Information on EC 1.17.7.1 - (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase

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

EC NUMBER
COMMENTARY
1.17.7.1
-
RECOMMENDED NAME
GeneOntology No.
(E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + H2O + 2 oxidized ferredoxin = 2-C-methyl-D-erythritol 2,4-cyclodiphosphate + 2 reduced ferredoxin
show the reaction diagram
-
-
-
-
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + H2O + 2 oxidized ferredoxin = 2-C-methyl-D-erythritol 2,4-cyclodiphosphate + 2 reduced ferredoxin
show the reaction diagram
reaction mechanism modelling, overview
-
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
oxidation
-
-
-
-
redox reaction
-
-
-
-
reduction
-
-
-
-
PATHWAY
KEGG Link
MetaCyc Link
Biosynthesis of secondary metabolites
-
Metabolic pathways
-
methylerythritol phosphate pathway
-
Terpenoid backbone biosynthesis
-
SYSTEMATIC NAME
IUBMB Comments
(E)-4-hydroxy-3-methylbut-2-en-1-yl-diphosphate:oxidized ferredoxin oxidoreductase
An iron-sulfur protein that contains a [4Fe-4S] cluster [1,2]. Forms, in the reverse direction, part of an alternative non-mevalonate pathway for isoprenoid biosynthesis that is found in most bacteria and in plant chloroplasts [4]. The enzyme from the plant Arabidopsis thaliana is active with photoreduced 5-deazaflavin but not with the flavodoxin/flavodoxin reductase/NADPH system that can be used as an electron donor by Escherichia coli [2]. Metabolites derived from isoprenoids play important roles in systems such as electron transport, photosynthesis, plant defense responses, hormonal regulation of development and membrane fluidity [1].
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
(E)-4-hydroxy-3-methylbut-2-enyl diphosphate synthase
-
-
1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate-synthase
-
-
GCEP
Solanum lycopersicum Mill.
-
-
-
GcpE
-
-
-
-
gcpE gene product
-
-
-
-
HDS
Solanum lycopersicum Mill.
-
-
-
hydroxymethylbutenyl 4-diphosphate synthase
-
-
hydroxymethylbutenyl 4-diphosphate synthase
Solanum lycopersicum Mill.
-
-
-
IspG protein
-
-
-
-
IspG-protein
-
-
CAS REGISTRY NUMBER
COMMENTARY
398144-56-4
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
gene ispG
-
-
Manually annotated by BRENDA team
gene ispG
-
-
Manually annotated by BRENDA team
Solanum lycopersicum Mill.
Mill.
-
-
Manually annotated by BRENDA team
; gene gcpE
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
metabolism
-
(E)-4-hydroxy-3-methylbut-2-enyl diphosphate synthase converts 2-C-methyl-D-erythritol-2,4-cyclodiphosphate into (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate in the penultimate step of the methyl-erythritol phosphate pathway for isoprene biosynthesis, pathway overview
physiological function
-
GcpE/IspG converts 2-C-methyl-D-erythritol-2,4-cyclodiphosphate into (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate for isoprene biosynthesis
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2-C-methyl-D-erythritol 2,4-cyclodiphosphate + dithionite
(E)-4-hydroxy-3-methylbut-2-enyl diphosphate + H2O + ?
show the reaction diagram
-
-
-
-
?
2-C-methyl-D-erythritol 2,4-cyclodiphosphate + dithionite
(E)-4-hydroxy-3-methylbut-2-enyl diphosphate + H2O + ?
show the reaction diagram
Q84GJ3, -
reaction in presence of dithionite as reductant
-
-
?
2-C-methyl-D-erythritol 2,4-cyclodiphosphate + protein-diol
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + H2O + protein disulfide
show the reaction diagram
-
-
-
?
2-C-methyl-D-erythritol 2,4-cyclodiphosphate + protein-diol
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + H2O + protein disulfide
show the reaction diagram
-
-
-
-
?
2-C-methyl-D-erythritol 2,4-cyclodiphosphate + protein-diol
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + H2O + protein disulfide
show the reaction diagram
P62620
-
-
?
2-C-methyl-D-erythritol 2,4-cyclodiphosphate + protein-diol
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + H2O + protein disulfide
show the reaction diagram
-
the enzyme is involved in deoxyxylulose phosphate pathway of isoprenoid biosynthesis
-
-
?
2-C-methyl-D-erythritol 2,4-cyclodiphosphate + protein-diol
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + H2O + protein disulfide
show the reaction diagram
Q84GJ3, -
part of an alternative, nonmevalonate pathway for terpenoid biosynthesis
-
?
