Information on EC 5.3.3.2 - isopentenyl-diphosphate DELTA-isomerase

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

EC NUMBER
COMMENTARY
5.3.3.2
-
RECOMMENDED NAME
GeneOntology No.
isopentenyl-diphosphate DELTA-isomerase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
Isopentenyl diphosphate = dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
Isopentenyl diphosphate = dimethylallyl diphosphate
show the reaction diagram
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
show the reaction diagram
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
show the reaction diagram
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
show the reaction diagram
interconversion of substrate is catalyzed by a stereoselective antarafacial [1.3] transposition of a proton involving residues C87, E149, W197 and Y137
Q13907
Isopentenyl diphosphate = dimethylallyl diphosphate
show the reaction diagram
in the rate determining step, the C2-H bond of isopentenyl diphosphate is cleaved. General acid/base catalysis may be involved during turnover
-
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
intramolecular oxidoreduction
-
-
-
-
isomerization
-
-
-
-
isomerization
-
-
isomerization
A9LRT7
-
PATHWAY
KEGG Link
MetaCyc Link
all-trans-farnesol biosynthesis
-
Biosynthesis of secondary metabolites
-
bisabolene biosynthesis
-
isoprene biosynthesis II (engineered)
-
Metabolic pathways
-
methylerythritol phosphate pathway
-
mevalonate pathway I
-
mevalonate pathway II (archaea)
-
mono-trans, poly-cis decaprenyl phosphate biosynthesis
-
Terpenoid backbone biosynthesis
-
trans, trans-farnesyl diphosphate biosynthesis
-
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.
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IPI
Q46822
-
IPP isomerase
-
-
-
-
IPP isomerase
Q46822
-
IPP isomerase
P61615
-
IPP-isomerase
-
-
-
-
IPPI1
-
-
-
-
IPPI2
-
-
-
-
IPPISOM
Vitis vinifera x Vitis riparia, Vitis vinifera x Vitis vinifera
-
-
Isomerase, isopentenylpyrophosphate DELTA-
-
-
-
-
Isopententenyl diphosphate:dimethylallyl diphosphate isomerase
-
-
-
-
isopentenyl diphosphate isomerase
-
-
isopentenyl diphosphate isomerase
Q46822
-
isopentenyl diphosphate isomerase
A9LRT7
-
isopentenyl diphosphate:dimethylallyl diphosphate isomerase
-
-
isopentenyl diphosphate:dimethylallyl diphosphate isomerase
P61615
-
Isopentenyl pyrophosphate isomerase
-
-
-
-
Isopentenyl pyrophosphate isomerase:dimethylallyl pyrophosphate isomerase
-
-
-
-
isopentenyl-diphosphate delta-isomerase 1
Vitis vinifera x Vitis riparia, Vitis vinifera x Vitis vinifera
-
-
Isopentenyldiphosphate DELTA-isomerase
-
-
-
-
Isopentenylpyrophosphate isomerase
-
-
-
-
Methylbutenylpyrophosphate isomerase
-
-
-
-
SlIPI
A9LRT7
-
type 2 isopentenyl diphosphate isomerase
-
-
type 2 isopentenyl diphosphate isomerase
P61615
-
type 2 isopentenyl-diphosphate isomerase
P61615
-
type I isopentenyl diphosphate isomerase
-
-
type II isopentenyl diphosphate isomerase
-
-
type II isopentenyl diphosphate:dimethylallyl diphosphate isomerase
-
-
CAS REGISTRY NUMBER
COMMENTARY
9033-27-6
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
isoform Idi1
UniProt
Manually annotated by BRENDA team
isoform IDI2
UniProt
Manually annotated by BRENDA team
isoform Ipi1
UniProt
Manually annotated by BRENDA team
isoform Ipi2
UniProt
Manually annotated by BRENDA team
type II isopentenyl diphosphate:dimethylallyl diphosphate isomerase
SwissProt
Manually annotated by BRENDA team
Cinchona robusta
-
-
-
Manually annotated by BRENDA team
Citrus sp.
-
-
-
Manually annotated by BRENDA team
Claviceps sp.
-
-
-
Manually annotated by BRENDA team
Claviceps sp.
strain SD58
-
-
Manually annotated by BRENDA team
Claviceps sp. SD58
strain SD58
-
-
Manually annotated by BRENDA team
Cucurbita sp.
