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Information on EC 5.3.3.2 - isopentenyl-diphosphate DELTA-isomerase
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5.3.3.2 isopentenyl-diphosphate DELTA-isomeraseIUBMB Comments
The enzyme from Streptomyces sp. strain CL190 requires FMN and NAD(P)H as cofactors. Activity is reduced if FMN is replaced by FAD, but the enzyme becomes inactive when NAD(P)H is replaced by NAD+ or NADP+. That enzyme also requires Mg2+, Mn2+ or Ca2+ for activity.
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Word Map
- 5.3.3.2
-
isoprenoids
- mevalonate
-
farnesyl
-
geranylgeranyl
-
geranyl
- isomerases
- isoprene
- prenyltransferase
- phosphomevalonate
- haematococcus
- synthesis
- 1-deoxy-d-xylulose-5-phosphate
- methylerythritol
- biotechnology
- industry
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Synonyms
fcd1, FNI, IDI, IDI-1, Idi-2, IDI1, IDP isomerase, IPI, IPI1, IPP isomerase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
IDI
Idi-2
IDI1
IPI
IPP isomerase
IPP-isomerase
-
-
-
-
IPPI
IPPI1
IPPI2
-
-
-
-
IPPISOM
Isomerase, isopentenylpyrophosphate DELTA-
-
-
-
-
Isopententenyl diphosphate:dimethylallyl diphosphate isomerase
-
-
-
-
isopentenyl diphosphate isomerase
isopentenyl diphosphate:dimethylallyl diphosphate isomerase
Isopentenyl pyrophosphate isomerase
-
-
-
-
Isopentenyl pyrophosphate isomerase:dimethylallyl pyrophosphate isomerase
-
-
-
-
isopentenyl-diphosphate delta-isomerase 1
Isopentenyldiphosphate DELTA-isomerase
-
-
-
-
Isopentenylpyrophosphate isomerase
-
-
-
-
Methylbutenylpyrophosphate isomerase
-
-
-
-
type 2 isopentenyl diphosphate isomerase
type 2 isopentenyl diphosphate: dimethylallyl diphosphate isomerase
type 2 isopentenyl diphosphate:dimethylallyl diphosphate isomerase
-
-
type II isopentenyl diphosphate:dimethylallyl diphosphate isomerase
-
-
IPP isomerase
-
-
-
-
IPPI1
-
-
-
-
type 2 isopentenyl diphosphate: dimethylallyl diphosphate isomerase
-
type 2 isopentenyl diphosphate: dimethylallyl diphosphate isomerase
-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
Isopentenyl diphosphate = dimethylallyl diphosphate
-
-
-
-
Isopentenyl diphosphate = dimethylallyl diphosphate
catalytic mechanism in which a cysteine initiates the reaction by protonating the carbon-carbon double bond, with the antarafacial rearrangement ultimately achieved by one of the glutamates involved in the metal coordination sphere
-
Isopentenyl diphosphate = dimethylallyl diphosphate
reaction involves protonation and deprotonation of the isoprenoid unit and proceeds through a carbocationic transition state. Glu116/Tyr104 and Cys67 are involved in the antarafacial addition/elimination of protons during isomerization
-
Isopentenyl diphosphate = dimethylallyl diphosphate
the mechanism of isomerizaion reaction involves protonation of the unactivated carbon-carbon double bond in the substrate, Glu116 is involved in the protonation step and Cys67 is involved in the elimination step
-
Isopentenyl diphosphate = dimethylallyl diphosphate
interconversion of substrate is catalyzed by a stereoselective antarafacial [1.3] transposition of a proton involving residues C87, E149, W197 and Y137
Isopentenyl diphosphate = dimethylallyl diphosphate
in the rate determining step, the C2-H bond of isopentenyl diphosphate is cleaved. General acid/base catalysis may be involved during turnover
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
intramolecular oxidoreduction
-
-
-
-
isomerization
isomerization
-
-
-
-
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PATHWAY SOURCE
PATHWAYS
BRENDA
KEGG
MetaCyc
all-trans-farnesol biosynthesis, bisabolene biosynthesis (engineered), isoprene biosynthesis II (engineered), methylerythritol phosphate pathway I, methylerythritol phosphate pathway II, mevalonate pathway I, mevalonate pathway II (archaea), mevalonate pathway III (archaea), mono-trans, poly-cis decaprenyl phosphate biosynthesis, trans, trans-farnesyl diphosphate biosynthesis
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SYSTEMATIC NAME
IUBMB Comments
isopentenyl-diphosphate DELTA3-DELTA2-isomerase
The enzyme from Streptomyces sp. strain CL190 requires FMN and NAD(P)H as cofactors. Activity is reduced if FMN is replaced by FAD, but the enzyme becomes inactive when NAD(P)H is replaced by NAD+ or NADP+. That enzyme also requires Mg2+, Mn2+ or Ca2+ for activity.
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CAS REGISTRY NUMBER
COMMENTARY
9033-27-6
-
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
(Z)-3-(difluoromethyl)-2-buten-1-yl diphosphate
?
-
about 2% of the activity with isopenteyl diphosphate
-
-
-
(Z)-3-(fluoromethyl)-2-buten-1-yl diphosphate
?
-
about 2% of the activity with isopenteyl diphosphate
-
-
-
3-(fluoromethyl)-3-buten-1-yl diphosphate
?
-
competition between isomerization and alkylation of the flavin cofactor
-
-
?
3-cyclopropyl-3-buten-1-yl diphosphate
(2Z)-3-cyclopropylbut-2-en-1-yl diphosphate
-
-
-
-
r
3-methylene-4-penten-1-yl diphosphate
?
