay at
30
-
assay at
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Geobacillus kaustophilus (strain HTA426)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Staphylococcus aureus (strain COL)
Synechocystis sp. (strain PCC 6803 / Kazusa)
Synechocystis sp. (strain PCC 6803 / Kazusa)
Synechocystis sp. (strain PCC 6803 / Kazusa)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
185000
Q5HH38
gel filtration
677390
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
hexamer
Q5HH38
gel filtration
hexamer
-
crystallization
hexamer
-
6 * 30000, SDS-PAGE, crystallization
homotrimer
-
3 * 30000, gel filtration
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
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, 22C, X-ray diffraction structure determination and analysis at 2.30 A resolution
-
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
-
sitting drop vapor diffusion technique, PEG 3350, in complex with o-succinylbenzoyl-amino-CoA
-
sitting drop vapour diffusion method with 30% (v/v) pentaerythritol ethocylate, 0.05 M ammonium sulfate, and 0.05 M bis-Tris pH 6.5
-
hanging drop vapor diffusion technique, PEG 6000, in complex with o-succinylbenzoyl-aminoCoA
-
sitting-drop or hanging-drop vapour-diffusion method, structure of native enzyme determined at 2.15 A resolution and structure of the naphthoyl-CoA complex is determined at 2.3 A resolution
-
sitting drop vapour diffusion method with 0.1 M NaHEPES pH 7.5, 1.6 M ammonium sulfate, 0.2 M NaCl
Q5HH38
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
-
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, 22C, X-ray diffraction structure determination and analysis at 2.04 A resolution
-
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
DMSO stabilizes during purification
-
unstable in the presence of ammonium sulfate
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20C, E. coli K-12, not less than 6 weeks
-
-20C, Mycobacterium phlei, in 3-(N-morpholino)propanesulfonic acid buffer, pH 6.9, 0.2 mM DTT, 20% DMSO, not less than 6 weeks
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ammonium sulfate precipitation, ion exchange chromatography (DEAE), gel filtration
-
His-tag affinity chromatography, tag removed
-
recombinant enzyme
-
recombinant wild-type and mutant enzymes from Escherichia coli strain BL21 (DE3) too over 95% purity
-
HisTrap Chelating HP5 Superdex 200 gel filtration and HiLoad 16/60 Superdex 200 gel filtration
-
HiTrap Chelating HP column chromatography and HiTrap column chromatography
Q5HH38
recombinant enzyme
-
recombinant enzyme from Escherichia coli strain BL21(DE3) too over 95% purity
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expression of wild-type and mutant enzymes in Escherichia coli strain BL21(DE3). K273A mutant forms inclusion bodies
-
His-tagged version expressed in Escherichia coli BL21(DE3)
-
recombinant expression
-
expressed in Escherichia coli strain BL21-CodonPlus(DE3)-RIL
-
expressed in Escherichia coli BL21(DE3)
-
expression in Escherichia coli BL21(DE3)
-
expressed in Escherichia coli strain BL21(DE3)
Q5HH38
expression of enzyme in Escherichia coli strain BL21(DE3)
-
recombinant expression
-
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D163A
-
loss of the ligand binding ability
D163E
-
14% 1,4-dihydroxy-2-naphthoyl-CoA synthetic activity
D163N
-
no 1,4-dihydroxy-2-naphthoyl-CoA synthetic activity
F270A
-
site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
G156D
-
no activity
K89A
-
site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
K91A
-
site-directed mutagenesis, inactive mutant
R267A
-
site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
R91A
-
no 1,4-dihydroxy-2-naphthoyl-CoA synthetic activity
S161A
-
expressed in inclusion bodies and unavailable for the binding test
Y258F
-
no 1,4-dihydroxy-2-naphthoyl-CoA synthetic activity
Y94F
-
wild type level activity
Y97F
-
no activity
Y97F
-
no 1,4-dihydroxy-2-naphthoyl-CoA synthetic activity
D185E
-
reduced kcat
D185G
-
no activity
D185N
-
reduced kcat
D192N
-
no activity
S190A
-
reduced kcat
Y287F
-
no activity
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
drug development
-
the enzyme is a target for development of antibacterial agents
drug development
-
the enzyme is a target for development of antibacterial agents
-
medicine
-
mutations in the menB gene, the gene encoding naphthoate synthase, cause the small-colony variant phenotype, small-colony variants are associated with persistent infections and may be selectively enriched during antibody therapy