-
-
-
Manually annotated by BRENDA team
type I enzyme
-
-
Manually annotated by BRENDA team
type I isopentenyl-diphosphate D-isomerase
-
-
Manually annotated by BRENDA team
wild type and strain Y104F
UniProt
Manually annotated by BRENDA team
4 enzyme forms: I, II, III, and IV
-
-
Manually annotated by BRENDA team
-
SwissProt
Manually annotated by BRENDA team
isoform IDI2
-
-
Manually annotated by BRENDA team
type I enzyme
SwissProt
Manually annotated by BRENDA team
type II enzyme, isoform IDI-2
-
-
Manually annotated by BRENDA team
type II isopentenyl diphosphate isomerase
-
-
Manually annotated by BRENDA team
isoform IDI2
UniProt
Manually annotated by BRENDA team
expressed in Escherichia coli
-
-
Manually annotated by BRENDA team
strain IDI-2, type II enzyme
-
-
Manually annotated by BRENDA team
type II isopentenyl diphosphate/dimethylallyl diphosphate isomerase
-
-
Manually annotated by BRENDA team
Staphylococcus aureus IDI-2
strain IDI-2, type II enzyme
-
-
Manually annotated by BRENDA team
type 2 isopentenyl diphosphate isomerase
SwissProt
Manually annotated by BRENDA team
strain PCC 6803 ORF sll 1556
-
-
Manually annotated by BRENDA team
isoform IDI-2
-
-
Manually annotated by BRENDA team
isoform IDI2
-
-
Manually annotated by BRENDA team
strain HB 27
-
-
Manually annotated by BRENDA team
type II enzyme, recombinant protein
-
-
Manually annotated by BRENDA team
Thermus thermophilus HB 27
strain HB 27
-
-
Manually annotated by BRENDA team
Vitis vinifera x Vitis riparia
-
-
-
Manually annotated by BRENDA team
Vitis vinifera x Vitis vinifera
-
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
physiological function
A9LRT7
isopentenyl diphosphate and dimethylallyl diphosphate are essential precursors for terpenoid biosynthesis
physiological function
Vitis vinifera x Vitis riparia, Vitis vinifera x Vitis vinifera
-
involved in terpenoid metabolism
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(Z)-3-(difluoromethyl)-2-buten-1-yl diphosphate
?
show the reaction diagram
-
about 2% of the activity with isopenteyl diphosphate
-
-
-
(Z)-3-(fluoromethyl)-2-buten-1-yl diphosphate
?
show the reaction diagram
-
about 2% of the activity with isopenteyl diphosphate
-
-
-
3-(fluoromethyl)-3-buten-1-yl diphosphate
?
show the reaction diagram
-
competition between isomerization and alkylation of the flavin cofactor
-
-
?
3-Ethylbut-3-enyl diphosphate
trans-3-Methylpent-3-enyl diphosphate
show the reaction diagram
-
ir
-
-
3-methylene-4-penten-1-yl diphosphate
?
show the reaction diagram
-
competition between isomerization and alkylation of the flavin cofactor
-
-
?
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
?
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
r
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
r
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
?
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
r
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
Q46822
-
-
?
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
?
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
r
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
?
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
O35760
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
?
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
O35586
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
Cucurbita sp., Citrus sp., Acholeplasma laidlawii
-
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
Claviceps sp.
-
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
Claviceps sp.
-
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
?
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
?
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
r
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
P61615, -
-
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
P61615, -
-
-
-
?
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
?
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-, P50740
-
-
-
r
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
?
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
A9LRT7
-
-
-
r
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
r
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
Cinchona robusta
-
r
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
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
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
Q46822
the enzyme catalyzes a crucial activation step in the isoprenoid biosynthesis pathway
-
?
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
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
show the reaction diagram
-
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
-
-
r
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
Claviceps sp. SD58
-
-
-
-
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
Staphylococcus aureus IDI-2
-
-
-
-
?
Isopentenyl diphosphate
?
show the reaction diagram
-
-
-
-
-
Isopentenyl diphosphate
?
show the reaction diagram
-
-
-
-
-
Isopentenyl diphosphate
?
show the reaction diagram
-
essential activation step in isoprenoid biosynthetic pathway
-
-
-
pyruvate
lactate
show the reaction diagram
-
-
-
-
?
trans-3-Methylpent-3-enyl diphosphate
trans-3-Methylpent-2-enyl diphosphate
show the reaction diagram
-
r
-
-
isopentenyl diphosphate
dimethylallyl phosphate
show the reaction diagram
-
-
-
-
?
additional information
?
-
P61615, -
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
?
-
-
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
?
-
-
enzyme of the isoprenoid pathway
-
-
-
additional information
?
-
-
enzyme in the pathway of conversion of isopentenyl diphosphate to phytoene
-
-
-
additional information
?
-
-
enzyme in the pathway of conversion of isopentenyl diphosphate to phytoene
-
-
-
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
?
-
-
key enzyme in biosynthesis of isoprenoids
-
?
additional information
?
-
-
key enzyme in biosynthesis of isoprenoids
-
?
additional information
?
-
-
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
-
-
-
additional information
?
-
-
3-butyn-1-yl diphosphate and 2,3-butadien-1-yl diphosphate are no substrates for IDI-1
-
-
-
additional information
?
-
-
3-butyn-1-yl diphosphate and 2,3-butadien-1-yl diphosphate are no substrates for IDI-2
-
-
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
?
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
P61615, -
-
-
-
?
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
?
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
-
-
-
?
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
A9LRT7
-
-
-
r
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
Q46822
the enzyme catalyzes a crucial activation step in the isoprenoid biosynthesis pathway
-
?