-
competition between isomerization and alkylation of the flavin cofactor
-
-
?
trans-3-Methylpent-3-enyl diphosphate
trans-3-Methylpent-2-enyl diphosphate
-
r
-
-
Isopentenyl diphosphate
?
-
essential activation step in isoprenoid biosynthetic pathway
-
-
-
isopentenyl diphosphate
dimethylallyl diphosphate
-
steady-state equilibrium ratio of isopentenyl diphosphate/dimethylallyl diphosphate of approximately 1:7
-
-
r
isopentenyl diphosphate
dimethylallyl diphosphate
the enzyme catalyzes a crucial activation step in the isoprenoid biosynthesis pathway
-
?
isopentenyl diphosphate
dimethylallyl diphosphate
-
-
-
-
?
isopentenyl diphosphate
dimethylallyl diphosphate
-
-
-
?
isopentenyl diphosphate
dimethylallyl diphosphate
-
the enzyme catalyzes the interconversion of the fundamental five carbon homoallylic and allylic diphosphate building blocks required for biosynthesis of isoprenoid compounds
-
?
isopentenyl diphosphate
dimethylallyl diphosphate
-
a mechanism is proposed where the reduced flavin cofactor acts as a general acid/base catalyst and helps stabilize the carbocationic intermediate formed by protonation
-
-
?
isopentenyl diphosphate
dimethylallyl diphosphate
-
the enzyme catalyses the interconversion of isopentenyl diphosphate and dimethylallyl diphosphate with a rather low degree of stereochemical fidelity. At least three kinetically distinguishable exchange processes are detected
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-
isopentenyl diphosphate
dimethylallyl diphosphate
-
accumulation of a reduced neutral dihydroflavin intermediate upon incubation of the reduced enzyme with isopentenyl diphosphate or dimethylallyl diphosphate. The intermediate forms and decays at kinetically competent rates in the pre-steady-state
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-
r
isopentenyl diphosphate
dimethylallyl diphosphate
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-
-
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r
isopentenyl diphosphate
dimethylallyl diphosphate
-
-
-
r
additional information
?
-
Cinchona robusta
-
induced after addition of a homogenate of the phytopathogenic fungus Phytophthora cinnamomi. Enzyme may be involved in the biosynthesis of anthraquinone phytoalexins that accumulate rapidly after elicitation of Cinchona cells
-
-
-
additional information
?
-
-
zinc is located in an unusual six-coordinate pocket and may facilitate protonation of the unactivated carbon-carbon double bond in isopentenyl diphosphate. The sulfhydryl moiety C67, perhaps in the thiolate form, is in position to remove a proton from the resulting tertiary carbocation to complete the reaction
-
?
additional information
?
-
-
key enzyme in biosynthesis of isoprenoids
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?
additional information
?
-
-
key enzyme in biosynthesis of isoprenoids
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?
additional information
?
-
-
3-butyn-1-yl diphosphate and 2,3-butadien-1-yl diphosphate are no substrates for IDI-1
-
-
-
additional information
?
-
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enzyme in the pathway of conversion of isopentenyl diphosphate to phytoene
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-
-
additional information
?
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the enzyme also has NADH dehydrogenase activity although it catalyzes the isomerase reaction without consuming any detectable amount of NADH. O2 acts as electron acceptor in the NADH dehydrogenase reaction
-
?
additional information
?
-
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the enzyme also has NADH dehydrogenase activity although it catalyzes the isomerase reaction without consuming any detectable amount of NADH. O2 acts as electron acceptor in the NADH dehydrogenase reaction
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?
additional information
?
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enzyme in the pathway of conversion of isopentenyl diphosphate to phytoene
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-
-
additional information
?
-
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substrate binds to the inactive oxidized and active reduced form of enzyme with similar affinities. Substrate-dependent accumulation of the neutral flavin semiquinone during both the flavoenzyme reduction and reoxidation processes
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additional information
?
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3-butyn-1-yl diphosphate and 2,3-butadien-1-yl diphosphate are no substrates for IDI-2
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-
-
additional information
?
-
-
ìsoform IDI-2 catalyzes exchange of the vinyl hydrogens in 1-OPP without concomitant isomerization
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-
-
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
Isopentenyl diphosphate
?
-
essential activation step in isoprenoid biosynthetic pathway
-
-
-
isopentenyl diphosphate
dimethylallyl diphosphate
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steady-state equilibrium ratio of isopentenyl diphosphate/dimethylallyl diphosphate of approximately 1:7
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-
r
isopentenyl diphosphate
dimethylallyl diphosphate
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-
-
-
?
isopentenyl diphosphate
dimethylallyl diphosphate
Q46822
the enzyme catalyzes a crucial activation step in the isoprenoid biosynthesis pathway
-
?
isopentenyl diphosphate
dimethylallyl diphosphate
-
the enzyme catalyzes the interconversion of the fundamental five carbon homoallylic and allylic diphosphate building blocks required for biosynthesis of isoprenoid compounds
-
?
isopentenyl diphosphate
dimethylallyl diphosphate
-
-
-
-
r
isopentenyl diphosphate
dimethylallyl diphosphate
B2ILS5
-
-
-
r
additional information
?
-
Cinchona robusta
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induced after addition of a homogenate of the phytopathogenic fungus Phytophthora cinnamomi. Enzyme may be involved in the biosynthesis of anthraquinone phytoalexins that accumulate rapidly after elicitation of Cinchona cells
-
-
-
additional information
?
-
-
key enzyme in biosynthesis of isoprenoids
-
?
additional information
?
-
-
key enzyme in biosynthesis of isoprenoids
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?
additional information
?
-
-
enzyme in the pathway of conversion of isopentenyl diphosphate to phytoene
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-
-
additional information
?
