Information on EC 2.2.1.9 - 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase

Word Map on EC 2.2.1.9
Please wait a moment until all data is loaded. This message will disappear when all data is loaded.
Specify your search results
Select one or more organisms in this record:
Show additional data
Do not include text mining results
Include (text mining) results (more...)
Include results (AMENDA + additional results, but less precise; more...)

The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
2.2.1.9
-
RECOMMENDED NAME
GeneOntology No.
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
isochorismate + 2-oxoglutarate = 5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate + CO2
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
decarboxylation
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
1,4-dihydroxy-2-naphthoate biosynthesis
-
-
vitamin K metabolism
-
-
Ubiquinone and other terpenoid-quinone biosynthesis
-
-
Metabolic pathways
-
-
Biosynthesis of secondary metabolites
-
-
SYSTEMATIC NAME
IUBMB Comments
isochorismate:2-oxoglutarate 4-oxopentanoatetransferase (decarboxylating)
Requires Mg2+ for maximal activity. This enzyme is involved in the biosynthesis of vitamin K2 (menaquinone). In most anaerobes and all Gram-positive aerobes, menaquinone is the sole electron transporter in the respiratory chain and is essential for their survival. It had previously been thought that the products of the reaction were (1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate (SHCHC), pyruvate and CO2 but it is now known that two separate enzymes are involved: this enzyme and EC 4.2.99.20, 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase. Under basic conditions, the product can spontaneously lose pyruvate to form SHCHC.
CAS REGISTRY NUMBER
COMMENTARY hide
122007-88-9
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
UniProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(+)-5-(carboxymethoxy)-6-hydroxycyclohexa-2,4-diene-1-carboxylic acid + 2-oxoglutarate
? + CO2
show the reaction diagram
-
analogue of isochorismate, weaker binding to enzyme. Only the (+)-enantiomer is a substrate
-
-
?
2,3-dihydroxybenzaldehyde + 2-oxoglutarate
(5R)-5-(2,3-dihydroxyphenyl)-5-hydroxy-4-oxopentanoic acid + CO2
show the reaction diagram
-
assay at pH 8
-
-
-
2-bromobenzaldehyde + 2-oxoglutarate
(5R)-5-(2-bromophenyl)-5-hydroxy-4-oxopentanoic acid + CO2
show the reaction diagram
-
assay at pH 8
-
-
-
2-chlorobenzaldehyde + 2-oxoglutarate
(5R)-5-(2-chlorophenyl)-5-hydroxy-4-oxopentanoic acid + CO2
show the reaction diagram
-
assay at pH 8
-
-
-
2-fluorobenzaldehyde + 2-oxoglutarate
(5R)-5-(2-fluorophenyl)-5-hydroxy-4-oxopentanoic acid + CO2
show the reaction diagram
-
assay at pH 8
-
-
-
2-fluorobenzaldehyde + oxaloacetate
(1R)-1-(2-fluorophenyl)-1-hydroxypropan-2-one + 2 CO2
show the reaction diagram
-
assay at pH 8
-
-
-
2-fluorobenzaldehyde + pyruvate
(1R)-1-(2-fluorophenyl)-1-hydroxypropan-2-one + CO2
show the reaction diagram
-
assay at pH 8
-
-
-
2-iodobenzaldehyde + 2-oxoglutarate
(5R)-5-hydroxy-5-(2-iodophenyl)-4-oxopentanoic acid + CO2