Isopentenyl diphosphate
Dimethylallyl diphosphate
show the reaction diagram
-
the enzyme catalyzes the interconversion of the fundamental five carbon homoallylic and allylic diphosphate building blocks required for biosynthesis of isoprenoid compounds
-
?
Isopentenyl diphosphate
?
show the reaction diagram
-
-
-
-
-
Isopentenyl diphosphate
?
show the reaction diagram
-
-
-
-
-
Isopentenyl diphosphate
?
show the reaction diagram
-
essential activation step in isoprenoid biosynthetic pathway
-
-
-
additional information
?
-
-
enzyme of the isoprenoid pathway
-
-
-
additional information
?
-
-
enzyme in the pathway of conversion of isopentenyl diphosphate to phytoene
-
-
-
additional information
?
-
-
enzyme in the pathway of conversion of isopentenyl diphosphate to phytoene
-
-
-
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
?
-
-
key enzyme in biosynthesis of isoprenoids
-
?
additional information
?
-
-
key enzyme in biosynthesis of isoprenoids
-
?
COFACTOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
FMN
P61615
strictly dependent on
FMN
-, P50740
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
-
nearly no activity with the flavin analogue 5-deazaFMN
FMN
-, P50740
maximal activity with 10 microM FMN
FMN
-
required under aerobic and anaerobic conditions
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, 37C
FMN
-
FMN must be in reduced state to be catalytically active
FMN
-
required, IDI-2 reconstituted with cofactor analogues such as 5-deaza-FMN show no activity
FMN
-
IDI-2 requires reduced flavin
NAD(P)H
P61615
required
NAD(P)H
-
proposed mechanism: reduction of FMN
NAD(P)H
-
used only for the reduction of FMN, can be replaced with Na2S2O4
NADH
-
or NADPH required under aerobic, not under anaerobic conditions
NADPH
-, P50740
maximal acitivity with 1 mM NADPH
NADPH
-
or NADH required under aerobic, not under anaerobic conditions
NADPH
-
required for reductive activation of inactive oxidized enzyme. Kd value is 0.11 mM at pH 7.0, 37C
NADPH
-
needed only in catalytic amounts to activate the enzyme for multiple turnovers. Hydride transfer from NADPH to reduce FMN is pro-S stereospecific
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
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
-
METALS and IONS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Ca2+
-, P50740
lower activity as with Mg2+
Ca2+
-
10mM, relative activity 100%
Cd2+
-
reconstitution of metal-free enzyme with Mg2+, Mn2+, Zn2+, Co2+, Ni2+ or Cd2+ generates active enzyme
Co2+
-
slight activation
Co2+
-
10mM, relative activity under 0.005%
Co2+
-
reconstitution of metal-free enzyme with Mg2+, Mn2+, Zn2+, Co2+, Ni2+ or Cd2+ generates active enzyme
Cu2+
-
10mM, relative activity under 0.005%
Mg2+
-
required
Mg2+
-
maximal activation at 5 mM; restores activity after EDTA treatment
Mg2+
-
slight activation
Mg2+
-
Mn2+ or Mg2+ required
Mg2+
-
Mn2+ is a better activator than Mg2+; Mn2+ or Mg2+ required
Mg2+
Claviceps sp.
-
maximal activation at 0.2 mM; Mn2+ or Mg2+ required
Mg2+
-
-
Mg2+
-
Mn2+ or Mg2+ required
Mg2+
-
maximal activation at 20 mM; Mn2+ or Mg2+ required
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+
P61615
required
Mg2+
-
the enzyme is fully active in the absence of Mn2+ as long as Mg2+ is present in the buffer
Mg2+
-
required. The enzyme requires the combined presence of FMN, NADPH and Mg2+
Mg2+
-, P50740
maximal acitivity
Mg2+
-
10mM, relative activity 65%
Mg2+
-
Kd value is 0.13 mM at pH 7.0, 37C
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 for activity
Mn2+
-
maximal activation at 2 mM, activity maximum obtained with Mn2+ is about 3times that with Mg2+; restores activity after EDTA treatment
Mn2+
-
isomerase I: maximal activation at 0.5 mM, isomerase II, III or IV: maximal activation at 0.25 mM
Mn2+
-
Mn2+ or Mg2+ required
Mn2+
-
Mn2+ is a better activator than Mg2+; Mn2+ or Mg2+ required
Mn2+
Claviceps sp.