2-C-methyl-D-erythritol 2,4-cyclodiphosphate + protein-diol
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + H2O + protein disulfide
show the reaction diagram
-
involved in carotenoid biosynthesis
-
-
?
2-C-methyl-D-erythritol 2,4-cyclodiphosphate + protein-diol
(E)-4-hydroxy-3-methylbut-2-en-1-yl 4-diphosphate + H2O + protein disulfide
show the reaction diagram
-
-, involved in carotenoid biosynthesisduring fruit ripening
-
-
?
2-C-methyl-D-erythritol 2,4-cyclodiphosphate + protein-diol
(E)-4-hydroxy-3-methylbut-2-en-1-yl 4-diphosphate + H2O + protein disulfide
show the reaction diagram
Solanum lycopersicum Mill.
-
-, involved in carotenoid biosynthesisduring fruit ripening
-
-
?
2-C-methyl-D-erythritol 2,4-cyclodiphosphate + reduced deazaflavin
(E)-4-hydroxy-3-methylbut-2-enyl diphosphate + H2O + oxidized deazaflavin
show the reaction diagram
-
-
-
-
?
2-C-methyl-D-erythritol 2,4-cyclodiphosphate + reduced ferredoxin
(E)-4-hydroxy-3-methylbut-2-enyl diphosphate + H2O + oxidized ferredoxin
show the reaction diagram
-
flavodoxin serves best as electron donor
-
-
?
2-C-methyl-D-erythritol 2,4-cyclodiphosphate + reduced flavodoxin
(E)-4-hydroxy-3-methylbut-2-enyl diphosphate + H2O + oxidized flavodoxin
show the reaction diagram
-
flavodoxin serves best as electron donor
-
-
?
2-C-methyl-D-erythritol-2,4-cyclodiphosphate + protein dithiol
(E)-4-hydroxy-3-methylbut-2-enyl diphosphate + H2O + protein-disulfide
show the reaction diagram
-
-, the penultimate step in the 1-deoxy-D-xylulose 5-phosphate pathway for isoprene biosynthesis, overview
-
-
?
2-C-methyl-D-erythritol-2,4-cyclodiphosphate + reduced dithionite
(E)-4-hydroxy-3-methyl-but-2-enyl diphosphate + dithionite
show the reaction diagram
-
for a full conversion, the presence of only the artificial electron donor dithionite is sufficient. GcpE/IspG converts 2-C-methyl-D-erythritol-2,4-cyclodiphosphate into (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate. 2-C-methyl-D-erythritol-2,4-cyclodiphosphate is a cyclic compound and the reaction involves the opening of the ring and removal of the C3 hydroxyl group consuming a total of two electrons
-
-
?
2-C-methyl-D-erythritol-2,4-cyclodiphosphate + reduced methyl viologen
(E)-4-hydroxy-3-methyl-but-2-enyl diphosphate + methyl viologen
show the reaction diagram
-
GcpE/IspG converts 2-C-methyl-D-erythritol-2,4-cyclodiphosphate into (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate. 2-C-methyl-D-erythritol-2,4-cyclodiphosphate is a cyclic compound and the reaction involves the opening of the ring and removal of the C3 hydroxyl group consuming a total of two electrons
-
-
?
methyl-D-erythritol-2,4-cyclodiphosphate + reduced electron donor
4-hydroxy-3-methyl-butenyl diphosphate + oxidized electron donor
show the reaction diagram
-
via epoxy-4-hydroxy-3-methyl-butenyl diphosphate, overview
-
-
r
additional information
?
-
-
in Arabidopsis thaliana, electron flow from photosynthesis can directly act as reducer in the 2-C-methyl-D-erythritol 4-phosphate pathway. In the dark, the plant catalysis requires in addition of ferredoxin NADP+/ferredoxin oxido-reductase and NADPH as electron shuttle
-
-
-
additional information
?
-
-
the enzyme is a 1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate-synthase involved in the biosynthesis of ginseng saponins, overview, the enzyme is a 1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate-synthase, i.e. HMPP synthase
-
-
-
additional information
?
