Information on EC 4.2.1.79 - 2-Methylcitrate dehydratase

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

EC NUMBER
COMMENTARY
4.2.1.79
-
RECOMMENDED NAME
GeneOntology No.
2-Methylcitrate dehydratase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
(2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate = (Z)-but-2-ene-1,2,3-tricarboxylate + H2O
show the reaction diagram
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
addition
-
-
double bond; of H2O to double bond
-
elimination of H2O
-
-
-
-
syn-elimination
-, P77243
-
PATHWAY
KEGG Link
MetaCyc Link
2-methylcitrate cycle I
-
Propanoate metabolism
-
SYSTEMATIC NAME
IUBMB Comments
(2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate hydro-lyase [(Z)-but-2-ene-1,2,3-tricarboxylate-forming]
Not identical with EC 4.2.1.4, citrate dehydratase. The enzyme is specific for (2S,3S)-methylcitrate, showing no activity with (2R,3S)-methylcitrate [2]. The enzyme can also use cis-aconitate as a substrate but more slowly [2]. Both this enzyme and EC 4.2.1.3, aconitate hydratase, are required to complete the isomerization of (2S,3S)-methylcitrate to (2R,3S)-2-methylisocitrate [2]
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
2-MC dehydratase
-
-
2-MC dehydratase
Salmonella enterica JE2170
-
-
-
2-methylcitrate dehydratase
-
-
2-methylcitrate dehydratase
Salmonella enterica JE2170
-
-
-
2-methylcitrate dehydratase 1
-
-
2-methylcitrate dehydratase 1
-
-
-
2-Methylcitrate hydro-lyase
-
-
-
-
Dehydratase, 2-methylcitrate
-
-
-
-
methylcitrate dehydratase
P77243
-
methylcitrate dehydratase
-
-
methylcitrate dehydratase
Mycobacterium smegmatis mc2155
-
-
-
PrpD
P77243
-
PrpD
-
-
-
PrpD
P74840
-
PrpD
Salmonella enterica JE2170
-
-
-
CAS REGISTRY NUMBER
COMMENTARY
80891-26-5
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
gene prpD, part of the prp operon, induction and expression depends on propionate during growth
SwissProt
Manually annotated by BRENDA team
K12, several strains, gene prpD of the propionate catabolism operon prpRBCDE, the enzyme is identical with aconitase AcnC
-
-
Manually annotated by BRENDA team
strain M1
-
-
Manually annotated by BRENDA team
strain M1
-
-
Manually annotated by BRENDA team
Rhodobacter capsulatus B10
strain B10
-
-
Manually annotated by BRENDA team
gene prpD
-
-
Manually annotated by BRENDA team
prpBCDE operon; serovar Typhimurium LT2, gene prpD of the prpBCDE operon
SwissProt
Manually annotated by BRENDA team
gene acnD and prpF are both needed for full enzyme activity, they exist in place of or in addition to prpD
-
-
Manually annotated by BRENDA team
gene acnD and prpF are both needed for full enzyme activity, they exist in place of or in addition to prpD
-
-
Manually annotated by BRENDA team
formerly Saccaromycopsis lipolytica
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
metabolism
-
2-methylcitrate dehydratase and 1, 2-methylcitrate synthase are involved in energy metabolism and participate in the methylcitrate cycle, which is an important source of energy in the cell
metabolism
-
2-methylcitrate dehydratase and 1, 2-methylcitrate synthase are involved in energy metabolism and participate in the methylcitrate cycle, which is an important source of energy in the cell
-
additional information
-
ipon silver stess 2-methylcitrate dehydratase and 2-methylcitrate synthase are strongly overexpressed
additional information
-
ipon silver stess 2-methylcitrate dehydratase and 2-methylcitrate synthase are strongly overexpressed
-
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(2S,3S)-hydroxybutane-1,2,3-tricarboxylate
(Z)-but-2-ene-1,2,3-tricarboxylate + H2O
show the reaction diagram
-, P77243
i.e. 2-methylcitrate, highly specific for, stereospecific for (2S,3S)-methylcitrate, the reverse reaction is an unusual syn-elimination
i.e. 2-methyl-cis-aconitate
?