-
Mn2+ or Mg2+ required
Mn2+
-
-
Mn2+
-
maximal activation at 0.5 mM; Mn2+ or Mg2+ required
Mn2+
-
maximal activation at 0.1 mM; Mn2+ or Mg2+ required
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+
-, P50740
lower activity as with Mg2+
Mn2+
-
10mM, relative activity 17%
Mn2+
-
0.10 mol per mol of enzyme. Reconstitution of metal-free enzyme with Mg2+, Mn2+, Zn2+, Co2+, Ni2+ or Cd2+ generates active enzyme
Ni2+
-
slight activation
Ni2+
-
10mM, relative activity under 0.005%
Ni2+
-
reconstitution of metal-free enzyme with Mg2+, Mn2+, Zn2+, Co2+, Ni2+ or Cd2+ generates active enzyme
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+
-
10mM, relative activity 0.2%
Zn2+
-
0.92 mol per mol of enzyme. Reconstitution of metal-free enzyme with Mg2+, Mn2+, Zn2+, Co2+, Ni2+ or Cd2+ generates active enzyme
Zn2+
-
IDI-1 is a zinc-metalloprotein
Mn2+
-
maximal activity at 0.01 mM
additional information
-, P50740
no effects of other divalent cations such as Co2+, Cu2+, Zn2+ at 5mM
INHIBITORS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
(+/-)-cis/trans-Chrysanthemyl diphosphate
-
-
(+/-)-cis/trans-Chrysanthemyl monophosphate
-
-
(E/Z)-3-cyclopropyl-2-buten-1-yl diphosphate
-
-
(N,N-dimethylamino)-1-ethyl diphosphate
-
transition state analogue
(Z)-3-difluoromethyl-2-buten-1-yl diphosphate
-
reversible
(Z)-3-fluoromethyl-2-buten-1-yl diphosphate
-
reversible
(Z)-4-Fluoro-3-methyl-2-buten-1-yl diphosphate
Claviceps sp.
-
inactivates through an active-site-directed covalent modification
2,2-Diphenyl-1-(beta-dimethylaminoethoxy)pentane hydrochloride
-
-
2,3-butadien-1-yl diphosphate
-
competitive inhibitor
-
2,3-cis,6,7-trans-farnesyl diphosphate
-
-
2-(Dimethylamino)ethyl phosphate
-
competitive
2-(Dimethylamino)ethyl phosphate
Claviceps sp.
-
may function as a transition state or reactive intermediate analogue of a carbocation that binds extremely tightly
2-(Dimethylamino)ethyl phosphate
Cinchona robusta
-
-
3,4-Epoxy-1-butenyl diphosphate
-
active-site directed irreversible inhibitor
3,4-epoxy-3-methyl-1-butyl diphosphate
-
-
3,4-epoxy-3-methylbutyl diphosphate
-
i.e. EIPP, mechanism-based inhibitor of type I enzyme, covalent modification of reduced FMN in N5 position
3,4-epoxy-3-methylbutyl diphosphate
-
irreversible inhibition
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-(Fluoromethyl)-3-buten-1-yl diphosphate
Claviceps sp.
-
inactivates through an active-site-directed covalent modification
3-(Fluoromethyl)-3-buten-1-yl diphosphate
-
-
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-Bromo-3-butenyl diphosphate
-
competitive
3-butyn-1-yl diphosphate
-
competitive inhibitor
-
3-cyclopropyl-3-buten-1-yl diphosphate
-
reversible
3-cyclopropyl-3-buten-1-yl diphosphate
-
-
3-cyclopropylbut-3-en-1-yl trihydrogen diphosphate
-
cyclopropyl-derivative of isopentenyl diphosphate, mechanism-based inhibitor
3-Methyl-3,4-epoxybutyl diphosphate
-
-
3-Methyl-3,4-epoxybutyl diphosphate
-
time-dependent first-order loss of activity
3-Methyl-5-oxo-hexyl diphosphate
-
-
3-Methyl-5-oxo-hexyl diphosphate ethylene glycol acetal
-
-
3-methylene-4-penten-1-yl diphosphate
-
inactivation through formation of covalent adducts with the reduced flavin
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
3-oxiranyl-3-buten-1-yl diphosphate
-
irreversible
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
ATP
-
partial
beta-Diethylaminoethyldiphenylpropylacetate hydrochloride
-
i.e. SKF-525A
bromohydrin
-
-
dimethylallyl diphosphate
-
-
dimethylallyl diphosphate
-
-
Dimethylallyl diphosphate containing fluorine, epoxy, and ammonium function groups
-
-
-
diphosphate
-
inhibitory effect decreases in the order of isomerases I, II, III, and IV
diphosphate
Claviceps sp., Gallus gallus
-
-
EDTA
-, P50740
addditon of 5mM EDTA results in almost complete loss of activity
epoxide of isopentenyl diphosphate
-
-
farnesyl diphosphate
Claviceps sp., Gallus gallus
-
-
geranyl diphosphate
-
-
geranyl diphosphate
-
-
geranyl diphosphate
Claviceps sp., Gallus gallus
-
-
geranyl diphosphate
Cinchona robusta
-
-
geranyl monophosphate
-
-
iodoacetamide
Cucurbita sp.
-
-
iodoacetamide
-
-
iodoacetamide
-
inhibitory effect decreases in the order of isomerases I, II, III, no inhibition of isomerase IV
iodoacetic acid
-
-
iodoacetic acid
Claviceps sp.
