Information on EC 1.1.1.87 - homoisocitrate dehydrogenase

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

EC NUMBER
COMMENTARY hide
1.1.1.87
-
RECOMMENDED NAME
GeneOntology No.
homoisocitrate dehydrogenase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate + NAD+ = 2-oxoadipate + CO2 + NADH + H+
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
oxidation
-
-
-
-
oxidative decarboxylation
-
-
-
-
reduction
-
-
-
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reductive carboxylation
-
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
lysine metabolism
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Lysine biosynthesis
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Metabolic pathways
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Microbial metabolism in diverse environments
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Biosynthesis of antibiotics
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L-lysine biosynthesis V
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coenzyme B biosynthesis
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L-lysine biosynthesis IV
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SYSTEMATIC NAME
IUBMB Comments
(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate:NAD+ oxidoreductase (decarboxylating)
Forms part of the lysine biosynthesis pathway in fungi [3].
CAS REGISTRY NUMBER
COMMENTARY hide
37250-23-0
-
9067-90-7
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
gene LYS12
-
-
Manually annotated by BRENDA team
isoform Rdh10
-
-
Manually annotated by BRENDA team
gene PH1722 or hdh
SwissProt
Manually annotated by BRENDA team
Saccharomycopsis lipolytica
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-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
the enzyme is a member of the family of pyridine dinucleotide-dependent beta-hydroxyacid oxidative decarboxylating dehydrogenases, specifically the family that has (R)-beta-hydroxyacid substrates, including isocitrate dehydrogenase (ICDH) among others. Superposition of available structures of the malic enzyme, isopropylmalate dehydrogenase, IcDH, and HIcDH show a similar overall geometry of residues in the substrate and metal ion binding sites. A Lys (general base)-Tyr (general acid) pair is conserved among these enzymes. The similar structural geometry in the active site suggests a similar general chemical mechanism. Three aspartate residues are conserved in the active sites of all HIcDHs sequenced to data, and are also conserved across the family of pyridine nucleotide-dependent oxidative decarboxylases including malic enzyme
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,2S)-1-hydroxybutane-1,2,4-tricarboxylate + NAD+
2-oxoadipate + CO2 + NADH + H+
show the reaction diagram
(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate + NAD+
2-oxoadipate + NADH + H+ + CO2
show the reaction diagram
(2R,3S)-3-(2-hydroxyethyl)malate + NAD+
?
show the reaction diagram
(2R,3S)-3-(3-aminopropyl)malate + NAD+
?
show the reaction diagram
(2R,3S)-3-(3-hydroxypropyl)malate + NAD+
?
show the reaction diagram
(2R,3S)-3-(4-hydroxybutyl)malate + NAD+
?
show the reaction diagram
(2R,3S)-3-(4-pentenyl)malic acid + NAD+
?
show the reaction diagram
(2R,3S)-3-allylmalic acid + NAD+
?
show the reaction diagram
(2R,3S)-3-propylmalic acid + NAD+
?
show the reaction diagram
1-hydroxy-1,2,3-propanetricarboxylate + NAD+
?
show the reaction diagram
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more effective substrate than 1-hydroxy-1,2,4-butanetricarboxylate
-
-
?
1-hydroxy-1,2,4-butanetricarboxylate + NAD+
2-oxoadipate + CO2 + NADH
show the reaction diagram
2(R),3(S)-homoisocitrate + NAD+
alpha-ketoadipate + NADH + CO2 + H+
show the reaction diagram
-
with homoisocitrate as the substrate, no primary deuterium isotope effect is observed, and a small 13C kinetic isotope effect indicates that the decarboxylation step contributes only slightly to rate limitation
-
-
?
