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Information on EC 5.3.3.2 - isopentenyl-diphosphate DELTA-isomerase and Organism(s) Bacillus subtilis and UniProt Accession P50740

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EC Tree
     5 Isomerases
         5.3 Intramolecular oxidoreductases
             5.3.3 Transposing C=C bonds
                5.3.3.2 isopentenyl-diphosphate DELTA-isomerase
IUBMB 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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Bacillus subtilis
UNIPROT: P50740
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The taxonomic range for the selected organisms is: Bacillus subtilis
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Synonyms
ipp isomerase, isopentenyl diphosphate isomerase, idi-2, isopentenyl pyrophosphate isomerase, idi-1, slipi, isopentenyl-diphosphate delta-isomerase, isopentenyl diphosphate:dimethylallyl diphosphate isomerase, type 2 isopentenyl diphosphate isomerase, type 2 isopentenyl diphosphate:dimethylallyl diphosphate isomerase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
isopentenyl diphosphate:dimethylallyl diphosphate isomerase
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IPP isomerase
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IPP-isomerase
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IPPI1
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IPPI2
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Isomerase, isopentenylpyrophosphate DELTA-
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Isopententenyl diphosphate:dimethylallyl diphosphate isomerase
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Isopentenyl pyrophosphate isomerase
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Isopentenyl pyrophosphate isomerase:dimethylallyl pyrophosphate isomerase
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Isopentenyldiphosphate DELTA-isomerase
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Isopentenylpyrophosphate isomerase
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Methylbutenylpyrophosphate isomerase
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-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
isomerization
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-
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intramolecular oxidoreduction
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-
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PATHWAY SOURCE
PATHWAYS
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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.
CAS REGISTRY NUMBER
COMMENTARY hide
9033-27-6
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
isopentenyl diphosphate
dimethylallyl diphosphate
show the reaction diagram
-
-
-
r
isopentenyl diphosphate
dimethylallyl diphosphate
show the reaction diagram
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-
-
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r
pyruvate
lactate
show the reaction diagram
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-
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-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
NADPH
maximal acitivity with 1 mM NADPH
FMN
-
required under aerobic and anaerobic conditions
NADH
-
or NADPH required under aerobic, not under anaerobic conditions
NADPH
-
or NADH required under aerobic, not under anaerobic conditions
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ca2+
lower activity as with Mg2+
Mg2+
maximal acitivity
Mn2+
lower activity as with Mg2+
Ca2+
-
10mM, relative activity 100%
Co2+
-
10mM, relative activity under 0.005%
Cu2+
-
10mM, relative activity under 0.005%
Mg2+
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10mM, relative activity 65%
Mn2+
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10mM, relative activity 17%
Ni2+
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10mM, relative activity under 0.005%
Zn2+
-
10mM, relative activity 0.2%
additional information
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
EDTA
addditon of 5mM EDTA results in almost complete loss of activity
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.001
-
pyruvate, C13-labeled at positions 2 and 3, aerobic, pH 8, 37°C
0.08
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dimethylallyl diphosphate, C13-labeled at positions 3, 4 and 5, aerobic, pH 8, 37°C
0.19
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dimethylallyl diphosphate, anaerobic, pH 8, 37°C
0.23
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dimethylallyl diphosphate, aerobic, pH 8, 37°C
0.62
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isopentenyl diphosphate, anaerobic, pH 8, 37°C
0.63
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isopentenyl diphosphate, aerobic, pH 8, 37°C
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
45000
8 * 45000
38460
39000
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SDS-PAGE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
octamer
8 * 45000
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
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Steinbacher, S.; Kaiser, J.; Gerhardt, S.; Eisenreich, W.; Huber, R.; Bacher, A.; Rohdich, F.
Crystal structure of the type II isopentenyl diphosphate:dimethylallyl diphosphate isomerase from Bacillus subtilis
J. Mol. Biol.
329
973-982
2003
Bacillus subtilis (P50740), Bacillus subtilis
Manually annotated by BRENDA team
Takagi, M.; Kaneda, K.; Shimizu, T.; Hayakawa, Y.; Seto, H.; Kuzuyama, T.
Bacillus subtilis ypgA gene is fni, a nonessential gene encoding type 2 isopentenyl diphosphate isomerase
Biosci. Biotechnol. Biochem.
68
132-137
2004
Bacillus subtilis (P50740), Bacillus subtilis
Manually annotated by BRENDA team
Laupitz, R.; Hecht, S.; Amslinger, S.; Zepeck, F.; Kaiser, J.; Richter, G.; Schramek, N.; Steinbacher, S.; Huber, R.; Arigoni, D.; Bacher, A.; Eisenreich, W.; Rohdich, F.
Biochemical characterization of Bacillus subtilis type II isopentenyl diphosphate isomerase, and phylogenetic distribution of isoprenoid biosynthesis pathways
Eur. J. Biochem.
271
2658-2669
2004
Bacillus subtilis
Manually annotated by BRENDA team