Information on EC 4.2.1.9 - dihydroxy-acid dehydratase

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

EC NUMBER
COMMENTARY hide
4.2.1.9
-
RECOMMENDED NAME
GeneOntology No.
dihydroxy-acid dehydratase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
2,3-dihydroxy-3-methylbutanoate = 3-methyl-2-oxobutanoate + H2O
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
elimination
-
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Biosynthesis of antibiotics
-
-
Biosynthesis of secondary metabolites
-
-
isoleucine metabolism
-
-
L-isoleucine biosynthesis I (from threonine)
-
-
L-isoleucine biosynthesis II
-
-
L-isoleucine biosynthesis III
-
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L-isoleucine biosynthesis IV
-
-
L-valine biosynthesis
-
-
Metabolic pathways
-
-
Pantothenate and CoA biosynthesis
-
-
pyruvate fermentation to isobutanol (engineered)
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-
valine metabolism
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Valine, leucine and isoleucine biosynthesis
-
-
SYSTEMATIC NAME
IUBMB Comments
2,3-dihydroxy-3-methylbutanoate hydro-lyase (3-methyl-2-oxobutanoate-forming)
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CAS REGISTRY NUMBER
COMMENTARY hide
9024-32-2
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
-
-
Manually annotated by BRENDA team
strain 15150; wild type strain BD-413
-
-
Manually annotated by BRENDA team
strain 15150
-
-
Manually annotated by BRENDA team
Chromatium sp.
strain D
-
-
Manually annotated by BRENDA team
Chromatium sp. D
strain D
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
gene Rv0189c or ilvD
-
-
Manually annotated by BRENDA team
gene Rv0189c or ilvD
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-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
-
deletion Dilv3A strain requires supplementation with isoleucine and valine for growth; mutants lacking AfIlv3A and ilv3B exhibit reduced levels of virulence in murine infection models
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
(+)-2,3-dihydroxy-3-ethylpentanoate
?
show the reaction diagram
-
20% of the activity with 2,3-dihydroxyisovalerate
-
-
?
2,3-dihydroxy-3-methylbutanoate
2-methyl-2-oxobutanoate + H2O
show the reaction diagram
2,3-dihydroxy-3-methylbutanoate
2-oxoisovalerate + H2O
show the reaction diagram
2,3-dihydroxy-3-methylbutanoate
3-methyl-2-oxobutanoate + H2O
show the reaction diagram
2,3-dihydroxy-3-methylpentanoate
3-methyl-2-oxopentanoate + H2O
show the reaction diagram
2,3-dihydroxy-3-methylpentanoate
?
show the reaction diagram
2,3-dihydroxy-3-methylvalerate
3-methyl-2-oxovalerate
show the reaction diagram
-
-
-
-
?
2,3-dihydroxy-isovalerate
2-oxoisovalerate
show the reaction diagram
-
-
-
-
?
2,3-dihydroxybutanoate
?
show the reaction diagram
-
-
-
-
-
2,3-dihydroxyisovalerate
2-oxovalerate + H2O
show the reaction diagram
-
IlvD, an iron-sulfur enzyme, catalyses the conversion from 2,3-dihydroxyisovalerate to 2-keto-isovalerate and is essential for the branchend-chain amino acid biosynthesis
-
-
?
2,3-dihydroxyisovalerate
?
show the reaction diagram
3-cyclopropyl-2,3-dihydroxybutanoate
?
show the reaction diagram
-
-
-
-
-
D,L-2,3-dihydroxy-isovalerate
?
show the reaction diagram
-
-
-
-
?
D-arabonate
?
show the reaction diagram
-
-
-
-
?
D-erythronate
?
show the reaction diagram
-
-
-
-
?
D-fuconate
?
show the reaction diagram
-
-
-
-
?
D-Galacturonate
?
show the reaction diagram
-
-
-
-
?
D-gluconate
2-dehydro-3-deoxy-D-gluconate + H2O
show the reaction diagram
D-gluconate
2-keto-3-deoxygluconate + H2O
show the reaction diagram
-
-
-
-
?
D-Glucuronate
?
show the reaction diagram
-
-
-
-
?
D-glycerate
pyruvate + H2O
show the reaction diagram
D-xylonate
?
show the reaction diagram
-
-
-
-
?
DL-2,3-dihydroxyisovalerate
2-oxo-isovalerate + H2O
show the reaction diagram
-
-
-
-
?
DL-2,3-dihydroxyisovalerate
?
show the reaction diagram
L-threonate
?
show the reaction diagram
threo-2,3-dihydroxybutanoate
?
show the reaction diagram
-
at 45% of the activity with 2,3-dihydroxyisovalerate
-
-
?
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
2,3-dihydroxy-3-methylbutanoate
3-methyl-2-oxobutanoate + H2O
show the reaction diagram
2,3-dihydroxy-3-methylpentanoate
?
show the reaction diagram
2,3-dihydroxy-3-methylvalerate
3-methyl-2-oxovalerate
show the reaction diagram
-
-
-
-
?
