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Information on EC 5.3.3.2 - isopentenyl-diphosphate DELTA-isomerase and Organism(s) Escherichia coli and UniProt Accession Q46822

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     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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Escherichia coli
UNIPROT: Q46822
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Word Map
The taxonomic range for the selected organisms is: Escherichia coli
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
IPP isomerase
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isopentenyl diphosphate isomerase
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IPP isomerase
-
-
-
-
IPP-isomerase
-
-
-
-
IPP:DMAPP
-
-
IPPI1
-
-
-
-
IPPI2
-
-
-
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Isomerase, isopentenylpyrophosphate DELTA-
-
-
-
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Isopententenyl diphosphate:dimethylallyl diphosphate isomerase
-
-
-
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isopentenyl diphosphate isomerase
-
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Isopentenyl pyrophosphate isomerase
-
-
-
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Isopentenyl pyrophosphate isomerase:dimethylallyl pyrophosphate isomerase
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-
-
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Isopentenyldiphosphate DELTA-isomerase
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-
-
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Isopentenylpyrophosphate isomerase
-
-
-
-
Methylbutenylpyrophosphate isomerase
-
-
-
-
type I isopentenyl diphosphate isomerase
-
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
Isopentenyl diphosphate = dimethylallyl diphosphate
show the reaction diagram
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
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
isomerization
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isomerization
intramolecular oxidoreduction
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-
-
-
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
-
-
-
-
?
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
Cd2+
-
reconstitution of metal-free enzyme with Mg2+, Mn2+, Zn2+, Co2+, Ni2+ or Cd2+ generates active enzyme
Co2+
-
reconstitution of metal-free enzyme with Mg2+, Mn2+, Zn2+, Co2+, Ni2+ or Cd2+ generates active enzyme
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
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(N,N-dimethylamino)-1-ethyl diphosphate
-
transition state analogue
2,3-butadien-1-yl diphosphate
-
competitive inhibitor
3,4-epoxy-3-methyl-1-butyl diphosphate
-
-
3-butyn-1-yl diphosphate
-
competitive inhibitor
bromohydrin
-
-
epoxide of isopentenyl diphosphate
-
-
N,N-dimethylaminoethyl diphosphate
-
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0008 - 0.0225
isopentenyl diphosphate
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
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
0.049
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
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.9
isoelectric focusing
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
metabolism
IPP isomerase activity is a rate-limiting step in terpenoid synthesis
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
24500
x * 24500, SDS-PAGE
21760
-
x * 21760, selenomethionyl form of the enzyme, mass spectrometry
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
x * 24500, SDS-PAGE
?
-
x * 21760, selenomethionyl form of the enzyme, mass spectrometry
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
crystallographic investigation of phosphoantigen binding
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
of wild-type and mutants Y104A, Y104F
crystal structure of the isomerase-bromohydrin complex
-
crystals soaked with transition state analogue (N,N-dimethylamino)-1-ethyl diphosphate
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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 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
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C67A
inactive mutant enzyme
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
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
E116Q
-
inactive mutant enzyme
E87Q
-
inactive mutant enzyme
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
48
melting temperature of mutant Y104A
55
melting temperature of mutant Y104F
69
melting temperature of wild-type
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
by affinity chromatography on Ni-NTA resin
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
expressed in Escherichia coli
-
for expression in Escherichia coli BL21DE3 cells
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overexpression in Escherichia coli
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RENATURED/Commentary
ORGANISM
UNIPROT
LITERATURE
reconstitution of metal-free enzyme with Mg2+, Mn2+, Zn2+, Co2+, Ni2+ or Cd2+ generates active enzyme
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
biotechnology
an Escherichia coli strain is engineered for isoprenoid ether lipid biosynthesis through digeranylgeranylglycerylphosphate, DGGGP
biotechnology
-
the prenyl alcohol production by Escherichia coli transformants with overexpression of isoprenoid biosynthesis genes is examined
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
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Oudjama, Y.; Durbecq, V.; Sainz, G.; Clantin, B.; Tricot, C.; Stalon, V.; Villeret, V.; Droogmans, L.
Preliminary structural studies of Escherichia coli isopentenyl diphosphate isomerase
Acta Crystallogr. Sect. D
57
287-288
2001
Escherichia coli
Manually annotated by BRENDA team
Durbecq, V.; Sainz, G.; Oudjama, Y.; Clantin, B.; Bompard-Gilles, C.; Tricot, C.; Caillet, J.; Stalon, V.; Droogmans, L.; Villeret, V.
Crystal structure of isopentenyl diphosphate:dimethylallyl diphosphate isomerase
EMBO J.
