Information on EC 4.1.3.30 - Methylisocitrate lyase

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

EC NUMBER
COMMENTARY hide
4.1.3.30
-
RECOMMENDED NAME
GeneOntology No.
Methylisocitrate lyase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = succinate + pyruvate
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
elimination
-
-
of an oxo-acid, C-C bond cleavage
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
2-methylcitrate cycle I
-
-
2-methylcitrate cycle II
-
-
Propanoate metabolism
-
-
propionate fermentation
-
-
SYSTEMATIC NAME
IUBMB Comments
(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate pyruvate-lyase (succinate-forming)
The enzyme acts on threo-Ds-2-methylisocitrate, but not on threo-Ds-isocitrate, threo-DL-isocitrate or erythro-Ls-isocitrate.
CAS REGISTRY NUMBER
COMMENTARY hide
57827-77-7
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
IFO 6662
-
-
Manually annotated by BRENDA team
strain IFO 0966
-
-
Manually annotated by BRENDA team
strain IFO 0966
-
-
Manually annotated by BRENDA team
strain IFO 0750, no activity in the strains NPA-1 and IFO 1364
-
-
Manually annotated by BRENDA team
strain IFO 0750, no activity in the strains NPA-1 and IFO 1364
-
-
Manually annotated by BRENDA team
strain Z03643
-
-
Manually annotated by BRENDA team
strain Z03643
-
-
Manually annotated by BRENDA team
Mucor rouxianus
strain IFO 5773
-
-
Manually annotated by BRENDA team
Mucor rouxianus IFO 5773
strain IFO 5773
-
-
Manually annotated by BRENDA team
strain mc2155
-
-
Manually annotated by BRENDA team
strain mc2155
-
-
Manually annotated by BRENDA team
strain IFO 6067
-
-
Manually annotated by BRENDA team
strain IFO 6067
-
-
Manually annotated by BRENDA team
strain IAM 6003
-
-
Manually annotated by BRENDA team
serovar typhimurium LT2
-
-
Manually annotated by BRENDA team
gene prpB
UniProt
Manually annotated by BRENDA team
gene mcl
-
-
Manually annotated by BRENDA team
Ustilago crus-galli
strain F-B-6
-
-
Manually annotated by BRENDA team
Ustilago crus-galli F-B-6
strain F-B-6
-
-
Manually annotated by BRENDA team
Ustilago utriculosa
strain F-B-5
-
-
Manually annotated by BRENDA team
Ustilago utriculosa F-B-5
strain F-B-5
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
the 2-methylcitrate cycle enzymes have been acquired via horizontal gene transfer, PrpB phylogenetic analysis, overview
malfunction
metabolism
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
(2S,3R)-3-Hydroxybutane-1,2,3-tricarboxylate
?
show the reaction diagram
(2S,3R)-3-Hydroxybutane-1,2,3-tricarboxylate
Pyruvate + succinate
show the reaction diagram
(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate
succinate + pyruvate
show the reaction diagram
2-methylisocitrate lactone
succinate + pyruvate
show the reaction diagram
methylisocitrate
succinate + pyruvate
show the reaction diagram
additional information
?
-
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
(2S,3R)-3-Hydroxybutane-1,2,3-tricarboxylate
?
show the reaction diagram
(2S,3R)-3-Hydroxybutane-1,2,3-tricarboxylate
Pyruvate + succinate
show the reaction diagram
-
one of the key enzymes of the methylcitrate cycle. Deletion mutants do not grow on propionate as sole carbon and energy source and are severely inhibited during growth on alternative carbon sources, when propionate is present. The strongest inhibitory effect is observed, when glycerol is the main carbon source, followed by glucose and acetate. In addition, asexual conidiation is strongly impaired in the presence of propionate
-
-
?