3-carboxy-2-hydroxyadipate + NAD+
2-oxoadipate + CO2 + NADH
show the reaction diagram
3-isopropylmalate + NAD+
?
show the reaction diagram
3-vinylmalate + NAD+
?
show the reaction diagram
ethylmalate + NAD+
?
show the reaction diagram
homoisocitrate + NAD+
2-oxoadipate + CO2 + NADH + H+
show the reaction diagram
-
-
-
r
homoisocitrate + NAD+
?
show the reaction diagram
homoisocitrate + NAD+
alpha-ketoadipate + NADH + CO2
show the reaction diagram
-
-
-
-
r
homoisocitrate + NAD+
alpha-ketoadipate + NADH + CO2 + H+
show the reaction diagram
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-
-
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r
isocitrate + NAD+
?
show the reaction diagram
isocitrate + NAD+
? + NADH + H+
show the reaction diagram
-
low activity
-
-
?
isopropylmalate + NAD+
?
show the reaction diagram
-
-
-
-
?
threo-D-isocitric acid + NAD+
?
show the reaction diagram
-
with isocitrate as the substrate, primary deuterium and 13C isotope effects indicate that hydride transfer and decarboxylation steps contribute to rate limitation, and that the decarboxylation step is the more rate-limiting of the two. The multiple-substrate deuterium/13C isotope effects suggest a stepwise mechanism with hydride transfer preceding decarboxylation
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-
?
trisodium (2S,3R)-2-(carboxylatomethoxy)-3-hydroxybutanedioate + NAD+
? + NADH + CO2
show the reaction diagram
-
-
-
-
?
trisodium (2S,3R)-2-[(carboxylatomethyl)amino]-3-hydroxybutanedioate + NAD+
? + NADH + CO2
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
(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate + NAD+
2-oxoadipate + CO2 + NADH + H+
show the reaction diagram
(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate + NAD+
2-oxoadipate + NADH + H+ + CO2
show the reaction diagram
-
-
-
-
?
1-hydroxy-1,2,4-butanetricarboxylate + NAD+
2-oxoadipate + CO2 + NADH
show the reaction diagram
3-carboxy-2-hydroxyadipate + NAD+
2-oxoadipate + CO2 + NADH
show the reaction diagram
-
intermediate in lysine biosynthesis
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-
?
3-isopropylmalate + NAD+
?
show the reaction diagram
A4CYJ9
-
-
-
?
homoisocitrate + NAD+
2-oxoadipate + CO2 + NADH + H+
show the reaction diagram
P40495
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-
-
r
homoisocitrate + NAD+
?
show the reaction diagram
A4CYJ9
-
-
-
?
isocitrate + NAD+
?
show the reaction diagram
A4CYJ9
-
-
-
?
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
NADP+
-
NADP+ can replace NAD+
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
NH4+
-
activates
additional information
-
selectivity of the activator site for monovalent ions, K+ is the best activator, and NH4+ and Rb+ are also activators of the reaction, while Cs+, Li+, and Na+ are not, overview. Substitution of potassium acetate for KCl changes the kinetic mechanism of HIcDH from a steady state random to a fully ordered mechanism with the binding of Mg-HIc followed by K+ and NAD+
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(2R,3S)-3-(p-carboxybenzyl)malate
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(2S)-thiahomocitrate
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(2S,3S)-(-)-3-methylmercaptomalic acid
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(2S,3S)-thiahomoisocitrate
interacts through hydrogen bonding to Arg 118, Tyr 125 and Lys 171 in the active site, enzyme binding structure, overview
(R,E)-(3-carboxypropylidene)malic acid
(R,E)-(3-hydroxypropylidene)malic acid
(R,Z)-(3-carboxypropylidene)malic acid
(R,Z)-(3-hydroxypropylidene)malic acid
2-oxoadipate
Saccharomycopsis lipolytica
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3-acetylpyridine adenine dinucleotide 3'-phosphate
3-AcPyrADP, competitive versus NAD+
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3-carboxypropylidenemalate
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3-vinylmalate
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3-[(carboxymethyl)sulfanyl]-2-oxopropanoic acid
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acetate
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slight inhibition
homoisocitrate
Mg-homoisocitrate
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NAD+