-
-
enzyme in the pathway of conversion of isopentenyl diphosphate to phytoene
-
-
-
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
-
IDI showed almost the same activity in the presence of NADH or dithionite. Data indicate that the reduced form of FMN is sufficient
-
FMN
bound only with very moderate affinity and is therefore completely lost during purification. However, the enzyme can be reconstituted in the crystals by soaking with FMN
FMN
-
reduced flavin is required. The neutral semiquinone state of the flavin is stabilized thermodynamically relative to free FMN in solution. Kd value is 0.0047 mM at pH 7.0, 37°C
FMN
-
required, IDI-2 reconstituted with cofactor analogues such as 5-deaza-FMN show no activity
FMN
-
the reduced FMN coenzyme of IDI-2 functions as an acid/base catalyst, with the N5 atom of the flavin likely playing a critical role in the deprotonation of isopentenyl diphosphate en route to dimethylallyl diphosphate formation
FMN
-
a mechanism is proposed where the reduced flavin cofactor acts as a general acid/base catalyst and helps stabilize the carbocationic intermediate formed by protonation
NAD(P)H
-
used only for the reduction of FMN, can be replaced with Na2S2O4
NADPH
-
required for reductive activation of inactive oxidized enzyme. Kd value is 0.11 mM at pH 7.0, 37°C
NADPH
-
needed only in catalytic amounts to activate the enzyme for multiple turnovers. Hydride transfer from NADPH to reduce FMN is pro-S stereospecific
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Ca2+
Cd2+
-
reconstitution of metal-free enzyme with Mg2+, Mn2+, Zn2+, Co2+, Ni2+ or Cd2+ generates active enzyme
Co2+
Mg2+
Mn2+
Ni2+
Zinc
-
essential cofactor. Type I enzyme contains an atom of tinc. The metal is located in an unusual six-coordinate pocket and may facilitate protonation of the unactivated carbon-carbon double bond in isopentenyl diphosphate
Zn2+
additional information
Co2+
-
reconstitution of metal-free enzyme with Mg2+, Mn2+, Zn2+, Co2+, Ni2+ or Cd2+ generates active enzyme
Mg2+
Cinchona robusta
-
activation by a mixture of Mg2+ and Mn2+ gives the highest activity; isomerase II: maximal activation at 2-8 mM Mg2+, the maximal activation is 35% lower than the activation obtained with Mn2+; isomerase I is activated by concentrations below 1 mM of Mn2+ or Mg2+, increasing concentrations are inhibitory; Mn2+ or Mg2+ required
Mg2+
-
the enzyme requires one Mn2+ or Mg2+ ion to fold in its active conformation, forming a distorted octahedral metal coordination site composed of three histidines and two glutamates and located in the active site
Mg2+
-
the enzyme is fully active in the absence of Mn2+ as long as Mg2+ is present in the buffer
Mg2+
-
0.72 mol per mol of enzyme. Reconstitution of metal-free enzyme with Mg2+, Mn2+, Zn2+, Co2+, Ni2+ or Cd2+ generates active enzyme
Mg2+
-
IDI-2 requires a divalent cation such as Mg2+ for activity
Mg2+
-
required. The enzyme requires the combined presence of FMN, NADPH and Mg2+
Mn2+
Cinchona robusta
-
activation by a mixture of Mg2+ and Mn2+ gives the highest activity; isomerase I is activated by concentrations below 1 mM of Mn2+ or Mg2+, increasing concentrations are inhibitory; Mn2+ or Mg2+ required
Mn2+
-
the enzyme requires one Mn2+ or Mg2+ ion to fold in its active conformation, forming a distorted octahedral metal coordination site composed of three histidines and two glutamates and located in the active site
Mn2+
-
the enzyme is fully active in the absence of Mn2+ as long as Mg2+ is present in the buffer
Mn2+
-
0.10 mol per mol of enzyme. Reconstitution of metal-free enzyme with Mg2+, Mn2+, Zn2+, Co2+, Ni2+ or Cd2+ generates active enzyme
Mn2+
-
isomerase I: maximal activation at 0.5 mM, isomerase II, III or IV: maximal activation at 0.25 mM
Mn2+
-
maximal activation at 2 mM, activity maximum obtained with Mn2+ is about 3times that with Mg2+; restores activity after EDTA treatment
Ni2+
-
reconstitution of metal-free enzyme with Mg2+, Mn2+, Zn2+, Co2+, Ni2+ or Cd2+ generates active enzyme
Zn2+
-
0.92 mol per mol of enzyme. Reconstitution of metal-free enzyme with Mg2+, Mn2+, Zn2+, Co2+, Ni2+ or Cd2+ generates active enzyme
additional information
-
no effects of other divalent cations such as Co2+, Cu2+, Zn2+ at 5mM
additional information
no effects of other divalent cations such as Co2+, Cu2+, Zn2+ at 5mM
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
(Z)-4-Fluoro-3-methyl-2-buten-1-yl diphosphate
-
inactivates through an active-site-directed covalent modification
3,4-Epoxy-1-butenyl diphosphate
-
active-site directed irreversible inhibitor
3,4-oxido-3-methyl-1-butyl diphosphate
-
inactivation through formation of covalent adducts with the reduced flavin, modification of the isoalloxazine ring at position N5
