Information on EC 4.2.1.113 - o-succinylbenzoate synthase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
4.2.1.113
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RECOMMENDED NAME
GeneOntology No.
o-succinylbenzoate synthase
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
(1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate = 2-succinylbenzoate + H2O
show the reaction diagram
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-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dehydration
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
1,4-dihydroxy-2-naphthoate biosynthesis
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Biosynthesis of secondary metabolites
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Metabolic pathways
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Ubiquinone and other terpenoid-quinone biosynthesis
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vitamin K metabolism
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SYSTEMATIC NAME
IUBMB Comments
(1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate hydrolyase (2-succinylbenzoate-forming)
Belongs to the enolase superfamily and requires divalent cations, preferably Mg2+ or Mn2+, for activity. Forms part of the vitamin-K-biosynthesis pathway.
CAS REGISTRY NUMBER
COMMENTARY hide
97089-83-3
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
strain T-1-60
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Manually annotated by BRENDA team
strain AN 154
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Manually annotated by BRENDA team
gene menC
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Manually annotated by BRENDA team
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UniProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
metabolism
additional information
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate
4-(2-carboxyphenyl)-4-oxobutanoic acid + H2O
show the reaction diagram
(1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate
2-succinylbenzoate + H2O
show the reaction diagram
2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylic acid
4-(2-carboxyphenyl)-4-oxobutyrate + H2O
show the reaction diagram
additional information
?
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
(1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate
4-(2-carboxyphenyl)-4-oxobutanoic acid + H2O
show the reaction diagram
(1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate
2-succinylbenzoate + H2O
show the reaction diagram
2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylic acid
4-(2-carboxyphenyl)-4-oxobutyrate + H2O
show the reaction diagram
additional information
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
thiamine diphosphate
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tightly bound to the enzyme
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
EDTA
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loses all activity during treatment with EDTA, activity is most efficiently restored by Mn2+
additional information
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docking of potential inhibitors, inhibitor development via competitive binding of the substrate, overview. Design of a substrate-based analogue, evaluation of auxiliary molecule interaction energies through molecular docking and molecular dynamic simulation studies
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.48
(1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate
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0.007 - 0.668
(1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate
additional information
additional information
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substrate affinity is as much as 40fold higher for Escherichia coli OSBS than for OSBS of Amycolatopsis, also stated by analysis on phylogeny, structure, sequence conservation
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
120
(1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate
Amycolatopsis sp.
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0.1 - 210
(1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.61 - 2600
(1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate
24567
additional information
additional information
Exiguobacterium sp.
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catalytic efficiency for the N-succinylamino acid racemization reaction is 0.041 mM/s
2
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5 - 9
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pH 7.5: about 60% of maximal activity, pH 9.0: about 60% of maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
37 - 60
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about 30% of maximal activity at 37°C and at 60°C
PDB
SCOP
CATH
ORGANISM
UNIPROT
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Staphylococcus aureus (strain COL)
Thermobifida fusca (strain YX)
Thermobifida fusca (strain YX)
Thermosynechococcus elongatus (strain BP-1)
Thermosynechococcus elongatus (strain BP-1)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
35760
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mass spectrometry
37740
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mass spectrometry
66500
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x * 66500, SDS-PAGE
195500
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gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
hanging-drop vapor diffusion method, the best crystals are observed growing at room temperature from poly(ethylene glycol) 8000 at pH 8.0, space group R32 with unit cell dimensions of a = b = 216.0 A and c = 261.0 A and contains 4 subunits in the asymmetric unit. Three-dimensional structures of liganded complexes of the enzyme with o-succinylbenzoate, N-acetylmethionine, N-succinylmethionine, succinylphenylglycine to 2.2, 2.3, 2.1, and 1.9 A resolution, respectively
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striking differences in overall structure, altered oligomeric structure, length variation, orientation of the capping domain, active site structure, differences in substrate binding, conformation and position of the 20s loop structure, evolution of new protein functions by promiscuous binding and reactions with new substrates due to structural flexibility
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co-crystallization of the K133R mutant with 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylic acid
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crystallization of the apoenzyme and a complex with Mg2+ and 4-(2-carboxyphenyl)-4-oxobutyrate
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
purification of a recombinant His-tagged enzyme by affinity chromatography followed by tag cleavage and anion-exchange chromatography
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recombinant N-terminally His-tagged enzyme from Escherichia coli strain BW25113 menC- by metal affinity chromatography
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recombinant N-terminally His-tagged wild-type and mutant enzymes from Escherichia coli strain BW25113 menC- by nickel affinity chromatography