-
-
iodoacetic acid
-
-
Isoamyl diphosphate
-
competitive
Isopentenyl diphosphates containing fluorine, epoxy, and ammonium functional groups
-
-
-
KH2PO4
-
-
Linaloyl diphosphate
-
-
Linaloyl monophosphate
-
-
Methyl diphosphate
-
competitive
Mg2+
Cinchona robusta
-
isomerase I is activated by concentrations below 1 mM of Mn2+ or Mg2+, increasing concentrations are inhibitory
Mn2+
Cinchona robusta
-
isomerase I is activated by concentrations below 1 mM of Mn2+ or Mg2+, increasing concentrations are inhibitory
Mn2+
Q13907
inhibitory at high concentrations
N,N-dimethyl-2-amino-1-ethyl diphosphate
-
transition state analogue, competitive
N,N-dimethylaminoethyl diphosphate
-
-
neryl diphosphate
-
-
Neryl monophosphate
-
-
O2
-
the overall reaction is sensitive to O2
Octyl diphosphate
-
-
p-hydroxymercuribenzoate
-
-
Sodium acetate
-
-
Terpene diphosphate esters
-
-
-
Terpene monophosphate esters
-
-
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
2-mercaptoethanol
-
activates
2-mercaptoethanol
-
activates isomerase III and IV
dithiothreitol
-
activates
dithiothreitol
-
activates
FMN
-
required as cofactor. The enzyme requires the combined presence of FMN, NADPH and Mg2+
glutathione
-
activates
L-Cysteine hydrochloride
-
activates
mevalonic acid
-
activates
Mevalonic acid lactone
-
weakly activates
NADPH
-
required as cofactor. The enzyme requires the combined presence of FMN, NADPH and Mg2+
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.017
-
dimethylallyl diphosphate
Cinchona robusta
-
isomerase I
0.0008
-
isopentenyl diphosphate
-
mutant enzyme W161F
0.001
-
isopentenyl diphosphate
Cinchona robusta
-
isomerase II
0.0013
-
isopentenyl diphosphate
-
isomerase II and III
0.0017
-
isopentenyl diphosphate
-
isomerase I
0.0025
-
isopentenyl diphosphate
-
isomerase IV
0.0027
-
isopentenyl diphosphate
-
-
0.003
-
isopentenyl diphosphate
-
mutant enzyme R83K
0.0035
-
isopentenyl diphosphate
-
wild-type enzyme
0.004
-
isopentenyl diphosphate
-
-
0.0048
-
isopentenyl diphosphate
-
aerobic, presence of NADPH, pH 7.0, 37C
0.0051
-
isopentenyl diphosphate
Cinchona robusta
-
isomerase I
0.0054
-
isopentenyl diphosphate
Claviceps sp.
-
-
0.0056
-
isopentenyl diphosphate
-
pH 7.0, 37C
0.0057
-
isopentenyl diphosphate
-
-
0.006
-
isopentenyl diphosphate
-
-
0.00714
-
isopentenyl diphosphate
-
pH 6.0, 60C, mutant enzyme E13R/R235E
0.0076
-
isopentenyl diphosphate
-
-
0.0095
-
isopentenyl diphosphate
-
wild-type, pH 7.4, 37C
0.0115
-
isopentenyl diphosphate
-
mutant enzyme E87Q
0.012
-
isopentenyl diphosphate
-
aerobic, presence of dithionite, pH 7.0, 37C
0.014
-
isopentenyl diphosphate
-
mutant enzyme K55A
0.0142
-
isopentenyl diphosphate
-
mutant Y104F, pH 7.4, 37C
0.015
-
isopentenyl diphosphate
-
mutant enzyme K55R
0.0168
-
isopentenyl diphosphate
-
anaerobic, presence of NADPH, pH 7.0, 37C
0.0185
-
isopentenyl diphosphate
-
mutant enzyme R51K
0.02
-
isopentenyl diphosphate
-
-
0.021
-
isopentenyl diphosphate
-
mutant enzyme E116Q
0.0225
-
isopentenyl diphosphate
-
mutant Y104A, pH 7.4, 37C
0.0228
-
isopentenyl diphosphate
-
pH 8.0
0.033
-
isopentenyl diphosphate
-
-
0.035
-
isopentenyl diphosphate
-
-
0.036
-
isopentenyl diphosphate
-
-
0.043
-
isopentenyl diphosphate
-
-
0.046
-
isopentenyl diphosphate
-
pH 8.0, 50C
0.0463
-
isopentenyl diphosphate
-
pH 6.0, 60C, wild-type enzyme
0.047
-
isopentenyl diphosphate
-
pH 8.0, 55C
0.063
-
isopentenyl diphosphate
P61615
pH 6.0, 60C
0.063
-
isopentenyl diphosphate
-
pH 8.0, 60C
0.064
-
isopentenyl diphosphate
-
-
0.065
-
isopentenyl diphosphate
-
pH 8.0, 70C
0.071
-
isopentenyl diphosphate
-
pH 8.0, 65C
0.077
-
isopentenyl diphosphate
-
pH 8.0, 75C
0.084
-
isopentenyl diphosphate
-
pH 8.0, 80C
0.0841
-
isopentenyl diphosphate
-
pH 6.0
0.093
-
isopentenyl diphosphate
-
pH 8.0, 90C
0.187
-
isopentenyl diphosphate
-