3-cyclopropylbut-3-en-1-yl trihydrogen diphosphate
-
cyclopropyl-derivative of isopentenyl diphosphate, mechanism-based inhibitor
3-oxiran-2-ylbut-3-en-1-yl trihydrogen diphosphate
-
epoxy-derivative of isopentenyl diphosphate, mechanism-based inhibitor. The enzyme catalyzes formation of a stable covalent adduct between the inhibitor and FMNH2 in a reaction catalyzed by protonation of the epoxide moiety followed by nucleophilic addition of the cofactor
4-aminophenyl-2-ethane-1,1-bisphosphonic acid
-
weak. Due to inhibition of more than one enzyme in the mevalonate pathway may lead to an increase in antiresorptive potency compared to bisphosphonates that only inhibit farnesyl diphosphate synthase
Dimethylallyl diphosphate containing fluorine, epoxy, and ammonium function groups
-
-
-
EDTA
addditon of 5mM EDTA results in almost complete loss of activity
Isopentenyl diphosphates containing fluorine, epoxy, and ammonium functional groups
-
-
-
Mg2+
Cinchona robusta
-
isomerase I is activated by concentrations below 1 mM of Mn2+ or Mg2+, increasing concentrations are inhibitory
N,N-dimethyl-2-amino-1-ethyl diphosphate
-
transition state analogue, competitive
additional information
-
not inhibited by 2-[ethyl(propyl)amino]ethyl trihydrogen diphosphate
-
2-(dimethylamino)ethyl phosphate
-
may function as a transition state or reactive intermediate analogue of a carbocation that binds extremely tightly
3,4-epoxy-3-methylbutyl diphosphate
-
i.e. EIPP, mechanism-based inhibitor of type I enzyme, covalent modification of reduced FMN in N5 position
3-(Fluoromethyl)-3-buten-1-yl diphosphate
-
inactivates through an active-site-directed covalent modification
3-(Fluoromethyl)-3-buten-1-yl diphosphate
-
active site-directed inhibitor
3-(Fluoromethyl)-3-buten-1-yl diphosphate
-
active site-directed inhibitor; irreversible
3-(Fluoromethyl)-3-buten-1-yl diphosphate
-
inactivation through formation of covalent adducts with the reduced flavin
3-Methyl-3,4-epoxybutyl diphosphate
-
time-dependent first-order loss of activity
3-methylene-4-penten-1-yl diphosphate
-
irreversible inhibition; the covalent adduct formed between irreversible mechanism based inhibitors, 3-methylene-4-penten-1-yl diphosphate or 3-oxiranyl-3-buten-1-yl diphosphate, and the flavin cofactor are investigated by X-ray crystallography and UV-visible spectroscopy. Both the crystal structures of enzyme binding the flavin-inhibitor adduct and the UV-visible spectra of the adducts indicate that the covalent bond is formed at C4a of flavin rather than at N5
3-methylene-4-penten-1-yl diphosphate
-
inactivation through formation of covalent adducts with the reduced flavin
3-oxiranyl-3-buten-1-yl diphosphate
-
irreversible inhibition; the covalent adduct formed between irreversible mechanism based inhibitors, 3-methylene-4-penten-1-yl diphosphate or 3-oxiranyl-3-buten-1-yl diphosphate, and the flavin cofactor are investigated by X-ray crystallography and UV-visible spectroscopy. Both the crystal structures of enzyme binding the flavin-inhibitor adduct and the UV-visible spectra of the adducts indicate that the covalent bond is formed at C4a of flavin rather than at N5
diphosphate
-
inhibitory effect decreases in the order of isomerases I, II, III, and IV
iodoacetamide
-
inhibitory effect decreases in the order of isomerases I, II, III, no inhibition of isomerase IV
Mn2+
Cinchona robusta
-
isomerase I is activated by concentrations below 1 mM of Mn2+ or Mg2+, increasing concentrations are inhibitory
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
FMN
-
required as cofactor. The enzyme requires the combined presence of FMN, NADPH and Mg2+
NADPH
-
required as cofactor. The enzyme requires the combined presence of FMN, NADPH and Mg2+
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DISEASE
TITLE OF PUBLICATION
LINK TO PUBMED
Amyotrophic Lateral Sclerosis
Segmental copy-number gain within the region of isopentenyl diphosphate isomerase genes in sporadic amyotrophic lateral sclerosis.
Bacterial Infections
Characterization and mechanistic studies of type II isopentenyl diphosphate:dimethylallyl diphosphate isomerase from Staphylococcus aureus.
isopentenyl-diphosphate delta-isomerase deficiency
Isopentenyl diphosphate isomerase deficiency in Synechocystis sp. strain PCC6803.
Neoplasms
Proliferation of NS0 cells in protein-free medium: the role of cell-derived proteins, known growth factors and cellular receptors.
Paralysis
Isopentenyl-diphosphate isomerase is essential for viability of Caenorhabditis elegans.
Zellweger Syndrome
Cholesterol biosynthesis in Zellweger syndrome: normal activity of mevalonate kinase, mevalonate-5'-pyrophosphate decarboxylase and IPP-isomerase in patients' fibroblasts but deficient mevalonate kinase activity in liver.