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ExiOSBS is encoded in the menaquinone synthesis operon, phylogenetic analysis and tree of the NSAR/OSBS subfamily, expression of N-terminally His-tagged enzyme in Escherichia coli strain BW25113 menC-
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expression in Escherichia coli of several recombinant mutant enzymes
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expression of a recombinant enzyme in Escherichia coli
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gene menC, expression of N-terminally His-tagged wild-type and mutant enzymes in Escherichia coli strain BW25113 menC-
gene menC, phylogenetic analysis
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gene menC, phylogenetic analysis, expression of wild-type enzme in Escherichia coli strain BL21(DE3), expression of mutant enzymes in Escherichia coli strain BW25113 (menC::kan), which is converted into a DE3 strain to express T7 RNA polymerase
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
K163R
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no o-succinylbenzoate synthase activity and no N-acylamino acid racemase activity, mutant enzyme catalyzes the stereospecific exchange of the alpha-hydrogen of N-succinyl-(S)-phenylglycine with solvent hydrogen
K163S
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no o-succinylbenzoate synthase activity and no N-acylamino acid racemase activity, mutant enzyme catalyzes the stereospecific exchange of the alpha-hydrogen of N-succinyl-(S)-phenylglycine with solvent hydrogen
K263R
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no o-succinylbenzoate synthase activity and no N-acylamino acid racemase activity, mutant enzyme catalyzes the stereospecific exchange of the alpha-hydrogen of N-succinyl-(R)-phenylglycine with solvent hydrogen
K263S
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no o-succinylbenzoate synthase activity and no N-acylamino acid racemase activity, mutant enzyme catalyzes the stereospecific exchange of the alpha-hydrogen of N-succinyl-(R)-phenylglycine with solvent hydrogen
F51A
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site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
F51Y
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site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
G16P/V17F/V18R/L19T/R20S/D21F/R22G/R23T/L24QL48A
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site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
G288A
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site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme, G288A introduces a steric clash with the substrate, reducing kcat/KM over 500fold
G295A
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site-directed mutagenesis, the mutant enzyme activity is reduced compared to the wild-type enzyme
I265A
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site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
K133A
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inactive mutant
K133R
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inactive mutant
K133S
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inactive mutant
K235A
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inactive mutant
K235R
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inactive mutant
K235S
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inactive mutant
L109A
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site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
L19A
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site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
L48A/F51A
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site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
L48M
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site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
L48M/F51Y
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site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
R159M
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site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
S262A/S263A/S264A/I265A
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site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
S262G
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site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
S262T
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site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
S263G
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site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
S264A
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site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
T291S
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site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
V233N
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site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
F16A
site-directed mutagenesis, the mutant enzyme activity is reduced compared to the wild-type enzyme
F39A
site-directed mutagenesis, the mutant enzyme activity is reduced compared to the wild-type enzyme
G254A
site-directed mutagenesis, the mutant enzyme activity is reduced compared to the wild-type enzyme
G254T
site-directed mutagenesis, the mutant enzyme activity is reduced compared to the wild-type enzyme
N73A
site-directed mutagenesis, the mutant enzyme activity is reduced compared to the wild-type enzyme
N73A/T75A
site-directed mutagenesis, the mutant is inactive
N73A/T75L
site-directed mutagenesis, the mutant enzyme activity is reduced compared to the wild-type enzyme
N73L/T75V
site-directed mutagenesis, the mutant enzyme activity is reduced compared to the wild-type enzyme
R128M
site-directed mutagenesis, the mutant enzyme activity is reduced compared to the wild-type enzyme
R15G/F16G/R17G/G18G/I19G
site-directed mutagenesis, the mutant enzyme activity is reduced compared to the wild-type enzyme
R17A
site-directed mutagenesis, the mutant enzyme activity is reduced compared to the wild-type enzyme
R17A/F39A
site-directed mutagenesis, the mutant enzyme activity is reduced compared to the wild-type enzyme
R17A/Y42A
site-directed mutagenesis, the mutant enzyme activity is reduced compared to the wild-type enzyme
T75A
site-directed mutagenesis, the mutant enzyme activity is reduced compared to the wild-type enzyme
T75L
site-directed mutagenesis, the mutant enzyme activity is reduced compared to the wild-type enzyme
V230L
site-directed mutagenesis, the mutant enzyme activity is reduced compared to the wild-type enzyme
Y42A
site-directed mutagenesis, the mutant enzyme activity is reduced compared to the wild-type enzyme
additional information
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20s loop is truncated by deleting residues V17, V18, L19, R20, D21, R22, R23, and L24 resulting in a mutant with highly reduced activity compared to the wild-type enzyme
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
drug development
Show AA Sequence (4463 entries)
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