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substrate inhibition at high concentrations and in absence of K+, kinetics, overview
Oxaloglutarate
Saccharomycopsis lipolytica
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thiahomoisocitrate
competitive versus homoisocitrate
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trisodium (2S,3R)-2-(carboxylatomethoxy)-3-hydroxybutanedioate
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trisodium (2S,3R)-2-[(carboxylatomethyl)amino]-3-hydroxybutanedioate
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trisodium (2S,3S)-2-[(carboxylatomethyl)sulfanyl]-3-hydroxybutanedioate
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-
additional information
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2-oxoadipate
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required for reductive carboxylation
NaHCO3-CO2
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required for reductive carboxylation
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.074 - 7.5
(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate
0.59 - 2.1
(2R,3S)-3-(2-hydroxyethyl)malate
0.51 - 0.58
(2R,3S)-3-(3-hydroxypropyl)malate
0.44 - 0.47
(2R,3S)-3-(4-hydroxybutyl)malate
2.7 - 9.4
(2R,3S)-3-(4-pentenyl)malic acid
0.41 - 2.8
(2R,3S)-3-allylmalic acid
0.29 - 0.78
(2R,3S)-3-propylmalic acid
0.4
1-hydroxy-1,2,3-propanetricarboxylate
-
purified enzyme, pH 8.0, 60C
7.5
1-hydroxy-1,2,4-butanetricarboxylate
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purified enzyme, pH 8.0, 60C
1.4
3-carboxy-2-hydroxyadipate
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-
1.33
3-isopropylmalate
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pH 7.8, 25C, recombinant wild-type enzyme
0.083 - 3.4
3-vinylmalate
1.5
alpha-ketoadipate
-
-
16.3
CO2
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reductive carboxylation of alpha-ketoadipate
0.6 - 1
ethylmalate
0.01 - 1.5
homoisocitrate
1.4
homoisocitric acid
-
-
0.0164 - 0.521
isocitrate
1.33
isopropylmalate
-
pH 7.8, 28C, recombinant enzyme
0.0042 - 3.2
Mg-homoisocitrate
0.042 - 9
NAD+
0.065 - 0.09
NADH
0.02
trisodium (2S,3R)-2-(carboxylatomethoxy)-3-hydroxybutanedioate
-
-
0.15
trisodium (2S,3R)-2-[(carboxylatomethyl)amino]-3-hydroxybutanedioate
-
-
additional information
additional information
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.38 - 0.4
(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate
0.78 - 25
(2R,3S)-3-(2-hydroxyethyl)malate
4.8 - 29
(2R,3S)-3-(3-hydroxypropyl)malate
2 - 8
(2R,3S)-3-(4-hydroxybutyl)malate
0.14 - 3
(2R,3S)-3-(4-pentenyl)malic acid
0.34 - 37
(2R,3S)-3-allylmalic acid
0.7 - 53
(2R,3S)-3-propylmalic acid
171
1-hydroxy-1,2,3-propanetricarboxylate
-
purified enzyme, pH 8.0, 60C
171
1-hydroxy-1,2,4-butanetricarboxylate
-
purified enzyme, pH 8.0, 60C
0.371
3-isopropylmalate
-
pH 7.8, 25C, recombinant wild-type enzyme
0.5 - 0.77
3-vinylmalate
0.61 - 43
ethylmalate
5.46 - 46.2
homoisocitrate
10.9 - 438
isocitrate
0.37
isopropylmalate
-
pH 7.8, 28C, recombinant enzyme
0.38 - 0.4
NAD+
0.59
trisodium (2S,3R)-2-(carboxylatomethoxy)-3-hydroxybutanedioate
-
-
2
trisodium (2S,3R)-2-[(carboxylatomethyl)amino]-3-hydroxybutanedioate
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
5.16 - 8.75
(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate
0.35 - 0.44
NAD+
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.013
(2S,3S)-thiahomoisocitrate
pH 7.8, 60C
0.79 - 3.1
(R,E)-(3-carboxypropylidene)malic acid
1.4 - 5.2
(R,E)-(3-hydroxypropylidene)malic acid
0.072 - 0.26
(R,Z)-(3-carboxypropylidene)malic acid
0.51 - 15.3
(R,Z)-(3-hydroxypropylidene)malic acid
0.088
3-vinylmalate
-
pH 7.8, 28C, recombinant enzyme
12
3-[(carboxymethyl)sulfanyl]-2-oxopropanoic acid
-
-
0.002
Mg-homoisocitrate
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oxidate decarboxylation of homoisocitrate
77
NAD+
-
pH 8.0, 25C, in absence of KOAc
0.01
trisodium (2S,3R)-2-(carboxylatomethoxy)-3-hydroxybutanedioate
-
-
0.000097
trisodium (2S,3S)-2-[(carboxylatomethyl)sulfanyl]-3-hydroxybutanedioate
-
-
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2.97 - 3.78
(2R,3S)-3-(p-carboxybenzyl)malate
0.000097
(2S)-thiahomocitrate
Candida albicans