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
-
substrate binds to the inactive oxidized and active reduced form of enzyme with similar affinities
-
0.00152
isopentenyl diphosphate
-
mutant enzyme Q160L, in 50 mM MOPS-NaOH, pH 6.0, at 60°C
0.00323
isopentenyl diphosphate
-
mutant enzyme Q160N, in 50 mM MOPS-NaOH, pH 6.0, at 60°C
0.0033
isopentenyl diphosphate
-
wild type enzyme, in 25 mM Tris-HCl, pH 7.0, at 37°C
0.0048
isopentenyl diphosphate
-
aerobic, presence of NADPH, pH 7.0, 37°C
0.00595
isopentenyl diphosphate
-
wild type enzyme, at anaerobic conditions, at pH 7.0 and 37°C
0.006
isopentenyl diphosphate
-
mutant enzyme E169Q, in 25 mM Tris-HCl, pH 7.0, at 37°C; mutant enzyme Y105F, in 25 mM Tris-HCl, pH 7.0, at 37°C
0.00713
isopentenyl diphosphate
-
mutant enzyme Q160H, in 50 mM MOPS-NaOH, pH 6.0, at 60°C
0.00714
isopentenyl diphosphate
-
pH 6.0, 60°C, mutant enzyme E13R/R235E
0.00739
isopentenyl diphosphate
-
wild type enzyme, in 50 mM MOPS-NaOH, pH 6.0, at 60°C
0.00826
isopentenyl diphosphate
-
mutant enzyme Q160E, in 50 mM MOPS-NaOH, pH 6.0, at 60°C
0.0116
isopentenyl diphosphate
-
mutant enzyme W216F, in 25 mM Tris-HCl, pH 7.0, at 37°C
0.012
isopentenyl diphosphate
-
aerobic, presence of dithionite, pH 7.0, 37°C
0.0128
isopentenyl diphosphate
-
mutant enzyme Y159F, in 25 mM Tris-HCl, pH 7.0, at 37°C
0.0168
isopentenyl diphosphate
-
anaerobic, presence of NADPH, pH 7.0, 37°C
0.0376
isopentenyl diphosphate
mutant enzyme L141H/Y195F/W256C, at pH 7.5 and 30°C
0.0408
isopentenyl diphosphate
-
wild type enzyme, at aerobic conditions, at pH 7.0 and 37°C
0.0415
isopentenyl diphosphate
wild type enzyme, at pH 7.5 and 30°C
0.2768
isopentenyl diphosphate
-
in 0.4 M Tris, 1 mM dithiothreitol, 10 mM MgCl2, pH 8.0, at 50°C
0.572
isopentenyl diphosphate
-
mutant enzyme N37A, at aerobic conditions, at pH 7.0 and 37°C
0.0874
NADH
dehydrogenase reaction without isopentenyl diphosphate
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.065
isopentenyl diphosphate
-
aerobic, presence of NADPH, pH 7.0, 37°C
0.57
isopentenyl diphosphate
-
aerobic, presence of dithionite, pH 7.0, 37°C
0.69
isopentenyl diphosphate
-
anaerobic, presence of NADPH, pH 7.0, 37°C
0.875
isopentenyl diphosphate
-
wild type enzyme, at anaerobic conditions, at pH 7.0 and 37°C
0.983
isopentenyl diphosphate
-
wild type enzyme, at aerobic conditions, at pH 7.0 and 37°C
1.31
isopentenyl diphosphate
-
mutant enzyme N37A, at aerobic conditions, at pH 7.0 and 37°C
8.27
isopentenyl diphosphate
wild type enzyme, at pH 7.5 and 30°C
10.57
isopentenyl diphosphate
mutant enzyme L141H/Y195F/W256C, at pH 7.5 and 30°C
197
isopentenyl diphosphate
-
mutant enzyme Q160N, in 50 mM MOPS-NaOH, pH 6.0, at 60°C
221
isopentenyl diphosphate
-
mutant enzyme Q160L, in 50 mM MOPS-NaOH, pH 6.0, at 60°C
1210
isopentenyl diphosphate
-
mutant enzyme Q160H, in 50 mM MOPS-NaOH, pH 6.0, at 60°C
3280
isopentenyl diphosphate
-
mutant enzyme Q160E, in 50 mM MOPS-NaOH, pH 6.0, at 60°C
29900
isopentenyl diphosphate
-
wild type enzyme, in 50 mM MOPS-NaOH, pH 6.0, at 60°C
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.031
isopentenyl diphosphate
-
mutant enzyme Q160K, in 50 mM MOPS-NaOH, pH 6.0, at 60°C
0.061
isopentenyl diphosphate
-
mutant enzyme Q160N, in 50 mM MOPS-NaOH, pH 6.0, at 60°C
0.145
isopentenyl diphosphate
-
mutant enzyme Q160L, in 50 mM MOPS-NaOH, pH 6.0, at 60°C
0.17
isopentenyl diphosphate
-
mutant enzyme Q160H, in 50 mM MOPS-NaOH, pH 6.0, at 60°C
0.397
isopentenyl diphosphate
-
mutant enzyme Q160E, in 50 mM MOPS-NaOH, pH 6.0, at 60°C
4.05
isopentenyl diphosphate
-
wild type enzyme, in 50 mM MOPS-NaOH, pH 6.0, at 60°C
200
isopentenyl diphosphate
wild type enzyme, at pH 7.5 and 30°C
280
isopentenyl diphosphate
mutant enzyme L141H/Y195F/W256C, at pH 7.5 and 30°C
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.031
2,3-butadien-1-yl diphosphate
-
in 50 mM HEPES (pH 7.2) containing 10 mM MgCl2, 200 mM KCl, 1 mg/ml bovine serum albumin, 0.5 mM dithiothreitol, at 37°C
0.036
2,3-butadien-1-yl diphosphate
-
in 200 mM HEPES (pH 7.0) containing 2 mM MgCl2, 0.04 mM FMN, 2 mM NADPH, at 37°C
0.048
3-butyn-1-yl diphosphate
-
in 200 mM HEPES (pH 7.0) containing 2 mM MgCl2, 0.04 mM FMN, 2 mM NADPH, at 37°C
0.049
3-butyn-1-yl diphosphate
-
in 50 mM HEPES (pH 7.2) containing 10 mM MgCl2, 200 mM KCl, 1 mg/ml bovine serum albumin, 0.5 mM dithiothreitol, at 37°C
0.0064
FMN
-
wild type enzyme, at anaerobic conditions, at pH 7.0 and 37°C
0.292
isopentenyl diphosphate
-
wild type enzyme, at aerobic conditions, at pH 7.0 and 37°C
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IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.158
(2Z)-3-methylhept-2-en-1-yl trihydrogen diphosphate
Choristoneura fumiferana
-
in 25 mM Tris-HCl, pH 7.0, at 37°C
0.156
(2Z)-3-methylhex-2-en-1-yl trihydrogen diphosphate
Choristoneura fumiferana
-
in 25 mM Tris-HCl, pH 7.0, at 37°C
0.234
(2Z)-3-methyloct-2-en-1-yl trihydrogen diphosphate
Choristoneura fumiferana
-