(2S,3S)-hydroxybutane-1,2,3-tricarboxylate
(Z)-but-2-ene-1,2,3-tricarboxylate + H2O
show the reaction diagram
-, P77243
enzyme performs the isomerization of (2S,3S)-methylcitrate to (2R,3S)-2-methylisocitrate together with aconitase, both enzymes are essential, overview
-
r
(S)-malate
?
show the reaction diagram
-
-
-
?
(Z)-But-2-ene-1,2,3-tricarboxylate + H2O
2-Hydroxybutane-1,2,3-tricarboxylate
show the reaction diagram
-
r
r, i.e. 2-methylcitrate
-
(Z)-But-2-ene-1,2,3-tricarboxylate + H2O
2-Hydroxybutane-1,2,3-tricarboxylate
show the reaction diagram
-
i.e. 2-methyl-cis-aconitate
r, i.e. 2-methylcitrate
-
2-Hydroxybutane-1,2,3-tricarboxylate
(Z)-But-2-ene-1,2,3-tricarboxylate + H2O
show the reaction diagram
-
-
-
?
2-Hydroxybutane-1,2,3-tricarboxylate
(Z)-But-2-ene-1,2,3-tricarboxylate + H2O
show the reaction diagram
P74840
-
-
?
2-Hydroxybutane-1,2,3-tricarboxylate
(Z)-But-2-ene-1,2,3-tricarboxylate + H2O
show the reaction diagram
-
r
r
-
2-Hydroxybutane-1,2,3-tricarboxylate
(Z)-But-2-ene-1,2,3-tricarboxylate + H2O
show the reaction diagram
-
i.e. 2-methylcitrate
-
-
-
2-Hydroxybutane-1,2,3-tricarboxylate
(Z)-But-2-ene-1,2,3-tricarboxylate + H2O
show the reaction diagram
-
i.e. 2-methylcitrate
-
-
2-Hydroxybutane-1,2,3-tricarboxylate
(Z)-But-2-ene-1,2,3-tricarboxylate + H2O
show the reaction diagram
-
i.e. 2-methylcitrate
r
-
2-Hydroxybutane-1,2,3-tricarboxylate
(Z)-But-2-ene-1,2,3-tricarboxylate + H2O
show the reaction diagram
-
i.e. 2-methylcitrate
i.e. 2-methyl-cis-aconitate
?
2-Hydroxybutane-1,2,3-tricarboxylate
(Z)-But-2-ene-1,2,3-tricarboxylate + H2O
show the reaction diagram
P74840
i.e. 2-methylcitrate
i.e. 2-methyl-cis-aconitate
?
2-Hydroxybutane-1,2,3-tricarboxylate
(Z)-But-2-ene-1,2,3-tricarboxylate + H2O
show the reaction diagram
-
i.e. 2-methylcitrate, best substrate
i.e. 2-methyl-cis-aconitate
?
2-Hydroxybutane-1,2,3-tricarboxylate
(Z)-But-2-ene-1,2,3-tricarboxylate + H2O
show the reaction diagram
-
i.e. 2-methylcitrate, best substrate
i.e. 2-methyl-cis-aconitate
?
2-Hydroxybutane-1,2,3-tricarboxylate
(Z)-But-2-ene-1,2,3-tricarboxylate + H2O
show the reaction diagram
-
metabolic function
-
?
2-Hydroxybutane-1,2,3-tricarboxylate
?
show the reaction diagram
-
methylcitric acid cycle, propionyl-CoA oxidation
-
-
-
2-methylcitrate
2-methyl-cis-aconitate + H2O
show the reaction diagram
-
-
-
-
?
2-methylcitrate
2-methyl-cis-aconitate + H2O
show the reaction diagram
-
-
-
-
?
2-methylcitrate
2-methyl-cis-aconitate + H2O
show the reaction diagram
-
-
-
-
?
2-methylcitrate
2-methyl-cis-aconitate + H2O
show the reaction diagram
Salmonella enterica JE2170
-
-
-
-
?
cis-aconitate
?
show the reaction diagram
P74840
-
-
?
cis-aconitate
?
show the reaction diagram
-, P77243
5fold lower activity than with 2-methylcitrate
-
?
citrate
cis-aconitate + H2O
show the reaction diagram
-
-
-
?
citrate
?
show the reaction diagram
-
-
-
?
citrate
?
show the reaction diagram
P74840
low activity with
-
?