pH 8.0, 82.5C
0.199
-
isopentenyl diphosphate
-
pH 8.0, 87.5C
0.211
-
isopentenyl diphosphate
-
pH 8.0, 85C
0.0874
-
NADH
P61615
dehydrogenase reaction without isopentenyl diphosphate
0.0904
-
NADH
P61615
isomerase reaction
15.3
-
isopentenyl diphosphate
-
pH 7.0, 85C
additional information
-
additional information
-
substrate binds to the inactive oxidized and active reduced form of enzyme with similar affinities
-
TURNOVER NUMBER [1/s]
TURNOVER NUMBER MAXIMUM[1/s]
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.065
-
isopentenyl diphosphate
-
aerobic, presence of NADPH, pH 7.0, 37C
0.2
-
isopentenyl diphosphate
P61615
pH 6.0, 60C
0.57
-
isopentenyl diphosphate
-
aerobic, presence of dithionite, pH 7.0, 37C
0.69
-
isopentenyl diphosphate
-
anaerobic, presence of NADPH, pH 7.0, 37C
1.6
-
isopentenyl diphosphate
-
-
17.9
-
isopentenyl diphosphate
-
pH 7.0, 37C
191
-
isopentenyl diphosphate
-
pH 7.0, 85C
Ki VALUE [mM]
Ki VALUE [mM] Maximum
INHIBITOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.383
-
(Z)-3-difluoromethyl-2-buten-1-yl diphosphate
-
pH 7.0, 37C
0.012
-
(Z)-3-fluoromethyl-2-buten-1-yl diphosphate
-
pH 7.0, 37C
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 37C
-
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 37C
-
0.0565
-
3,4-epoxy-3-methylbutyl diphosphate
-
pH 7.0, 85C
0.0486
-
3,4-oxido-3-methyl-1-butyl diphosphate
-
pH 7.0, 37C
0.0074
-
3-(Fluoromethyl)-3-buten-1-yl diphosphate
-
pH 7.0, 37C
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 37C
-
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 37C
-
0.054
-
3-cyclopropyl-3-buten-1-yl diphosphate
-
pH 7.0, 37C
0.008
-
3-methylene-4-penten-1-yl diphosphate
-
pH 7.0, 37C
0.0014
-
3-oxiranyl-3-buten-1-yl diphosphate
-
pH 7.0, 37C
0.00013
-
5-deaza-FMN
-
-
IC50 VALUE [mM]
IC50 VALUE [mM] Maximum
INHIBITOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.278
-
(E/Z)-3-cyclopropyl-2-buten-1-yl diphosphate
-
25C, pH 8.6
0.1
-
3-cyclopropyl-3-buten-1-yl diphosphate
-
25C, pH 8.6
0.00114
-
3-oxiranyl-3-buten-1-yl diphosphate
-
pH 7.0, 37C
SPECIFIC ACTIVITY [µmol/min/mg]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
0.001
-
-
pyruvate, C13-labeled at positions 2 and 3, aerobic, pH 8, 37C
0.046
-
Cinchona robusta
-
-
0.08
-
-
dimethylallyl diphosphate, C13-labeled at positions 3, 4 and 5, aerobic, pH 8, 37C
0.19
-
-
dimethylallyl diphosphate, anaerobic, pH 8, 37C
0.23
-
-
dimethylallyl diphosphate, aerobic, pH 8, 37C
0.62
-
-
isopentenyl diphosphate, anaerobic, pH 8, 37C
0.63
-
-
isopentenyl diphosphate, aerobic, pH 8, 37C
1.2
-
-
pH 8.0
5.92
-
-
-
52
-
-
isoenzyme type II, isopentenyl diphosphate, pH 7.0, 37 C
73
-
-
-
3000
-
Claviceps sp.
-
-
additional information
-
-
-
additional information
-
-
-
additional information
-
-
-
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%
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
6
8.5
Claviceps sp.
-
in presence of Mg2+. A sharper maximum is observed in presence of Mn2+
6
-
-
assay at
6.3
-
-
-
6.5
7
-, P50740
-
6.6
-
-
-
7
7.8
-
isomerase I
7
8
-
isomerase II
7
-
-
in presence of Mg2+
pH RANGE
pH RANGE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
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
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
37
-
-, P50740
-
60
-
-
assay at
80
-
-
maximum activity
TEMPERATURE RANGE
TEMPERATURE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
15
55
-, P50740
-
pI VALUE
pI VALUE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
5.06
-
A9LRT7
theoretical
5.8
-
Q0QYT2
calculated
SOURCE TISSUE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
SOURCE
Cinchona robusta
-
-
Manually annotated by BRENDA team
-
in normal fibroblasts and Zellweger fibroblasts, in which the synthesis of cholesterol is impaired
Manually annotated by BRENDA team
Cucurbita sp.