-
-
IspG-catalyzes reductive deoxygenation of methyl-D-erythritol-2,4-cyclodiphosphate to 4-hydroxy-3-methyl-butenyl diphosphate. IspG also can catalyze the production of MEcPP from epoxy-4-hydroxy-3-methyl-butenyl diphosphate, reversible C-O cleavage at the inactivated C2 position not only supports binding of methyl-D-erythritol-2,4-cyclodiphosphate to IspG, but also implies that C-O bond cleavage at such a inactivated C2 position occurs prior to subsequent reduction chemistries
-
-
-
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
2-C-methyl-D-erythritol 2,4-cyclodiphosphate + protein-diol
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + H2O + protein disulfide
show the reaction diagram
P62620
-
-
?
2-C-methyl-D-erythritol 2,4-cyclodiphosphate + protein-diol
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + H2O + protein disulfide
show the reaction diagram
-
the enzyme is involved in deoxyxylulose phosphate pathway of isoprenoid biosynthesis
-
-
?
2-C-methyl-D-erythritol 2,4-cyclodiphosphate + protein-diol
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + H2O + protein disulfide
show the reaction diagram
Q84GJ3, -
part of an alternative, nonmevalonate pathway for terpenoid biosynthesis
-
?
2-C-methyl-D-erythritol 2,4-cyclodiphosphate + protein-diol
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + H2O + protein disulfide
show the reaction diagram
-
involved in carotenoid biosynthesis
-
-
?
2-C-methyl-D-erythritol 2,4-cyclodiphosphate + protein-diol
(E)-4-hydroxy-3-methylbut-2-en-1-yl 4-diphosphate + H2O + protein disulfide
show the reaction diagram
Solanum lycopersicum, Solanum lycopersicum Mill.
-
involved in carotenoid biosynthesisduring fruit ripening
-
-
?
2-C-methyl-D-erythritol-2,4-cyclodiphosphate + protein dithiol
(E)-4-hydroxy-3-methylbut-2-enyl diphosphate + H2O + protein-disulfide
show the reaction diagram
-
the penultimate step in the 1-deoxy-D-xylulose 5-phosphate pathway for isoprene biosynthesis, overview
-
-
?
2-C-methyl-D-erythritol-2,4-cyclodiphosphate + reduced dithionite
(E)-4-hydroxy-3-methyl-but-2-enyl diphosphate + dithionite
show the reaction diagram
-
for a full conversion, the presence of only the artificial electron donor dithionite is sufficient. GcpE/IspG converts 2-C-methyl-D-erythritol-2,4-cyclodiphosphate into (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate. 2-C-methyl-D-erythritol-2,4-cyclodiphosphate is a cyclic compound and the reaction involves the opening of the ring and removal of the C3 hydroxyl group consuming a total of two electrons
-
-
?
2-C-methyl-D-erythritol-2,4-cyclodiphosphate + reduced methyl viologen
(E)-4-hydroxy-3-methyl-but-2-enyl diphosphate + methyl viologen
show the reaction diagram
-
GcpE/IspG converts 2-C-methyl-D-erythritol-2,4-cyclodiphosphate into (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate. 2-C-methyl-D-erythritol-2,4-cyclodiphosphate is a cyclic compound and the reaction involves the opening of the ring and removal of the C3 hydroxyl group consuming a total of two electrons
-
-
?
additional information
?
-
-
in Arabidopsis thaliana, electron flow from photosynthesis can directly act as reducer in the 2-C-methyl-D-erythritol 4-phosphate pathway. In the dark, the plant catalysis requires in addition of ferredoxin NADP+/ferredoxin oxido-reductase and NADPH as electron shuttle
-
-
-
additional information
?
-
-
the enzyme is a 1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate-synthase involved in the biosynthesis of ginseng saponins, overview
-
-
-
additional information
?
