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 ACCESSION NO.
LITERATURE
4-(2-carboxyphenyl)-4-oxobutanoyl-CoA = 1,4-dihydroxy-2-naphthoyl-CoA + H2O
show the reaction diagram
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Claisen condensation
-
-
Claisen condensation
-
-
cleavage of 3-hydroxy acid
-
-
-
-
cleavage of 3-hydroxy acid
-
-
PATHWAY
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
-
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 ACCESSION NO.
COMMENTARY
LITERATURE
1,4-dihydroxy-2-naphthoate synthetase
-
-
1,4-dihydroxy-2-naphthoyl-CoA synthase
-
-
1,4-dihydroxy-2-naphthoyl-CoA synthase
-
-
1,4-dihydroxy-2-naphthoyl-CoA synthase
O06414
-
1,4-dihydroxy-2-naphthoyl-CoA synthase
-
-
1,4-dihydroxy-2-naphthoyl-coenzyme synthase
-
-
DHNA synthetase
-
-
-
-
DHNA synthetase
-
-
dihydroxynaphthoate synthase
-
-
Dihydroxynaphthoic acid synthetase
-
-
-
-
naphthoate synthase
-
-
naphthoate synthase (MenB)
-
-
synthase, 1,4-dihydroxy-2-naphthoate
-
-
-
-
CAS REGISTRY NUMBER
COMMENTARY
72506-71-9
-
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
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-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 ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
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 ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
additional information
-
no cofactor required
-
METALS and IONS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
additional information
-
no metal ion required
INHIBITORS
ORGANISM
UNIPROT ACCESSION NO.
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
-
-
-
2,3-dihydroxybenzoyl-CoA
-
-
2,4-dihydroxybenzoyl-CoA
-
-
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
-
-
salicylyl-CoA
-
-
methyl (2Z)-[6-(ethylsulfonyl)-2-oxo-2H-1,4-benzoxazin-3(4H)-ylidene]ethanoate
-
-
additional information
-
little or no inhibition by dimethylamide
-
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
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
0.0259
-
o-succinylbenzoyl-CoA
-
pH 7.0, 25C
TURNOVER NUMBER [1/s]
TURNOVER NUMBER MAXIMUM[1/s]
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
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
0.062
-
o-succinylbenzoyl-CoA
-
pH 7.0, 25C
kcat/KM VALUE [1/mMs-1]
kcat/KM VALUE [1/mMs-1] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.0024
-
2-(3-carboxypropyl)-benzoyl-CoA
-
wild type protein protein, pH 7.0, 25C
316049
0.04
-
2-succinylbenzoyl-CoA
-
S190A mutant protein, pH 7.0, 25C
40185
0.07
-
2-succinylbenzoyl-CoA
-
D185N mutant protein, pH 7.0, 25C
40185
0.48
-
2-succinylbenzoyl-CoA
-
D185E mutant protein, pH 7.0, 25C
40185
21
-
2-succinylbenzoyl-CoA
-
wild type protein, pH 7.0, 25C
40185
2.4
-
o-succinylbenzoyl-CoA
-
pH 7.0, 25C
14731
Ki VALUE [mM]
Ki VALUE [mM] Maximum
INHIBITOR
ORGANISM
UNIPROT ACCESSION NO.
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
0.0091
-
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]
IC50 VALUE [mM] Maximum
INHIBITOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
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]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
additional information
-
-
-
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
30
-
-
assay at
30
-
-
assay at
SOURCE TISSUE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT ACCESSION NO.
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)
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
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
185000
-
Q5HH38, -
gel filtration
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
hexamer
Q5HH38, -
gel filtration
hexamer
-
6 * 30000, SDS-PAGE, crystallization
hexamer
-
crystallization
homotrimer
-
3 * 30000, gel filtration
Crystallization/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
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, -
GENERAL STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
DMSO stabilizes during purification
-
unstable in the presence of ammonium sulfate
-
STORAGE STABILITY
ORGANISM
UNIPROT ACCESSION NO.
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 ACCESSION NO.
LITERATURE
ammonium sulfate precipitation, ion exchange chromatography (DEAE), gel filtration
-
His-tag affinity chromatography, tag removed
-
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, -
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
His-tagged version expressed in Escherichia coli BL21(DE3)
-
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, -
ENGINEERING
ORGANISM
UNIPROT ACCESSION NO.
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
G156D
-
no activity
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 1,4-dihydroxy-2-naphthoyl-CoA synthetic activity
Y97F
-
no activity
D185E
-
reduced kcat
D185G
-
no activity
D185N
-
reduced kcat
D192N
-
no activity
S190A
-
reduced kcat
Y287F
-
no activity
APPLICATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
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