in 25 mM Tris-HCl, pH 7.0, at 37°C
0.007
2-[ethyl(propyl)amino]ethyl trihydrogen diphosphate
Choristoneura fumiferana
-
in 25 mM Tris-HCl, pH 7.0, at 37°C
0.092
dimethylallyl diphosphate
Choristoneura fumiferana
-
in 25 mM Tris-HCl, pH 7.0, at 37°C
0.131
homodimethylallyl diphosphate
Choristoneura fumiferana
-
in 25 mM Tris-HCl, pH 7.0, at 37°C
0.066
homoisopentenyl diphosphate
Choristoneura fumiferana
-
in 25 mM Tris-HCl, pH 7.0, at 37°C
0.003
2-[ethyl(methyl)amino]ethyl trihydrogen diphosphate
Choristoneura fumiferana
-
in 25 mM Tris-HCl, pH 7.0, at 37°C
0.0055
2-[ethyl(methyl)amino]ethyl trihydrogen diphosphate
Sus scrofa
-
in 50 mM Tris-HCl (pH 7.0), at 37°C
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
0.08
-
dimethylallyl diphosphate, C13-labeled at positions 3, 4 and 5, aerobic, pH 8, 37°C
additional information
additional information
-
mutant D216A, relative IPP isomerase activity 35%, wild-type enzyme 100%; mutant E161A, relative IPP isomerase activity 0.5%, wild-type enzyme 100%; mutant E194A, relative IPP isomerase activity 15%, wild-type enzyme 100%; mutant E229A, relative IPP isomerase activity 6.5%, wild-type enzyme 100%; mutant H11A, relative IPP isomerase activity 4%, wild-type enzyme 100%; mutant H155A, relative IPP isomerase activity 3%, wild-type enzyme 100%; mutant K193A, relative IPP isomerase activity 1%, wild-type enzyme 100%; mutant K8A, relative IPP isomerase activity 0.1%, wild-type enzyme 100%; mutant N125A, relative IPP isomerase activity 5%, wild-type enzyme 100%; mutant N157A, relative IPP isomerase activity 0.5%, wild-type enzyme 100%; mutant Q160A, relative IPP isomerase activity 0.1%, wild-type enzyme 100%; mutant R232A, relative IPP isomerase activity 2%, wild-type enzyme 100%; mutant R7A, relative IPP isomerase activity 0.1%, wild-type enzyme 100%; mutant S96A, relative IPP isomerase activity 3%, wild-type enzyme 100%; mutant T68A, relative IPP isomerase activity 6%, wild-type enzyme 100%
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
4.5 - 9.5
-
pH 4.5: about 39% of maximal activity, pH 9.5: about 60% of maximal activity
5.5 - 7.5
-
pH 5.5: about 35% of maximal activity, pH 7.5: about 30% of maximal activity
7 - 8.5
Cinchona robusta
-
pH 7.0-7.8: maximal activity, pH 8.5: 20% of maximal activity, isomerase I
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
5.9
6.1
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
type II isopentenyl diphosphate:dimethylallyl diphosphate isomerase
SwissProt
brenda
type II isopentenyl diphosphate/dimethylallyl diphosphate isomerase
-
-
brenda
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
-
in normal fibroblasts and Zellweger fibroblasts, in which the synthesis of cholesterol is impaired
brenda
in mature and tender leaf, expression is higher than in tubers
brenda
additional information
expression in stem is much higher than in root and tender leaf, no expression in mature leaf
brenda
-
expression is highest in stems, followed by leaf, and is lowest in root
brenda
in mature and tender leaf, expression is higher than in tubers
brenda
cDNA clone of the tomato IPI gene is amplified using cDNA from young leaves as template
brenda
expression in stem is much higher than in root and tender leaf
brenda
-
expression is highest in stems, followed by leaf, and is lowest in root
brenda
expression is much higher than in root and tender leaf
brenda
-
expression is highest in stems, followed by leaf, and is lowest in root
brenda
additional information
no expression in mature leaf and fruit
brenda
additional information
-
expression may be induced by Verticillium dahliae kleb, by methyl jasmonate and salicylic acid
brenda
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
enhanced green fluorescent protein fusions are found mainly in the mitochondrion
brenda
enhanced green fluorescent protein fusions are found mainly in the plastid
brenda
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
metabolism
physiological function
metabolism
-
IPP isomerase activity is a rate-limiting step in terpenoid synthesis
metabolism
IPP isomerase activity is a rate-limiting step in terpenoid synthesis
metabolism
the enzyme plays a critical role in terpenoid metabolic pathways
metabolism
-
the plastidial enzyme plays an important function in carotenoid biosynthesis
physiological function
isopentenyl diphosphate and dimethylallyl diphosphate are essential precursors for terpenoid biosynthesis
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PDB
SCOP
CATH
UNIPROT
ORGANISM
Bacillus subtilis (strain 168)
Escherichia coli (strain K12)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Streptococcus mutans serotype c (strain ATCC 700610 / UA159)
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)
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
29200
34000
35000
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
homotetramer
monomer
octamer
tetramer
?
x * 33680, calculated from amino acid sequence; x * 35000, SDS-PAGE
?