-
-
Manually annotated by BRENDA team
Citrus sp.
-
-
Manually annotated by BRENDA team
Q0QYT2
in mature and tender leaf, expression is higher than in tubers
Manually annotated by BRENDA team
-
expression is highest in stems, followed by leaf, and is lowest in root
Manually annotated by BRENDA team
-, Q0MW34
expression in stem is much higher than in root and tender leaf, no expression in mature leaf
Manually annotated by BRENDA team
A9LRT7
cDNA clone of the tomato IPI gene is amplified using cDNA from young leaves as template
Manually annotated by BRENDA team
Claviceps sp.
-
-
Manually annotated by BRENDA team
Claviceps sp. SD58
-
-
-
Manually annotated by BRENDA team
-
expression is highest in stems, followed by leaf, and is lowest in root
Manually annotated by BRENDA team
-, Q0MW34
expression in stem is much higher than in root and tender leaf
Manually annotated by BRENDA team
A9LRT7
highest expression level
Manually annotated by BRENDA team
-
isoform IDI2 is only expressed in skeletal muscle
Manually annotated by BRENDA team
-
expression is highest in stems, followed by leaf, and is lowest in root
Manually annotated by BRENDA team
-, Q0MW34
expression is much higher than in root and tender leaf
Manually annotated by BRENDA team
Q0QYT2
in mature and tender leaf, expression is higher than in tubers
Manually annotated by BRENDA team
additional information
-
no activity in heart muscle
Manually annotated by BRENDA team
additional information
Q0QYT2
no expression in veins
Manually annotated by BRENDA team
additional information
-
expression may be induced by Verticillium dahliae kleb, by methyl jasmonate and salicylic acid
Manually annotated by BRENDA team
additional information
-, Q0MW34
no expression in mature leaf and fruit
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
Q38929, Q42553
enhanced green fluorescent protein fusions are found mainly in the mitochondrion
Manually annotated by BRENDA team
Q38929, Q42553
enhanced green fluorescent protein fusions are found mainly in the plastid
Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
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 HB8 / ATCC 27634 / DSM 579)
MOLECULAR WEIGHT
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
27180
-
A9LRT7
theoretical
30000
-
A9LRT7
determined by SDS-PAGE
33500
-
-
gel filtration
34000
-
-
gel filtration
35000
-
-
gel filtration
35000
-
Claviceps sp.
-
gel filtration
38460
-
-
calculated; mass spectrometry
39000
-
-
SDS-PAGE
50000
-
-
SDS-PAGE
82500
-
-
gel filtration
197000
-
A6YQV2, -
gel filtration
345000
-
-
gel filtration chromatography
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
?
-
x * 26864, calculation from nucleotide sequence
?
Cinchona robusta
-
x * 29000, isomerase I, SDS-PAGE; x * 34000, isomerase II, SDS-PAGE
?
-
x * 33350, calculation from nucleotide sequence; x * 39000-40000, SDS-PAGE
?
-
x * 21760, selenomethionyl form of the enzyme, mass spectrometry
?
-
x * 39897, mass spectrometry
?
Q0QYT2
x * 33800, calculated
?
-
x * 34390, calculated
?
-
x * 40000, SDS-PAGE
monomer
Claviceps sp.
-
1 * 35000, SDS-PAGE
monomer
-
1 * 33500, SDS-PAGE
octamer
-, P50740
8 * 45000
octamer
-
8 * 41492, calculated
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
tetramer
P61615
-
tetramer
-
4 * 48000, SDS-PAGE
tetramer
A6YQV2, -
4 * 43000, SDS-PAGE
Crystallization/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
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
-, P50740
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
-
crystal structure of free and metal-bound C67A mutant enzyme
-
crystal structure of the isomerase-bromohydrin complex
-
crystallographic investigation of phosphoantigen binding
Q46822
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
-
of wild-type and mutants Y104A, Y104F
-
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
Q13907
native enzyme at 1.7 A and in complex with substrate at 1.9 A resolution. comparison with Escherichia coli enzyme structure
Q13907
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
A6YQV2, -
crystallized at 20C 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 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
-
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
-
TEMPERATURE STABILITY
TEMPERATURE STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
37
-
Claviceps sp.
-
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
48
-
-
melting temperature of mutant Y104A
55
-
-
melting temperature of mutant Y104F
69
-
-
melting temperature of wild-type
70
-
-
1h, IDI retained 50% of the activity
80
-
A6YQV2, -
10 min, more than 90% residual activity
GENERAL STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
high susceptibility to proteolysis
Claviceps sp.
-
unstable in dilute solutions
Claviceps sp.
-
STORAGE STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
-80C, 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
-
-15C, stable for several months
-
-20C, 0.1 M potassium phosphate buffer, pH 7.0, 2 mM dithiothreitol, stable for several weeks
-
Purification/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
partial
-
2 isoforms: I and II
Cinchona robusta
-
-
Claviceps sp.