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recombinant His-tagged enzyme, pH 7.8, 20C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.304
Saccharomycopsis lipolytica
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-
564
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purified enzyme, pH 8.0, 60C, with 1-hydroxy-1,2,4-butanetricarboxylate as substrate
8579
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purified enzyme, pH 8.0, 60C, with 1-hydroxy-1,2,3-propanetricarboxylate as substrate
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.5 - 9.5
pH independence of the catalytic reaction over the range of pH 5.5-9.5
7
-
reductive carboxylation
8.3 - 8.8
-
oxidative decarboxylation
additional information
-
mutant enzymes kinetics and pH-dependencies, overview
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.5 - 9.5
pH independence of the catalytic reaction over the range of pH 5.5-9.5, pH profiles
6.1 - 7.7
-
pH 6.1: about 60% of activity maximum, pH 7.7: about 50% of activity maximum, reductive carboxylation
6.5 - 8.5
-
activity drops sharply below pH 6.5 and above pH 8.5
7.4 - 9.3
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pH 7.4: about 50% of activity maximum, pH 9.3: about 90% of activity maximum, oxidative decarboxylation
additional information
-
pH-rate profile in the absence of K+, overview
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7
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reductive carboxylation
7.5
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oxidative decarboxylation
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
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mRNA level of isoform Rdh10 declines during development, with strong and lasting expression in the meninges and choroid plexuses. Expression is also present in the striatum
Manually annotated by BRENDA team
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mRNA level of isoform Rdh10 declines during development, with strong and lasting expression in the meninges and choroid plexuses. Expression is also present in the striatum
Manually annotated by BRENDA team
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mRNA level of isoform Rdh10 declines during development, with strong and lasting expression in the meninges and choroid plexuses. Expression is also present in the striatum
Manually annotated by BRENDA team
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inner ear, specific expression of isoform Rdh10 in the endolymphatic system and stria vascularis
Manually annotated by BRENDA team
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mRNA expression of isoform Rdh10 both in the prospective pigmented epithelium and neural retina
Manually annotated by BRENDA team
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mRNA level of isoform Rdh10 declines during development, with strong and lasting expression in the meninges and choroid plexuses. Expression is also present in the striatum
Manually annotated by BRENDA team
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and vibrissae follicles, expression of isoform Rdh10 from early stages in regions where sensory receptors appear and mesenchymal/epithelial interactions take place
Manually annotated by BRENDA team
-
mRNA expression of isoform Rdh10 both in the prospective pigmented epithelium and neural retina
Manually annotated by BRENDA team
-
mRNA expression of isoform Rdh10 both in the prospective pigmented epithelium and neural retina
Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
UNIPROT
Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
40000
-
4 * 40000, recombinant enzyme, SDS-PAGE
41491
-
4 * 42600, SDS-PAGE, x * 41491, sequence calculation
42600
-
4 * 42600, SDS-PAGE, x * 41491, sequence calculation
154000
-
recombinant enzyme, gel filtration
158000
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
Saccharomycopsis lipolytica
-
2 * 48000, at high protein concentration or in presence of substrate the enzyme exists as dimer
monomer
Saccharomycopsis lipolytica
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1 * 48000, native or denaturing PAGE
tetramer
additional information
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