-
x * 33350, calculation from nucleotide sequence; x * 39000-40000, SDS-PAGE
homotetramer
4 * 39868, calculated from amino acid sequence; 4 * 39874, purified His-tagged enzyme, electrospray ionization mass spectrometry
homotetramer
-
4 * 39868, calculated from amino acid sequence; 4 * 39874, purified His-tagged enzyme, electrospray ionization mass spectrometry
-
octamer
-
substrate binding causes the dissociation of an octamer into tetramers. The mutant enzyme E13R/R235E is in the tetrameric state even at a concentration where the wild-type enzyme dominantly forms an octamer
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CRYSTALLIZATION/commentary
ORGANISM
UNIPROT
LITERATURE
sitting drop vapor diffusion method, ligand-free form of the FMN-bound enzyme form at 2.8 A resolution. The octamer forms a D4 symmetrical open, cage-like structure. The monomers of 45000 Da display a classical TIM barrel fold
comparison of orthorhombic, monoclinic and trigonal crystal forms, up to 2.2 A resolution. Crystallization of free enzyme and in complex wih transition-state analogue N,N-dimethyl-2-amino-1-ethyl diphosphate
-
crystals soaked with transition state analogue (N,N-dimethylamino)-1-ethyl diphosphate
-
hanging drop vapor diffusion method, crystal structure of the C67A mutant of isopentenyl diphosphate isomerase complexed with the mechanism-based irreversible inhibitor 3,4-epoxy-3-methyl-1-butyl diphosphate
-
hanging drop vapor diffusion method, crystal structures of complexes with transition state analogue N,N-dimethyl-2-amino-1-ethyl diphosphate and the covalently attached irreversible inhibitors 3,4-epoxy-3-methyl-1-butyl diphosphate at 1.96 A resolution
-
hanging drop vapour diffusion method, selenomethionyl form, crystals display trigonal symmetry, with unit-cell parameters, a = b = 71.3 A, c = 61.7 A, and diffract to 1.45 A resolution
-
enzyme shows a flexible N-terminal alpha-helix covering the active pocket and blocking the entrance. Substrate binding induces conformational change in the active site. A water molecule is the direct proton donor for the substrate
native enzyme at 1.7 A and in complex with substrate at 1.9 A resolution. comparison with Escherichia coli enzyme structure
sitting drop vapor diffusion method, using 0.6 M calcium acetate and 50 mM HEPES pH 7.5
-
molecular modeling of structure and comparison with structures of Streptococcus pneumoniae and Thermus thermophilus enzymes
crystallized at 20°C using the hanging-drop vapor diffusion method with a reservoir solution containing 0.1 M Tris-HCl (pH 8.0), 0.2 M sodium citrate, and 30% (vol/vol) polyethylene glycol 400 (PEG 400)
-
the covalent adduct formed between irreversible mechanism based inhibitors, 3-methylene-4-penten-1-yl diphosphate or 3-oxiranyl-3-buten-1-yl diphosphate, and the flavin cofactor are investigated by X-ray crystallography and UV-visible spectroscopy. Both the crystal structures of enzyme binding the flavin-inhibitor adduct and the UV-visible spectra of the adducts indicate that the covalent bond is formed at C4a of flavin rather than at N5. The high-resolution crystal structures of enzyme-substrate complexes and the kinetic studies of new mutants confirm that only the flavin cofactor can catalyze protonation of the substrates and suggest that N5 of flavin is most likely to be involved in proton transfer
-
the crystal structures of the substrate-free enzyme and of the substrate-enzyme complexes, in the oxidized and reduced states, are solved to resolutions between 1.99 and 3.1 A, six distinct types of type 2 IDI crystals are obtained
-
sitting drop vapor diffusion method, using HEPES buffer (100 mM, pH 7.5 with 2 M (NH4)2SO4)
in complex with diphosphate. The diphosphate moiety is located near the conserved residues H10, R97, H152, Q157, E158, and W219, and the flavin cofactor. The putative active site may stabilize a carbocationic intermediate
-
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
E116Q
E87Q
K55A
-
the ratio of maximal velocity to turnover number is 66% of that of the wild-type enzyme
K55R
-
the ratio of maximal velocity to turnover number is 28% of that of the wild-type enzyme
R51K
-
the ratio of maximal velocity to turnover number is 4.2% of that of the wild-type enzyme
R83K
-
the ratio of maximal velocity to turnover number is 104% of that of the wild-type enzyme
W161F
-
the ratio of maximal velocity to turnover number is 0.8% of that of the wild-type enzyme
Y104A
-
0.1% of wild-type activity. Crystallization data. The M2+ metal-binding site is absent in the structure, but Mg2+ is still present and bound to C67, E87, and four water molecules
Y104F
-
0.1% of wild-type activity. Crystallization data. General fold of enzyme is similar to wild-type
E13R/R235E
-
the mutant and the wild-type enzyme show similar Vmax values, while the Km of E13R/R235E is smaller than that of the wild type. The mutant is in the tetrameric state even at a concentration where the wild-type enzyme dominantly forms an octamer
Q160E
-
10-fold decrease in kcat/Km; the mutant shows a 10fold decrease in kcat/Km
Q160H
-
23-fold decrease in kcat/Km; the mutant shows a 23fold decrease in kcat/Km
Q160K
-
130-fold decrease in kcat/Km; the mutant shows a 130fold decrease in kcat/Km
Q160L
-
28-fold decrease in kcat/Km; the mutant shows a 28fold decrease in kcat/Km
Q160N
-
150-fold decrease in kcat, kcat/Km decreases 66-fold; the mutant shows a 150fold decrease in kcat, although kcat/Km only decreases 66fold
L141H/W256C
the mutations enhance the enzyme activity 1.65fold
L141H/Y195F
the mutations enhance the enzyme activity 2.03fold
L141H/Y195F/W256C
the mutation enhances the enzyme activity 3.13fold
Y195F/W256C
the mutations enhance the enzyme activity 1.14fold
N37A
-
the mutant is a monomeric but active enzyme with by 20°C lowered melting temperature and reduced binding affinities of FMN (40fold) and a minimal effect on the kcat value compared to the wild type enzyme