-
-
IspG-catalyzes reductive deoxygenation of methyl-D-erythritol-2,4-cyclodiphosphate to 4-hydroxy-3-methyl-butenyl diphosphate. IspG also can catalyze the production of MEcPP from epoxy-4-hydroxy-3-methyl-butenyl diphosphate
-
-
-
COFACTOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
additional information
-
the enzyme contains a single [4Fe-4S] cluster in its active site. Characterization of the paramagnetic species present under turnover conditions by electron paramagnetic resonance, EPR, and ENDOR spectroscopies EPR, overview
-
METALS and IONS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Fe2+
-
the enzyme contains [4Fe-4S] clusters under anaerobic conditions, determination of Fe content, overview
Fe2+
-
the enzyme contains a single [4Fe-4S] cluster in its active site, determination of enzyme iron content, overview
Iron
Q84GJ3, -
the reaction is dependent on a [4Fe-4S] cluster as cofactor, which is sensitive to dioxygen and can be reduced by dithionite as an artificial one-electron donor
Iron
-
enzyme purified under exclusion of air contains solely [4Fe-4S] clusters. During the reaction an intermediate is directly bound to the active-site cluster
Iron
Q8DK70, -
[4Fe-4S]2+ cluster
Iron
-
protein contains 2.4 mol iron ions and 4.4 mol sulfide ions per mol of subunit
Iron-sulfur cluster
-
-
INHIBITORS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
additional information
-
NADH flavin oxidoreductase protein, can affect the expression level of the ispG gene
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
5-deazaflavin semiquinone radical
-
required for activity of recombinant protein
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.42
-
2-C-methyl-D-erythritol 2,4-cyclodiphosphate
Q84GJ3, -
pH 7.5, 55C
0.56
-
2-C-methyl-D-erythritol 2,4-cyclodiphosphate
-
wild-type, pH 8.0, 37C, radioassay in presence of flavodoxin, flavodoxin reductase and NADPH
0.7
-
2-C-methyl-D-erythritol 2,4-cyclodiphosphate
-
wild-type, pH 8.0, 37C, photometric assay
additional information
-
additional information
-
steady-state and pre-steady-state kinetic studies, overview
-
TURNOVER NUMBER [1/s]
TURNOVER NUMBER MAXIMUM[1/s]
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.4
-
2-C-methyl-D-erythritol 2,4-cyclodiphosphate
Q84GJ3, -
pH 7.5, 55C
SPECIFIC ACTIVITY [µmol/min/mg]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
0.074
-
-
wild-type, pH 8.0, 37C
0.16
-
-
purified and reconstituted enzyme, pH 8.0, 30C
0.6
-
Q84GJ3, -
-
160
-
-
pH 8.0, 30C, using spinach chloroplast preparation and light as electron donor system
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
7.5
8
Q84GJ3, -
-
8
-
-
assay at
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
55
-
Q84GJ3, -
-
55
-
-
assay at
SOURCE TISSUE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
SOURCE
Solanum lycopersicum Mill.
-
-
-
Manually annotated by BRENDA team
Solanum lycopersicum Mill.
-
-
-
Manually annotated by BRENDA team
Solanum lycopersicum Mill.
-
-
-
Manually annotated by BRENDA team
Solanum lycopersicum Mill.
-
-
-
Manually annotated by BRENDA team
Solanum lycopersicum Mill.
-
-
-
Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
Aquifex aeolicus (strain VF5)
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
?
-
x * 79500, SDS-PAGE
Purification/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
recombinant protein using His-tag
-
maE/IspG protein
-
recombinant Strep-tagged IspG from Escherichia coli by affinity chromatography
-
native enzyme, purification under anaerobic conditions; purification under exclusion of air leads to preparation containing solely [4Fe-4S] clusters
-
recombinant enzyme
Q84GJ3, -
recombinant GcpE from Escherichia coli XL1-Blue cells by two different steps of anion exchange chromatography
-
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
expressed in Escherichia coli EcAB3-3
-
gene ispG, expression as Strep-tagged protein in Escherichia coli
-
ispG gene is cloned into a expression vector to afford a fusion protein comprising a maltose binding protein domain and ab IspG protein domain
-
the ispG gene is amplified from bp 372 to 1024. The amplificate is ligated into the plasmid vector pBScyclo. The resulting plasmid pBSxispC-G is electrotransformed into Escherichia coli strain XL1-Blue, yielding the recombinant strain XL1-pBSxispC-G
P62620
gene ispG, DNA and amino acid sequence determination and analysis, semiquantitative expression analysis
-
expression in Escherichia coli
Q84GJ3, -
gene gcpE, expression in Escherichia coli XL1-Blue cells
-
gene gcpE, overexpression in Escherichia coli
-
ENGINEERING
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
C270S
-
no enzymatic activity. Less than 23% sulfide content and 6% iron content, compared with wild-type
C273S
-
no enzymatic activity. Less than 23% sulfide content and 6% iron content, compared with wild-type
C306S
-
no enzymatic activity. Less than 23% sulfide content and 6% iron content, compared with wild-type
additional information
Q8DK70, -
simultaneous expression of (E)-4-hydroxy-3-methylbut-2-enyl diphosphate synthase and ferredoxin I in Escherichia coli shows strong interaction of both proteins. Ferredoxin I is able to transfer electrons to the synthase
Renatured/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
reconstitution after purification of the recombinant protein, purified protein is fully inactive before reconstitution
-
enzyme inactivated by EDTA may be reactivated by Mn2+
-