2,3-dihydroxy-isovalerate
2-oxoisovalerate
show the reaction diagram
-
-
-
-
?
2,3-dihydroxyisovalerate
2-oxovalerate + H2O
show the reaction diagram
-
IlvD, an iron-sulfur enzyme, catalyses the conversion from 2,3-dihydroxyisovalerate to 2-keto-isovalerate and is essential for the branchend-chain amino acid biosynthesis
-
-
?
2,3-dihydroxyisovalerate
?
show the reaction diagram
DL-2,3-dihydroxyisovalerate
2-oxo-isovalerate + H2O
show the reaction diagram
-
-
-
-
?
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ni2+
-
divalent cation required. Mg2+, Mn2+, Ni2+, Co2+, and Fe2+ are nearly equally effective
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(NH4)2Fe(SO4)2
10 mM, 50C, 45% loss of activity, dehydration of D-gluconate
-
2,4,5,6-tetrahydroxyhexanoate
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-
2,4,5-trihydroxypentanoate
-
-
2,4-dihydroxybutanoate
-
-
2-hydroxy-3-methylbutyric acid
-
-
-
2-mercaptoethanol
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1 mM, 40% inhibition
3-(5-nitrofuran-2-yl)-5,6-dihydroimidazo[2,1-b][1,3]thiazole hydrochloride
-
-
4,7-dicyanobenzofurazan
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bacteriostatic effect due to inactivation of 2,3-dihydroxyisovalerate dehydratase
BaCl2
100 mM, 50C, 43% loss of activity, dehydration of D-gluconate
benzoquinone
-
-
CaCl2
10 mM, 50C, 77% loss of activity, dehydration of D-gluconate
CuSO4
10 mM, 50C, 86% loss of activity, dehydration of D-gluconate
D-glycerate
competitive. Presence of 20 mM D-glycerate decreases catalytic activity towards D-gluconate drastically to 5% residual activity
duroquinone
-
-
hydralazine
-
-
imidazole
leads to a complete elimination of enzyme activity towards D-gluconate
juglone
-
-
nitric oxide
-
nitric oxide halts bacterial growth via inhibition of the branched-chain amino acid biosynthesis enzyme dihydroxyacid dehydratase
Nitrofurantoin
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-
p-chloromercuribenzoic acid
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-
p-hydroxymercuribenzoic acid
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-
paraquat
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-
Plumbagin
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-
ZnCl2
10 mM, 50C, 95% loss of activity, dehydration of D-gluconate
additional information
-
formation of the IlvD-bound DNIC, dinitrosyl-iron complex, and inactivation of the enzyme activity under anaerobic conditions, reaction kinetics of NO and enzyme using diethylamine NONOate as NO donor. GSH fails to prevent the NO-mediated modification of the IlvD [4Fe-4S] cluster regardless of the presence of O2 in the medium, overview
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2-mercaptoethanol
increases activity up to 3fold. Activation modulates thermotolerance at 50C
additional information
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.97 - 2.1
2,3-Dihydroxy-3-methylbutanoate
2.16 - 8.5
2,3-dihydroxy-3-methylpentanoate
0.55
2,3-dihydroxybutanoate
-
-
0.54 - 2.8
2,3-dihydroxyisovalerate
0.33
2R,3R-2,3-dihydroxy-3-methylpentanoate
-
-
0.71
2R,3S-2,3-dihydroxy-3-methylpentanoate
-
-
1.78
3-cyclopropyl-2,3-dihydroxybutanoate
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-
1.75
D-erythronate
-
-
-
2.42 - 7.8
D-gluconate
3.7
DL-2,3-dihydroxyisovalerate
-
pH 8.0, temperature not specified in the publication
0.65 - 10.1
L-threonate
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.31 - 11.5
2,3-Dihydroxy-3-methylbutanoate
4.6
2,3-dihydroxybutanoate
Spinacia oleracea
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-
25 - 75.8
2,3-dihydroxyisovalerate
8.3
2R,3R-2,3-dihydroxy-3-methylpentanoate
Spinacia oleracea
-
-
12.3
2R,3S-2,3-dihydroxy-3-methylpentanoate
Spinacia oleracea
-
-
5.7
3-cyclopropyl-2,3-dihydroxybutanoate
Spinacia oleracea
-
-
0.4 - 48.5
D-gluconate
0.011 - 0.03
D-glycerate
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2.3
D-glycerate
50C, pH 7
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
8
2-hydroxy-3-methylbutyric acid
Aspergillus fumigatus
-
pH 8, 22C
-
additional information
butanol
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.024
-
purified native enzyme, pH 8.0, temperature not specified in the publication
10.7
pH 7, 50C, conversion of D-glycerate to pyruvate
18
-
pH 8, 22C
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.2
dehydration of D-gluconate
7.7 - 8
-
2,3-dihydroxy-3-methylpentanoate
8 - 8.3
-
2,3-dihydroxyisovalerate
8 - 8.2
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2,3-dihydroxy-3-methylpentanoate, 2,3-dihydroxyisovalerate
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.2 - 8.2
pH 5.2: about 40% of maximal activity, pH 8.2: about 40% of maximal activity, dehydration of D-gluconate
7 - 9
-
pH 7.0: about 40% of maximal activity, pH 9.0: about 25% of maximal activity, 2,3-dihydroxyisovalerate