additional information
E116Q
-
the ratio of maximal velocity to turnover number is 0.09%% of that of the wild-type enzyme
E87Q
-
the ratio of maximal velocity to turnover number is 0.07% of that of the wild-type enzyme
additional information
mutants lacking isoform idi1 activity have no major morphological or chemical differences from the wild-type. Mutants lacking both isoforms idi1 and idi2 are non-viable; mutants lacking isoform idi2 activity have no major morphological or chemical differences from the wild-type except for flowers with fused sepals and underdeveloped petals. Mutants lacking both isoforms idi1 and idi2 are non-viable
additional information
mutants lacking isoform idi1 activity have no major morphological or chemical differences from the wild-type. Mutants lacking both isoforms idi1 and idi2 are non-viable; mutants lacking isoform idi2 activity have no major morphological or chemical differences from the wild-type except for flowers with fused sepals and underdeveloped petals. Mutants lacking both isoforms idi1 and idi2 are non-viable
additional information
mutants lacking isoform ipi1 activity are phenotypically normal. Mutants lacking the activities of both isoforms ipi1 and ipi2 exhibit dwarfism and male sterility under long-day conditions, and decreased pigmentation under continuous light. The sterol and ubiquinone levels of the double mutant are less than 50% of wild-type level. The male-sterile phenotype is complemented by squalene; mutants lacking isoform ipi2 activity are phenotypically normal. Mutants lacking the activities of both isoforms ipi1 and ipi2 exhibit dwarfism and male sterility under long-day conditions, and decreased pigmentation under continuous light. The sterol and ubiquinone levels of the double mutant are less than 50% of wild-type level. The male-sterile phenotype is complemented by squalene
additional information
mutants lacking isoform ipi1 activity are phenotypically normal. Mutants lacking the activities of both isoforms ipi1 and ipi2 exhibit dwarfism and male sterility under long-day conditions, and decreased pigmentation under continuous light. The sterol and ubiquinone levels of the double mutant are less than 50% of wild-type level. The male-sterile phenotype is complemented by squalene; mutants lacking isoform ipi2 activity are phenotypically normal. Mutants lacking the activities of both isoforms ipi1 and ipi2 exhibit dwarfism and male sterility under long-day conditions, and decreased pigmentation under continuous light. The sterol and ubiquinone levels of the double mutant are less than 50% of wild-type level. The male-sterile phenotype is complemented by squalene
additional information
-
functional expression in engineered Escherichia coli restores the carotenoid pathway
additional information
functional expression in engineered Escherichia coli restores the carotenoid pathway
additional information
-
gene IPI can accelerate the accumulation of beta-carotene in Escherichia coli transformants
additional information
-
isoform IDI2 can complete isomerase function in an idi1-deficient yeast strain
additional information
recombinant expression in Escherichia coli. Gene IBI can take the role of Arabidopsis thaliana IDI to produce the orange beta-carotene
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37
-
half-life in dilute solution: 30 min. In more concentrated solutions of the protein or dilute enzyme in the presence of 0.01% bovine serum albumin, little loss of activity after 1 h
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, 0.1 M potassium phosphate buffer, pH 7.0, 2 mM dithiothreitol, stable for several weeks
-
-80°C, 0.05 M Tris/HCl, pH 7.5, containing 0.01 mM leupeptin, 2 mM dithiothreitol, 5% glycerol, 55% of the activity is recovered after 3 months
Cinchona robusta
-
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PURIFICATION/commentary
ORGANISM
UNIPROT
LITERATURE
DEAE Sepharose column chromatography and Resource Phe column chromatograpyh
-
on a HisTrap column, for crystallisation, the enzyme is loaded on a HiLoad 16/60 Superdex 200 column
-
partial. Dye-ligand and immobilized metal ion interaction chromatography are efficient techniques for the rapid batchwise fractionation, from crude plant extracts, of a series of enzymes of prenyl diphosphate metabolism
-
recombinant enzyme
recombinant protein, enzyme purified under aerobic conditions is inactive until the flavin cofactor is reduced by NADPH or dithionite or photochemically
-
TALON metal affinity resin column chromatography
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CLONED/commentary
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli
expressed in Escherichia coli BL21 cells
expressed in Escherichia coli BL21(DE3) cells
expressed in Escherichia coli Rosetta cells
expressed in Nicotiana tabacum and Escherichia coli BL-21 (DE3) cells
expression in Escherichia coli
expression in Escherichia coli, His6-tagged type II enzyme
-
into the vector pMD18-T for sequencing, and subsequently into pET-28a+ for expression in Escherichia coli BL21DE3 cells
overexpression in Escherichia coli
recombinantly expressed with a polyhistidine tag at its N terminus in Escherichia coli BL21
-
the plasmid pDL11, which contains the genes idi, gps and egsA, is constructed by inserting idi and egsA into pCW3, derived from pCL1920, pDL11 is transformed into Escherichia coli TOP10 cells
-
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
enzyme expression is increased about 4fold at 4°C, about 2.5fold at 0.1 mM NaCl, about 6fold at 0.15 mM mannitol, and about 7.5fold at 0.03 mM methyl jasmonate
enzyme expression is induced 6 and 24 h after treatment with 30 mM Ag+
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