(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate
succinate + pyruvate
show the reaction diagram
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
NAD+
-
activates
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mn2+
-
48% of the activition with Mg2+
Pb2+
-
11% activation, when added instead of Mg2+. 10 mM, in presence of 2.5 mM Mg2+, 14% inhibition
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
3-Bromopyruvate
-
complete inactivation at equimolar concentrations
Ca2+
-
40% inactivation at 2 mM; inhibition at 2 mM
Cu2+
-
10 mM, in presence of 2.5 mM Mg2+, 10% inhibition
Hg2+
-
10 mM, in presence of 2.5 mM Mg2+, 30% inhibition
iodoacetate
-
-
isocitrate
-
-
Itaconic acid
-
itaconic acid specifically inhibits growth of wild-type cells on acetate and propionate, but not dextrose, in an ICL-dependent manner, and elicited metabolomic changes similar to those observed with ICL-deficient cells. Enzyme ICL inhibition by itaconic acid results in a specific decrease in intrabacterial pH from pH 7.3 to pH 6.4 in propionat-grown cells, not in acetate-grown cells
NADH
-
noncompetitive
NADPH
-
noncompetitive
p-chloromercuribenzoate
-
-
Pb2+
-
10 mM, in presence of 2.5 mM Mg2+, 14% inhibition. 11% activation, when added instead of Mg2+
sulfhydryl reagents
-
-
Zn2+
-
10 mM, in presence of 2.5 mM Mg2+, 34% inhibition
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
dithiothreitol
-
5 mM, required for optimal ativity
glutathione
-
required for optimal ativity
sulfhydryl compound
-
required for optimal activity, Km for Cys: 0.43 mM
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.024 - 57
(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate
0.0181 - 0.0806
methylisocitrate
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.1 - 105
(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate
38
Mg2+
Salmonella enterica
-
pH 7.5, 37°C
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
92.8 - 1850
methylisocitrate
8275
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
additional information
-
0.258 mM isocitrate required to double the KM-value with methylisocitrate (wild type protein), 0.0598 mM isocitrate required to double the KM-value with methylisocitrate (L521F mutant protein), 0.0606 mM isocitrate required to double the KM-value with methylisocitrate (S523T mutant protein), 0.0119 mM isocitrate required to double the KM-value with methylisocitrate (L521F/L521F mutant protein)
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.00055
-
substrate isocitrate, S523T mutant protein, pH not specified in the publication, temperature not specified in the publication
0.00105
-
substrate isocitrate, L521F mutant protein, pH not specified in the publication, temperature not specified in the publication
0.0033
-
substrate isocitrate, L521F/S523T mutant protein, pH not specified in the publication, temperature not specified in the publication
4.33
-
L521F/S523T mutant protein, pH not specified in the publication, temperature not specified in the publication
7.52
-
S523T mutant protein, pH not specified in the publication, temperature not specified in the publication
27.43
-
L521F mutant protein, pH not specified in the publication, temperature not specified in the publication
32.33
-
wild type protein, pH not specified in the publication, temperature not specified in the publication
additional information
-
activity not detectable for substrate isocitrate and wild type protein, pH not specified in the publication, temperature not specified in the publication
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.3 - 7.8
-
-
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 8.5
-
16% activity at pH 6, 96% activity at pH 8.5
6.5 - 8
-
pH 6.5: about 50% of maximal activity, pH 8: about 65% of maximal activity
6.5 - 8.5
-
pH 6.5: about 60% of maximal activity, pH 8.5: about 35% of maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
20 - 50
-
20°C: about 50% of maximal activity, 50°C: about 30% of maximal activity
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
exclusively, subcellular localization analysis
Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
UNIPROT
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
40000
x * 40000, about, recombinant N-terminally myc-tagged pro-PrpB, SDS-PAGE
66000
-
4 * 66000, SDS-PAGE
120000
-
gel filtration
130000
-
gel filtration
244000
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
x * 40000, about, recombinant N-terminally myc-tagged pro-PrpB, SDS-PAGE
tetramer
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
proteolytic modification
recombinant N-terminally myc-tagged PrpB is produced as a precursor of about 40 kDa
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
crystals of the inactive mutant C123S MICL in complex with isocitrate are obtained at room temperature by vapor diffusion in hanging drops. A crystal of C123S MICL in complex with pyruvate and succinate was obtained by overnight incubation of a C123S MICL/isocitrate complex crystal in a solution containing 35% PEG3350, 100 mM pyruvate and 100 mM succinate. This crystal also belongs to space group C2
-
sitting drop vapor diffusion method
-
native enzyme and bound with pyruvate/Mg2+, sitting and hanging drop vapor diffusion method
-
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5
-
15°C, 20 h, fairly stable
5346
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0
-
stable for several days
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
enzyme becomes inactivated when incubated with oxygen, partial reactivation with dithiothreitol possible
-
OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
enzyme becomes inactivated when incubated with oxygen, partial reactivation with dithiothreitol possible
-
651100
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
immobilized metal ion affinity chromatography (Ni2+)
-
recombinant
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
-
fusion protein with green fluorescent protein
-
gene mcl, phylogenetic analysis
-
gene prpB, phylogenetic analysis, C-terminally Ty-tagged version of TgPrpB is located in the cytosolic fraction whereas an N-terminally myc-tagged TgPrpB is partitioned in both the cytosol and organellar fractions, mycPrpB is produced as a precursor of about 40 kDa that corresponds to the predicted size of full-length PrpB and this form is detectable with anti-myc
His-tagged version expressed in Escherichia coli BL21(DE3)Rosetta2
-
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
gene expression of mcl is not influenced by carbon sources or antagonistic interactions
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
L521F
-
L521 contributes to substrate specificity
L521F/S523T
-
L521 and S523 contribute to substrate specificity
S523T
-
S523 contributes to substrate specificity
L521F
-
L521 contributes to substrate specificity
-
L521F/S523T
-
L521 and S523 contribute to substrate specificity
-
S523T
-
S523 contributes to substrate specificity
-
C123A
-
no enzyme activity
D58A
-
no enzyme activity
H125A
-
decreased kcat
K121A
-
decreased kcat
R122K
-
decreased kcat
additional information
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