5.3.3.2: isopentenyl-diphosphate DELTA-isomerase

This is an abbreviated version!
For detailed information about isopentenyl-diphosphate DELTA-isomerase, go to the full flat file.

Reaction

Synonyms

fcd1, FNI, IDI, IDI-1, Idi-2, IDI1, IDP isomerase, IPI, IPI1, IPP isomerase, IPP-isomerase, IPP:DMAPP, IPPI, IPPI1, IPPI2, IPPISOM, Isomerase, isopentenylpyrophosphate DELTA-, Isopententenyl diphosphate:dimethylallyl diphosphate isomerase, isopentenyl diphosphate isomerase, isopentenyl diphosphate isomerase 1, 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, SlIPI, type 1 IPP isomerase, type 2 isopentenyl diphosphate isomerase, type 2 isopentenyl diphosphate: dimethylallyl diphosphate isomerase, type 2 isopentenyl diphosphate:dimethylallyl diphosphate isomerase, type 2 isopentenyl-diphosphate isomerase, type I isopentenyl diphosphate isomerase, type II isopentenyl diphosphate isomerase, type II isopentenyl diphosphate:dimethylallyl diphosphate isomerase, type-2 isopentenyl diphosphate isomerase, type-I isopentenyl pyrophosphate isomerase

ECTree

     5 Isomerases

         5.3 Intramolecular oxidoreductases

             5.3.3 Transposing C=C bonds

                5.3.3.2 isopentenyl-diphosphate DELTA-isomerase

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Results	in table
10	Activating Compound
23028	AA Sequence
9	Application
1	CAS Registry Number
44	Cloned(Commentary)
31	Cofactor
20	Crystallization (Commentary)
10	Disease/ Diagnostics
2	Expression
7	General Information
2	General Stability
13	IC50 Value
127	Inhibitors
8	kcat/KM [mM/s]
17	Ki Value [mM]
76	KM Value [mM]
21	Localization
83	Metals/Ions
35	Molecular Weight [Da]
40	Natural Substrates/ Products (Substrates)
125	Organism
15	Pathway
96	PDB ID
16	pH Optimum
3	pH Range
9	pI Value
63	Protein Variants
36	Purification (Commentary)
6	Reaction
8	Reaction Type
117	Reference
3	Renatured (Commentary)
66	Source Tissue
36	Specific Activity [micromol/min/mg]
3	Storage Stability
114	Substrates and Products (Substrate)
33	Subunits
90	Synonyms
1	Systematic Name
7	Temperature Optimum [°C]
2	Temperature Range [°C]
6	Temperature Stability [°C]
23	Turnover Number [1/s]

Cofactor

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Cofactor on EC 5.3.3.2 - isopentenyl-diphosphate DELTA-isomerase

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COFACTOR

ORGANISM

UNIPROT

COMMENTARY

LITERATURE

IMAGE

FMN

16 entries

FMNH2

2 entries

NAD(P)H

3 entries

NADH

Bacillus subtilis

-

or NADPH required under aerobic, not under anaerobic conditions

661638

NADPH

8 entries

additional information

Saccharolobus shibatae

-

IDI showed almost the same activity in the presence of NADH or dithionite. Data indicate that the reduced form of FMN is sufficient

660882

-

FMN

Staphylococcus aureus

-

-

746921

FMN

Streptococcus pneumoniae

-

-

747106

FMN

Synechocystis sp.

-

-

662026

FMN

Thermococcus kodakarensis

-

-

660902

FMN

Saccharolobus shibatae

P61615

-

704638

FMN

Saccharolobus shibatae

P61615

strictly dependent on

651170

FMN

Bacillus subtilis

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

652916

FMN

Bacillus subtilis

P50740

maximal activity with 10 microM FMN

661357

FMN

Saccharolobus shibatae

-

nearly no activity with the flavin analogue 5-deazaFMN

660882

FMN

Bacillus subtilis

-

required under aerobic and anaerobic conditions

661638

FMN

Staphylococcus aureus

-

FMN must be in reduced state to be catalytically active

678309

FMN

Thermus thermophilus

-

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

678278

FMN

Thermus thermophilus

-

IDI-2 requires reduced flavin

714202

FMN

Methanocaldococcus jannaschii

-

required, IDI-2 reconstituted with cofactor analogues such as 5-deaza-FMN show no activity

713655

FMN

Staphylococcus aureus

-

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

715286

FMN

Saccharolobus shibatae

P61615

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

728667

FMNH2

Streptococcus pneumoniae

-

-

747099

FMNH2

Streptococcus pneumoniae

B2ILS5

-

747530

NAD(P)H

Saccharolobus shibatae

P61615

required

651170

NAD(P)H

Saccharolobus shibatae

-

proposed mechanism: reduction of FMN

660882

NAD(P)H

Saccharolobus shibatae

P61615

used only for the reduction of FMN, can be replaced with Na2S2O4

704638

NADPH

Staphylococcus aureus

-

-

746921

NADPH

Thermus thermophilus

-

-

714202

NADPH

Synechocystis sp.

-

-

662026

NADPH

Thermococcus kodakarensis

-

-

660902

NADPH

Bacillus subtilis

P50740

maximal acitivity with 1 mM NADPH

661357

NADPH

Bacillus subtilis

-

or NADH required under aerobic, not under anaerobic conditions

661638

NADPH

Staphylococcus aureus

-

needed only in catalytic amounts to activate the enzyme for multiple turnovers. Hydride transfer from NADPH to reduce FMN is pro-S stereospecific

678309

NADPH

Thermus thermophilus

-

required for reductive activation of inactive oxidized enzyme. Kd value is 0.11 mM at pH 7.0, 37°C

678278