show the reaction diagram
-
assay at pH 8
-
-
-
2-methylbenzaldehyde + 2-oxoglutarate
(5R)-5-hydroxy-5-(2-methylphenyl)-4-oxopentanoic acid + CO2
show the reaction diagram
-
assay at pH 8
-
-
-
3,4-dihydroxybenzaldehyde + 2-oxoglutarate
(5R)-5-(3,4-dihydroxyphenyl)-5-hydroxy-4-oxopentanoic acid + CO2
show the reaction diagram
-
assay at pH 8
-
-
-
3-fluorobenzaldehyde + 2-oxoglutarate
(5R)-5-(3-fluorophenyl)-5-hydroxy-4-oxopentanoic acid + CO2
show the reaction diagram
-
assay at pH 8
-
-
-
3-iodobenzaldehyde + 2-oxoglutarate
(5R)-5-hydroxy-5-(3-iodophenyl)-4-oxopentanoic acid + CO2
show the reaction diagram
-
assay at pH 8
-
-
-
3-methoxybenzaldehyde + 2-oxoglutarate
(5R)-5-hydroxy-5-(3-methoxyphenyl)-4-oxopentanoic acid + CO2
show the reaction diagram
-
assay at pH 8
-
-
-
4-chlorbenzaldehyde + 2-oxoglutarate
(5R)-5-(4-chlorophenyl)-5-hydroxy-4-oxopentanoic acid + CO2
show the reaction diagram
-
assay at pH 8
-
-
-
4-fluorobenzaldehyde + 2-oxoglutarate
(5R)-5-(4-fluorophenyl)-5-hydroxy-4-oxopentanoic acid + CO2
show the reaction diagram
-
assay at pH 8
-
-
-
4-hydroxybenzaldehyde + 2-oxoglutarate
(5R)-5-hydroxy-5-(4-hydroxyphenyl)-4-oxopentanoic acid + CO2
show the reaction diagram
-
assay at pH 8
-
-
-
acetaldehyde + 2-oxoglutarate
(5R)-5-hydroxy-4-oxohexanoic acid + CO2
show the reaction diagram
-
assay at pH 8
-
-
-
benzaldehyde + 2-oxoglutarate
(5R)-5-hydroxy-4-oxo-5-phenylpentanoic acid + CO2
show the reaction diagram
-
assay at pH 8
-
-
-
benzaldehyde + oxaloacetate
(1R)-1-hydroxy-1-phenylpropan-2-one + 2 CO2
show the reaction diagram
-
assay at pH 8
-
-
-
benzaldehyde + pyruvate
(1R)-1-hydroxy-1-phenylpropan-2-one + 2 CO2
show the reaction diagram
-
assay at pH 8
-
-
-
cyclohex-1-ene-1-carbaldehyde + 2-oxoglutarate
(5R)-5-cyclohex-1-en-1-yl-5-hydroxy-4-oxopentanoic acid + CO2
show the reaction diagram
-
assay at pH 8
-
-
-
glyoxylate + 2-oxoglutarate
5-hydroxy-4-oxopentanoic acid + 2 CO2
show the reaction diagram
-
assay at pH 8
-
-
-
hexanal + 2-oxoglutarate
(5R)-5-hydroxy-4-oxodecanoic acid + CO2
show the reaction diagram
-
assay at pH 8
-
-
-
isochorismate + 2-oxoglutarate
(1R,2S,5S,6S)-5-[(1-carboxyethenyl)oxy]-2-(3-carboxypropanoyl)-6-hydroxycyclohex-3-ene-1-carboxylic acid + CO2
show the reaction diagram
isochorismate + 2-oxoglutarate
5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate + CO2
show the reaction diagram
pyruvate + 2-oxoglutarate
4-hydroxy-5-oxohexanoic acid + 2 CO2
show the reaction diagram
-
assay at pH 8
-
-
-
undec-10-enal + 2-oxoglutarate
(5R)-5-hydroxy-4-oxopentadec-14-enoic acid + CO2
show the reaction diagram
-
assay at pH 8
-
-
-
additional information
?
-
-
MenD participates in the menaquinone (vitamin K2) biosynthetic pathway
-
-
-
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
isochorismate + 2-oxoglutarate
5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate + CO2
show the reaction diagram
-
the enzyme is involved in biosynthesis of vitamin K2 (menoquinone). Under basic conditions, the product can spontaneously lose pyruvate to form (1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate
-
-
?
additional information
?