20
1530-1537
2001
Escherichia coli (Q46822), Escherichia coli
Manually annotated by BRENDA team
Wouters, J.; Oudjama, Y.; Ghosh, S.; Stalon, V.; Droogmans, L.; Oldfield, E.
Structure and mechanism of action of isopentenylpyrophosphate-dimethylallylpyrophosphate isomerase
J. Am. Chem. Soc.
125
3198-3199
2003
Escherichia coli
Manually annotated by BRENDA team
Carrigan, C.N.; Poulter, C.D.
Zinc is an essential cofactor for type I isopentenyl diphosphate:dimethylallyl diphosphate isomerase
J. Am. Chem. Soc.
125
9008-9009
2003
Escherichia coli
Manually annotated by BRENDA team
Wouters, J.; Oudjama, Y.; Barkley, S.J.; Tricot, C.; Stalon, V.; Droogmans, L.; Poulter, C.D.
Catalytic mechanism of Escherichia coli isopentenyl diphosphate isomerase involves Cys-67, Glu-116, and Tyr-104 as suggested by crystal structures of complexes with transition state analogues and irreversible inhibitors
J. Biol. Chem.
278
11903-11908
2003
Escherichia coli (Q46822), Escherichia coli
Manually annotated by BRENDA team
Wouters, J.; Oudjama, Y.; Stalon, V.; Droogmans, L.; Poulter, C.D.
Crystal structure of the C67A mutant of isopentenyl diphosphate isomerase complexed with a mechanism-based irreversible inhibitor
Proteins
54
216-221
2004
Escherichia coli
Manually annotated by BRENDA team
Wouters, J.; Yin, F.; Song, Y.; Zhang, Y.; Oudjama, Y.; Stalon, V.; Droogmans, L.; Morita, C.T.; Oldfield, E.
A crystallographic investigation of phosphoantigen binding to isopentenyl pyrophosphate/dimethylallyl pyrophosphate isomerase
J. Am. Chem. Soc.
127
536-537
2005
Escherichia coli (Q46822)
Manually annotated by BRENDA team
Lee, S.; Poulter, C.D.
Escherichia coli type I isopentenyl diphosphate isomerase: structural and catalytic roles for divalent metals
J. Am. Chem. Soc.
128
11545-11550
2006
Escherichia coli
Manually annotated by BRENDA team
de Ruyck, J.; Durisotti, V.; Oudjama, Y.; Wouters, J.
Structural role for Tyr-104 in Escherichia coli isopentenyl-diphosphate isomerase: site-directed mutagenesis, enzymology, and protein crystallography
J. Biol. Chem.
281
17864-17869
2006
Escherichia coli (Q46822), Escherichia coli
Manually annotated by BRENDA team
de Ruyck, J.; Oudjama, Y.; Wouters, J.
Monoclinic form of isopentenyl diphosphate isomerase: a case of polymorphism in biomolecular crystals
Acta Crystallogr. Sect. F
F64
239-242
2008
Escherichia coli (Q46822)
Manually annotated by BRENDA team
Ghimire, G.P.; Lee, H.C.; Sohng, J.K.
Improved squalene production via modulation of the methylerythritol 4-phosphate pathway and heterologous expression of genes from Streptomyces peucetius ATCC 27952 in Escherichia coli
Appl. Environ. Microbiol.
75
7291-7293
2009
Escherichia coli
Manually annotated by BRENDA team
Ohto, C.; Muramatsu, M.; Obata, S.; Sakuradani, E.; Shimizu, S.
Prenyl alcohol production by expression of exogenous isopentenyl diphosphate isomerase and farnesyl diphosphate synthase genes in Escherichia coli
Biosci. Biotechnol. Biochem.
73
186-188
2009
Escherichia coli
Manually annotated by BRENDA team
Lai, D.; Lluncor, B.; Schroeder, I.; Gunsalus, R.P.; Liao, J.C.; Monbouquette, H.G.
Reconstruction of the archaeal isoprenoid ether lipid biosynthesis pathway in Escherichia coli through digeranylgeranylglyceryl phosphate
Metab. Eng.
11
184-191
2009
Escherichia coli (Q46822)
Manually annotated by BRENDA team
Sharma, N.K.; Pan, J.J.; Poulter, C.D.
Type II isopentenyl diphosphate isomerase: probing the mechanism with alkyne/allene diphosphate substrate analogues
Biochemistry
49
6228-6233
2010
Escherichia coli, Thermus thermophilus
Manually annotated by BRENDA team
Berthelot, K.; Estevez, Y.; Deffieux, A.; Peruch, F.
Isopentenyl diphosphate isomerase: A checkpoint to isoprenoid biosynthesis
Biochimie
94
1621-1634
2012
Homo sapiens (Q13907), Escherichia coli (Q46822)
Manually annotated by BRENDA team