enzyme in binary complex with inhibitor (2S,3S)-thiahomoisocitrate, sitting drop vapour diffusion method, 0.00 ml of 8.7 mg/ml protein in 5 mM Tris-HCl, pH 7.8. 0.8 mM inhibitor, and 1.7 mM NAD, is mixed with 0.002 ml of reservoir solution containing 40% 2-methyl-2,4-pentandiol and 100 mM citrate pH 4.85, eqilibration against 1 ml resetvoir solution, X-ray diffrcation structure determination and analysis at 2.6 A resolution, molecular replacement
purified recombinant enzyme, hanging drop vapour diffusion method, 10 mg/ml protein with reservoir solution containing 24% PEG 400, and 0.1 M citrate, pH 4.8, addition of 0.003 ml drops of 0.1 M MgCl2, 5 mM isocitrate or homoisocitrate, and of a 0.001 ml drop 50 mM CdCl2, equilibration against 0.5 ml reservoir solution, 5 days at 20C, X-ray diffraction structure determination and analysis at 1.85 A resolution, molecular replacement
-
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
-
enzyme is stable when incubated for at least 15 min over the pH range of 5.0-10.0
685232
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
90
-
half life: 16.7 h
93.6
-
melting point
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
Mg2+ stabilizes
Saccharomycopsis lipolytica
-
Mn2+ stabilizes
Saccharomycopsis lipolytica
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20C, ammonium sulfate precipitate, partially purified, stable
-
-20C, stable as ammonium sulfate precipitate
Saccharomycopsis lipolytica
-
0C, pH 7.2, rapid loss of activity
Saccharomycopsis lipolytica
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0C, potassium phosphate 20 mM, pH 7.2, 4-5 hours
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
recombinant enzyme from Escherichia coli by anion exchange chromatography and gel filtration
-
recombinant enzyme from Escherichia coli strain OM17 by anion exchange and hydrophobic interaction chromatography, followed by another step of anion exchange chromatography
-
recombinant His-tagged enzyme from Escherichia coli strain TOP 10F by nickel affinity chromatography'
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recombinant His-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by nickel affinity chrmatography
recombinnat His-tagged enzyme from Escherichia coli by metal affinity chromatography
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
DNA and amino acid sequence determination and analysis, expression of His-tagged enzyme in Escherichia coli
DNA and amino acid sequence determination and analysis, overexpression in Escherichia coli strain OM17
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expressed in Escherichia coli BL21(DE3)
-
expression in Escherichia coli
-
expression of His-tagged enzyme in Escherichia coli strain TOP 10F'
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LYS1 gene codes for the alpha-aminoadipate pathway enzymes in fungi, can complement LYS1-deficient mutants of Candida albicans and Saccharomyces cerevisiae, amplification in Escherichia coli
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recombinant expression of His-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
A80del
-
site-directed mutagenesis, the mutant shows altered substrate specificity preferring isocitrate to homoisocitrate, it is unable to oxidize 3-isopropylmalate, the specificity is similar to the enzyme from Thermus thermophilus
R87T
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site-directed mutagenesis, the mutant oxidizes homoisocitrate, but not isocitrate and 3-isopropylmalate
R87V
-
site-directed mutagenesis, the mutant oxidizes homoisocitrate, but not isocitrate and 3-isopropylmalate
D271N
site-directed mutagenesis, mutation of a metal ion ligand and binding determinant for Mg2+, to N. The mutant enzyme shows a decrease of 520fold in V and V/Km_Mg2+, suggesting that the same step(s) limit the reaction at limiting and saturating MgHIc concentrations
R85V
-
complete loss of activity with isocitrate, significant activity with 3-isopropylmalate, no effect on activity with homoisocitrate
V135M
-
site-directed mutagenesis, tetramer-to-dimer structural transition enhances the activity with isocitrate 1.6fold
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
medicine
Show AA Sequence (165 entries)
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