-
-
MenD participates in the menaquinone (vitamin K2) biosynthetic pathway
-
-
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
thiamine diphosphate
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
4-[ethoxy(hydroxy)phosphoryl]-4-oxobutanoic acid
-
inhibitor shows no significant inhibition of Mycobacterium tuberculosis growth in vitro under aerobic and hypoxic conditions
4-[hydroxy(methoxy)phosphoryl]-4-oxobutanoic acid
methyl succinylphosphonate
-
dead-end inhibitor
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
thiamine diphosphate
-
required, Km: 0.0024 mM
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0042 - 0.109
(+)-5-(carboxymethoxy)-6-hydroxycyclohexa-2,4-diene-1-carboxylic acid
0.0026 - 1.5
2-oxoglutarate
0.0053 - 0.053
isochorismate
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.12 - 0.4
(+)-5-(carboxymethoxy)-6-hydroxycyclohexa-2,4-diene-1-carboxylic acid
0.01 - 0.37
2-oxoglutarate
0.05
isochorismate
Escherichia coli
-
pH 7.8, 22C
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1 - 1417
(+)-5-(carboxymethoxy)-6-hydroxycyclohexa-2,4-diene-1-carboxylic acid
4189
0.07 - 77
2-oxoglutarate
34
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.016
4-[ethoxy(hydroxy)phosphoryl]-4-oxobutanoic acid
-
pH 7.4, 25C
0.00013 - 0.0007
4-[hydroxy(methoxy)phosphoryl]-4-oxobutanoic acid
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7 - 8
-
phosphate buffer
PDB
SCOP
CATH
ORGANISM
UNIPROT
Bacillus subtilis (strain 168)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Listeria monocytogenes serotype 4b (strain F2365)
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)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
61400
-
gel filtration
62000
-
SDS-PAGE
290000
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
tetramer
dimer of dimer, crystallization data, 4 x 64100, calculated
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
to 2.35 A resolution, in complex with thiamine diphosphate and Mn2+. basic residues Arg32, Arg106, Arg409, Arg428, and Lys299 interact with carboxylate and hydroxyl groups to align substrates for catalysis in combination with a cluster of the non-polar residues Ile489, Phe490, and Leu493 on one side of the active site. Arg409 plays a significant role in binding both substrates while Arg428 contributes mainly to binding of 2-oxoglutarate. Arg32 and in particular Arg106 are critical for recognition of isochorismate
crystallization of the apoenzyme and holoenzyme forms of MenD. The apoenzyme crystals are obtained by sitting-drop vapour diffusion with 70% MPD. The crystals are too small to collect diffraction data and a search for better conditions is not successful. Single crystals of the holoenzyme with thiamin diphosphate and Mn2+ as cofactors are obtained by the hanging-drop vapour-diffusion method with 35% ethylene glycol as precipitant. Diffraction data are collected on a cryocooled crystal to a resolution of 2.0 A
-
sitting and hanging vapor diffusion method, hexagonal complex with thiamine diphosphate and Mn2+
-
tetragonal crystal form
-
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
-
melting temperature 53C, melting temperature 57.3C of protein complex with thiamin diphosphate, melting temperature 54C of protein complex with 2-oxoglutarate, melting temperature 54.5C of protein complex with FAD
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
2-oxoglutarate improves protein stability
-
FAD improves protein stability
-
thiamine diphosphate improves protein stability
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
4C, desalting buffer with 50 mM phosphate, 1 mM thiamine diphosphate and 2 mM MgCl2, pH 8.0, 4 weeks, no significant loss of activity
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
first step His-Trap chromatography, second step ion-exchange chromatography with Q column, third step chromatography with Superdex column
-
gel permeation chromatography
-
Ni2+ affinity column, size-exclusion column
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli BL21
-
overexpression in Escherichia coli BL21
-
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
F490A
0.6% of wild-type activity
I489A
1% of wild-type activity
K299A
150% of wild-type activity
L493A
80% of wild-type activity
R106A
mutation in the second subunit forming the active site, 10% of wild-type activity
R32A
mutation in the second subunit forming the active site, 30% of wild-type activity
R409A
3% of wild-type activity
R428A
1% of wild-type activity
E55D
-
about 30% decrease in catalytic efficiency
I148L
-
strong decrease in catalytic efficiency
K292Q
-
150% increase in catalytic efficiency
R107K
-
no decrease in catalytic efficiency
R293K
-
slight increase in catalytic efficiency
R395K
-
90% decrease in catalytic efficiency
R413K
-
strong decrease in catalytic efficiency
S32A
-
slight decrease in catalytic efficiency
S391A
-
slight decrease in catalytic efficiency
R395K
-
4fold increase in Km value, 50% decrease in kcat value
S391A
-
minor effect on activity
S391Y
-
trace activity
Show AA Sequence (3946 entries)
Please use the Sequence Search for a certain query.