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Information on EC 5.3.3.2 - isopentenyl-diphosphate DELTA-isomerase and Organism(s) Saccharolobus shibatae and UniProt Accession P61615

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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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Saccharolobus shibatae
UNIPROT: P61615
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Word Map
The taxonomic range for the selected organisms is: Saccharolobus shibatae
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 isomerase
-
isopentenyl diphosphate:dimethylallyl diphosphate isomerase
-
type 2 isopentenyl diphosphate isomerase
-
type 2 isopentenyl-diphosphate isomerase
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IPP isomerase
-
-
-
-
IPP-isomerase
-
-
-
-
IPPI1
-
-
-
-
IPPI2
-
-
-
-
Isomerase, isopentenylpyrophosphate DELTA-
-
-
-
-
Isopententenyl diphosphate:dimethylallyl diphosphate isomerase
-
-
-
-
Isopentenyl pyrophosphate isomerase
-
-
-
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Isopentenyl pyrophosphate isomerase:dimethylallyl pyrophosphate isomerase
-
-
-
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Isopentenyldiphosphate DELTA-isomerase
-
-
-
-
Isopentenylpyrophosphate isomerase
-
-
-
-
Methylbutenylpyrophosphate isomerase
-
-
-
-
type-2 isopentenyl diphosphate isomerase
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
isomerization
-
-
-
-
intramolecular oxidoreduction
-
-
-
-
PATHWAY SOURCE
PATHWAYS
-
-, -, -, -, -, -, -, -, -, -
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
-
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
isopentenyl diphosphate
dimethylallyl diphosphate
show the reaction diagram
additional information
?
-
NATURAL SUBSTRATE
NATURAL 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
isopentenyl diphosphate
dimethylallyl diphosphate
show the reaction diagram
-
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
NAD(P)H
FMN
-
nearly no activity with the flavin analogue 5-deazaFMN
NAD(P)H
-
proposed mechanism: reduction of FMN
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
COMMENTARY hide
LITERATURE
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
3-methylene-4-penten-1-yl diphosphate
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-oxiranyl-3-buten-1-yl diphosphate
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
irreversible inhibition
3-oxiranyl-3-buten-1-yl diphosphate
irreversible inhibition
5-deaza-FMN
-
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0015 - 0.063
isopentenyl diphosphate
0.0874 - 0.0904
NADH
0.00152 - 0.0841
isopentenyl diphosphate
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.000197 - 0.2
isopentenyl diphosphate
197 - 29900
isopentenyl diphosphate
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.031 - 4.05
isopentenyl diphosphate
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00013
5-deaza-FMN
-
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
IDI2_SACSH
368
0
40427
Swiss-Prot
-
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
Q160E
10-fold decrease in kcat/Km
Q160H
23-fold decrease in kcat/Km
Q160K
130-fold decrease in kcat/Km
Q160L
28-fold decrease in kcat/Km
Q160N
150-fold decrease in kcat, kcat/Km decreases 66-fold
R232A
mutation of highly conserved residue
R7A
mutation of highly conserved residue
S96A
mutation of highly conserved residue
T68A
mutation of highly conserved residue
Q160E
the mutant shows a 10fold decrease in kcat/Km
Q160H
the mutant shows a 23fold decrease in kcat/Km
Q160K
the mutant shows a 130fold decrease in kcat/Km
Q160L
the mutant shows a 28fold decrease in kcat/Km
Q160N
the mutant shows a 150fold decrease in kcat, although kcat/Km only decreases 66fold
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
on a HisTrap column, for crystallisation, the enzyme is loaded on a HiLoad 16/60 Superdex 200 column
recombinant enzyme
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
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
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Yamashita, S.; Hemmi, H.; Ikeda, Y.; Nakayama, T.; Nishino, T.
Type 2 isopentenyl diphosphate isomerase from a thermoacidophilic archaeon Sulfolobus shibatae
Eur. J. Biochem.
271
1087-1093
2004
Saccharolobus shibatae (P61615), Saccharolobus shibatae
Manually annotated by BRENDA team
Hemmi, H.; Ikeda, Y.; Yamashita, S.; Nakayama, T.; Nishino, T.
Catalytic mechanism of type 2 isopentenyl diphosphate:dimethylallyl diphosphate isomerase: verification of a redox role of the flavin cofactor in a reaction with no net redox change
Biochem. Biophys. Res. Commun.
322
905-910
2004
Saccharolobus shibatae
Manually annotated by BRENDA team
Unno, H.; Yamashita, S.; Ikeda, Y.; Sekiguchi, S.Y.; Yoshida, N.; Yoshimura, T.; Kusunoki, M.; Nakayama, T.; Nishino, T.; Hemmi, H.
New role of flavin as a general acid-base catalyst with no redox function in type 2 isopentenyl-diphosphate isomerase
J. Biol. Chem.
284
9160-9167
2009
Saccharolobus shibatae (P61615), Saccharolobus shibatae
Manually annotated by BRENDA team
Nakatani, H.; Goda, S.; Unno, H.; Nagai, T.; Yoshimura, T.; Hemmi, H.
Substrate-induced change in the quaternary structure of type 2 isopentenyl diphosphate isomerase from Sulfolobus shibatae
J. Bacteriol.
194
3216-3224
2012
Saccharolobus shibatae (P61615), Saccharolobus shibatae
Manually annotated by BRENDA team
Nagai, T.; Unno, H.; Janczak, M.W.; Yoshimura, T.; Poulter, C.D.; Hemmi, H.
Covalent modification of reduced flavin mononucleotide in type-2 isopentenyl diphosphate isomerase by active-site-directed inhibitors
Proc. Natl. Acad. Sci. USA
108
20461-20466
2011
Saccharolobus shibatae, Saccharolobus shibatae (P61615)
Manually annotated by BRENDA team