D-malate
?
show the reaction diagram
-
-
-
?
D-tartrate
?
show the reaction diagram
-
-
-
?
DL-citramalate
?
show the reaction diagram
-
-
-
?
DL-isocitrate
?
show the reaction diagram
-
-
-
?
L-tartrate
?
show the reaction diagram
-
-
-
?
meso-tartrate
?
show the reaction diagram
-
-
-
?
additional information
?
-
-
not: citrate, threo-DL-isocitrate, threo-D-2-methylisocitrate, DL-homocitrate, DL-citramalate
-
-
-
additional information
?
-
-, P77243
(2R,3S)-isocitrate and citrate are poor substrates, no activity with trans-aconitate, threo-2-methylisocitrate, erythro-2-methylisocitrate, (S)-malate and (R)-malate
-
?
additional information
?
-
-
2-methylisocitrate and isocitrate are no substrates for AcnD
-
?
additional information
?
-
P74840
enzyme does not catalyze the hydration of 2-methyl-cis-aconitate to 2-methylisocitrate, isocitrate is no substrate
-
?
additional information
?
-
-
substrate specificity, no activity with cis-aconitate and related substances containing double bonds, overview
-
?
additional information
?
-
P74840
the enzyme and the aconitase perform the 2-methylcitric acid cycle, overview
-
?
additional information
?
-
-
enzyme of the methylcitrate cycle
-
-
-
additional information
?
-
-
PrpD does not catabolize 2-methylcitrate which is produced by the Krebs cycle enzyme citrate synthase GltA
-
-
-
additional information
?
-
Mycobacterium smegmatis mc2155
-
enzyme of the methylcitrate cycle
-
-
-
additional information
?
-
Salmonella enterica JE2170
-
PrpD does not catabolize 2-methylcitrate which is produced by the Krebs cycle enzyme citrate synthase GltA
-
-
-
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
(2S,3S)-hydroxybutane-1,2,3-tricarboxylate
(Z)-but-2-ene-1,2,3-tricarboxylate + H2O
show the reaction diagram
-, P77243
enzyme performs the isomerization of (2S,3S)-methylcitrate to (2R,3S)-2-methylisocitrate together with aconitase, both enzymes are essential, overview
-
r
2-Hydroxybutane-1,2,3-tricarboxylate
(Z)-But-2-ene-1,2,3-tricarboxylate + H2O
show the reaction diagram
-
-
-
?
2-Hydroxybutane-1,2,3-tricarboxylate
(Z)-But-2-ene-1,2,3-tricarboxylate + H2O
show the reaction diagram
P74840
-
-
?
2-Hydroxybutane-1,2,3-tricarboxylate
(Z)-But-2-ene-1,2,3-tricarboxylate + H2O
show the reaction diagram
-
metabolic function
-
?
2-Hydroxybutane-1,2,3-tricarboxylate
?
show the reaction diagram
-
methylcitric acid cycle, propionyl-CoA oxidation
-
-
-
additional information
?
-
P74840
the enzyme and the aconitase perform the 2-methylcitric acid cycle, overview
-
?
additional information
?