-
by affinity chromatography on Ni-NTA resin
-
DEAE Sepharose column chromatography and Resource Phe column chromatograpyh
-
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
-
on a HisTrap column, for crystallisation, the enzyme is loaded on a HiLoad 16/60 Superdex 200 column
-
recombinant enzyme
P61615
nickel-nitrilotriacetic acid affinity chromatography
-
recombinant protein, enzyme purified under aerobic conditions is inactive until the flavin cofactor is reduced by NADPH or dithionite or photochemically
-
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
expression in Escherichia coli
-
expression in Escherichia coli
-, Q0MW34
expressed in Escherichia coli
-
for expression in Escherichia coli BL21DE3 cells
-
overexpression in Escherichia coli
-
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
-
expression in Escherichia coli
-
expression in Escherichia coli
-
overexpressed in Escherichia coli
-
expression in Escherichia coli
Q0QYT2
expressed in Escherichia coli
-
expression in Escherichia coli, His6-tagged type II enzyme
-
expression in Escherichia coli
-
expression in Escherichia coli
A6YQV2, -
expression in Escherichia coli
-
overexpression in Escherichia coli
-
expression in Escherichia coli
-
into the vector pMD18-T for sequencing, and subsequently into pET-28a+ for expression in Escherichia coli BL21DE3 cells
A9LRT7
expression in Escherichia coli
P61615
into a pET-vector for expression in Escherichia coli Bl21DE3 cells
-
recombinantly expressed with a polyhistidine tag at its N terminus in Escherichia coli BL21
-
expression in Escherichia coli strain JMSB0373a
-
expression in Escherichia coli strain BL21(DE3)
-
expressed in Escherichia coli
-
expression in Escherichia coli
-
ENGINEERING
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
C67A
-
inactive mutant enzyme
E116Q
-
the ratio of maximal velocity to turnover number is 0.09%% of that of the wild-type enzyme
E116Q
-
inactive mutant enzyme
E87Q
-
the ratio of maximal velocity to turnover number is 0.07% of that of the wild-type enzyme
E87Q
-
inactive mutant enzyme
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
Q154N
-
active site mutant
D216A
-
mutation of highly conserved residue
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
E161A
-
mutation of highly conserved residue
E194A
-
mutation of highly conserved residue
E229A
-
mutation of highly conserved residue
H11A
-
mutation of highly conserved residue
H155A
-
mutation of highly conserved residue
K193A
-
mutation of highly conserved residue
K8A
-
mutation of highly conserved residue
N125A
-
mutation of highly conserved residue
N157A
-
mutation of highly conserved residue
Q160A
-
mutation of highly conserved residue
R232A
-
mutation of highly conserved residue
R7A
-
mutation of highly conserved residue
S96A
-
mutation of highly conserved residue
T68A
-
mutation of highly conserved residue
additional information
Q38929, Q42553
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
Q38929, Q42553
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
-, Q0MW34
functional expression in engineered Escherichia coli restores the carotenoid pathway
Y104F
-
0.1% of wild-type activity. Crystallization data. General fold of enzyme is similar to wild-type
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
Q0QYT2
recombinant expression in Escherichia coli. Gene IBI can take the role of Arabidopsis thaliana IDI to produce the orange beta-carotene
Renatured/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
reconstitution of metal-free enzyme with Mg2+, Mn2+, Zn2+, Co2+, Ni2+ or Cd2+ generates active enzyme
-
reconstitution of apo-enzyme with 5-deaza-FMN results in an inactive enzyme, whereas reconstitution with 1-deaza-FMN leads to full recovery of activity
-
enzyme purified under aerobic conditions is inactive until the flavin cofactor is reduced by NADPH or dithionite or photochemically
-
APPLICATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
biotechnology
-
the prenyl alcohol production by Escherichia coli transformants with overexpression of isoprenoid biosynthesis genes is examined
biotechnology
-
an Escherichia coli strain is engineered for isoprenoid ether lipid biosynthesis through digeranylgeranylglycerylphosphate, DGGGP
industry
-
over-expression of isopentenyl diphosphate isomerase and 1-deoxy-D-xylulose 5-phosphate synthase in combination with heterologous expression of squalene/phytoene synthase and farnesyl diphosphate synthase of Streptomyces peucetius in Escherichia coli facilitates the synthesis of the industrially important compound squalene
synthesis
-
expression of the genes in E. coli is a useful method for maximizing the production of industrially valuable isoprenoids
synthesis
-
with the combination of the proper substrates and the enzymes farnesyl diphosphate synthetase and isopentenyl-diphosphate DELTA-isomerase, it is possible to use labeled derivatives of isopentenyl diphosphate and dimethylallyl diphosphate to selectively in
biotechnology
A9LRT7
overexpression of SlIPI in engineered Escherichia coli can promote the biosynthesis of beta-carotene in bacteria, the result provides a foundation for terpenoid metabolic engineering using the SlIPI gene
synthesis
-
synthesis of polyisoprenyl diphosphates in an organic-aeqous dual-liquid phase system by trans-isoprenyl diphosphate synthase mutant Y81S and isopentenyl diphosphate isomerase