7.4 - 9
-
pH 7.4: about 40% of maximal activity, pH 9.0: about 70% of maximal activity, 2,3-dihydroxy-3-methylpentanoate
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
37
-
assay at
77
dehydration of D-gluconate
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 9
-
pH 6.0: about 30% of maximal activity, pH 9.0: about 35% of maximal activity
60 - 90
-
60C: about 60% of maximal activity, 90C: about 60% of maximal activity
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
additional information
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
12000
-
gel filtration
65000
-
SDS-PAGE, recombinant enzyme
105000
-
gel filtration
110000
-
native PAGE
125000
-
native PAGE
155000
-
gel filtration, recombinant thioredoxin-His-tagged IlvD
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homodimer
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
40
-
20 min, stable
45
-
20 min, about 5% loss of activity
46.5
-
20 min, 50% loss of activity, mutant strain 332
55
-
20 min, about 55% loss of activity
56
-
20 min, 50% loss of activity, wild type
60
-
20 min, complete loss of activity
70
-
2 h, stable
80
-
30 min, 50% loss of activity
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
enzyme in crude extract is labile to heat and acid
-
OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
5% O2, at 25C, half-life: less than 6 min, under anaerobic conditions the enzyme is stable for more than 8 days
-
33983
exposure of E. coli cells to 4.2 atm O2 causes complete loss of activity
-
33973
hyperbaric oxygen results in rapid inactivation
-
33971, 33975
inactivation by exposure to hyperbaric O2 is due to the destruction of its catalytically active 4Fe-4S cluster. Reactivation occurs by reconstitution of the enzyme's Fe-S cluster
-
33977
oxidative degradation appears to lead to a complete breakdown of the Fe-S cluster, and the resulting protein cannot by reactivated with Fe2+ and thiol reducing agents
-
33976
when the recombinant enzyme is incubated in 50 mM Tris-HCl buffer at 30C for 2 h under aerobic or anaerobic conditions and the residual activity is measured, no difference is found between aerobic and anaerobic conditions
-
680539
when the recombinant enzyme is incubated in 50 mM Tris-HCl buffer at 30C for 2 h with organic peroxide, the enzyme activity is stable during exposure to 0.5% organic peroxide for 2 h
-
680539
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20C, about 85% loss of activity after 4 weeks, crude extract is unstable upon storage
-
-80C, after purification of His-tagged enzyme the total enzyme activity is decreased to 43% of the crude extract and even further to 17% when stored at -80 C for one day
-80C, specific activity for D-gluconate of the frozen/thawed enzyme is stable for 60 min, but loses about 70% after a maximum of 100 min
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
recombinant thioredoxin-His-tagged IlvD from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
-
expression in Escherichia coli BL21 (DE3)
gene ilvD, co-expression with other enzymes of the branched amino acid biosynthesis pathway in Bacillus subtilis strain 168 for production of isobutanol via the Ehrlich pathway, overview. Bacillus subtilis is engineered as the cell factory for isobutanol production due to its high tolerance to isobutanol. Subcloning in Escherichia coli strain JM109
-
gene ilvD, co-overexpression with genes ilvBCEGHN in Escherichia coli strain W for engineering of L-valine production in fed-batch fermentation, engineering method development and evaluation, overview
-
gene ilvD, expression in Escherichia coli DH5alpha, overexpression
-
gene Rv0189c or ilvD, overexpression of thioredoxin-His-tagged IlvD in Escherichia coli strain OrigamiBL21(DE3). Transcript levels of Rv0189c in sense and antisense transformants of Mycobacterium tuberculosis, phenotype, overview
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recombinant expression in Escherichia coli as a His-tagged fusion protein
-
recombinant expression of IlvD [4Fe-4S] cluster from Escherichia coli
-
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
upregulation of Rv0189c occurs during the early exponential phase of growth, under acid stress and ex vivo. Rv0189c expression is upregulated by 1.72fold at pH 4.5 and 1.42fold at pH 5.5, compared to that at pH 7.2, relative gene expression profiles of Rv0189c starved in PBS, overview
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
analysis
-
the enzyme is used to quantify and investigate the biological oxidant stress activity of various redox-cycling chemicals. High sensitivity to inactivation by oxidants makes the enzyme useful for identification of compounds which increase oxyradical flux in the cell and for probing their mechanism of action
drug development
synthesis
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