-
Mycobacterium smegmatis, Mycobacterium smegmatis mc2155
-
enzyme of the methylcitrate cycle
-
-
-
COFACTOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
additional information
P74840
the enzyme contains no iron-sulfur center
-
METALS and IONS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Fe2+
-
AcnD enzyme possesses 1 unstable iron-sulfur center per monomer, absolutely required for activity, can be reconstituted by Fe2+ under reducing conditions
Fe2+
-
enzyme possesses 1 unstable iron-sulfur center per monomer, required for activity, can be reconstituted by Fe2+ under reducing conditions
additional information
P74840
no requirement for metal ions and reducing agents
INHIBITORS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
citrate
-
competitive
DL-Fluorocitrate
-
competitive
p-chloromercuribenzoate
-
-
threo-Isocitrate
-
competitive
-
tricarballylate
-
competitive
additional information
-
not: chelating agents
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
Propionate
-
induces enzyme expression, enzyme is required for growth on propionate
Propionate
-
induces the enzyme expression from acnC and prpD
PrpF
-
seems to be an accessory protein required to prevent oxidative damage of the Fe/S center of active AcnD enzyme, or is involved in synthesis or repair of the Fe/S cluster present in AcnD
-
additional information
-, P77243
gene prpD, part of the prp operon, induction and expression depends on propionate during growth
-
additional information
-
no requirement for AMP, ADT, ATP, NAD(P)+, NAD(P)H, pyruvate
-
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.44
-
(2S,3S)-methylcitrate
-, P77243
-
0.19
-
2-Hydroxybutane-1,2,3-tricarboxylate
-
diastereomer
SPECIFIC ACTIVITY [µmol/min/mg]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
0.005
-
-
partially purified AcnC
0.2
-
P74840
purified recombinant His-tagged enzyme, substrate citrate
0.8
-
-
purified PrpD
2.6
-
P74840
purified recombinant His-tagged enzyme, substrate cis-aconitate
2.8
-
P74840
purified recombinant His-tagged enzyme, substrate 2-methylcitrate
additional information
-
-
substrate specificity
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
7
8
-
for AcnC and PrpD
7.5
-
-, P77243
assay at
8
-
P74840
assay at
pH RANGE
pH RANGE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
37
-
P74840
assay at
37
-
-
assay at
37
-
-
assay at
TEMPERATURE RANGE
TEMPERATURE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
pI VALUE
pI VALUE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
5.7
-
-, P77243
isoelectric focusing
5.8
-
-
isoelectric focusing
SOURCE TISSUE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
SOURCE
additional information
-
2-methylcitrate dehydratase is highly induced in cadmium-treated cells
Manually annotated by BRENDA team
additional information
Rhodobacter capsulatus B10
-
2-methylcitrate dehydratase is highly induced in cadmium-treated cells
-
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
Escherichia coli (strain K12)
MOLECULAR WEIGHT
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
54000
-
-, P77243
gel filtration
54000
-
-
gel filtration and native PAGE
78000
79000
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
?
-
x * 55000, SDS-PAGE
?
-
x * 55000, SDS-PAGE
-
monomer
-
1 * 79000, SDS-PAGE
monomer
-
1 * 54000, SDS-PAGE
Crystallization/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
purified recombinant His-tagged enzyme, 11.7 mg/ml, in 10 mM HEPES, pH 7.5, optimization of crystallization conditions with precipitant solution containing PEG or pentaerythriol propoxylate and pentaerythriol ethoxylate, overview, X-ray diffraction structure determination and analysis at beyond 2.0 A resolution
-
pH STABILITY
pH STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
TEMPERATURE STABILITY
TEMPERATURE STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
40
-
-
30 min, stable
50
-
-
half-life is 30 min for both AcnC and PrpD
60
-
-
30 min, complete inactivation
GENERAL STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
unstable in Tris-HCl buffer
-
STORAGE STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
liquid N2, 0.05 M potassium phosphate buffer, pH 6.5, stable for more than 6 months
-
Purification/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
AcnC partially 0.25fold from AcnABnull strain, PrpD 14.3fold from overexpression in AcnABnull strain
-
recombinant His-tagged enzyme from overexpressing strain
-, P77243
recombinant His-tagged enzyme from Escherichia coli BL21(DE3), to homogeneity
P74840
recombinant His-tagged AcnD and PrpF from Escherichia coli BL21(DE3)
-
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
DNA and amino acid sequence determination and analysis, genomic organization, expression of AcnC in AcnABnull strain, overexpression of PrpD in AcnABnull strain
-
genomic structure of prp operon, expression studies in Escherichia coli K12 strain W3350, and overexpression of the N-terminally His-tagged enzyme
-, P77243
gene prpD in the operon prpBCDE, DNA sequence determination nand analysis, overexpression as N-terminally His-tagged protein in Escherichia coli BL21(DE3)
P74840
expression of His-tagged AcnD and PrpF in Escherichia coli BL21(DE3), functional complementation of an enzyme-deficient mutant of Salmonella enterica only by expression of both AcnD and PrpF
-
structural genetic organization of prp operon
-
EXPRESSION
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
2-methylcitrate dehydratase is induced 3.6fold by treatment with Ag+, no induction by Co2+
-
2-methylcitrate dehydratase is induced 3.6fold by treatment with Ag+, no induction by Co2+
-
-