Information on EC 2.5.1.91 - all-trans-decaprenyl-diphosphate synthase

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

EC NUMBER
COMMENTARY hide
2.5.1.91
-
RECOMMENDED NAME
GeneOntology No.
all-trans-decaprenyl-diphosphate synthase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
(2E,6E)-farnesyl diphosphate + 7 isopentenyl diphosphate = 7 diphosphate + all-trans-decaprenyl diphosphate
show the reaction diagram
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-
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
all-trans-decaprenyl diphosphate biosynthesis
-
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Terpenoid backbone biosynthesis
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ubiquinol-10 biosynthesis (eukaryotic)
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SYSTEMATIC NAME
IUBMB Comments
(2E,6E)-farnesyl-diphosphate:isopentenyl-diphosphate farnesyltranstransferase (adding 7 isopentenyl units)
This enzyme catalyses the condensation reactions resulting in the formation of all-trans-decaprenyl diphosphate, the isoprenoid side chain of ubiquinone-10 and menaquinone-10. The enzyme adds seven isopentenyl diphosphate molecules sequentially to farnesyl diphosphate with trans stereochemistry.
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
strain LBA4404
UniProt
Manually annotated by BRENDA team
strain B10
UniProt
Manually annotated by BRENDA team
strain B10
UniProt
Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
the enzyme contains six conserved motifs (from I to V), i.e., motif I (GKxxR), motif II (DDxxD(x)4RRG), motif III (GExxQ), motif IV (Y(x)6KT), motif V (FQLxDDxxD) and motif VI (K(x)4DxxxGxxTxPxL), occurring in all DPPS-1s examined, including insect, vertebrate, yeast and plant DPPS-1s, and bacterial DPPSs; the enzyme contains six conserved motifs (from I to V), i.e., motif I (GKxxR), motif II (DDxxD(x)4RRG), motif III (GExxQ), motif IV (Y(x)6KT), motif V (FQLxDDxxD) and motif VI (K(x)4DxxxGxxTxPxL), occurring in all DPPS-1s examined, including insect, vertebrate, yeast and plant DPPS-1s, and bacterial DPPSs
malfunction
physiological function
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(2E,6E)-farnesyl diphosphate + 7 isopentenyl diphosphate
7 diphosphate + all-trans-decaprenyl diphosphate
show the reaction diagram
(2E,6E)-farnesyl diphosphate + 7 isopentenyl diphosphate
7 diphosphate + decaprenyl diphosphate
show the reaction diagram
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plus solanesyl diphosphate
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?
(2E,6E)-farnesyl diphosphate + 7 isopentenyl diphosphate
7 diphosphate + octaprenyl diphosphate
show the reaction diagram
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-
-
-
?
(2E,6E,10E)-geranylgeranyl diphosphate + isopentenyl diphosphate
diphosphate + ?
show the reaction diagram
(2E,6E,10E)-geranylgeranyl diphosphate + isopentenyl diphosphate
diphosphate + octaprenyl diphosphate
show the reaction diagram
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plus, in decreasing order, nonaprenyl diphosphate, decaprenyl diphosphate, and heptaprenyl diphosphate
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?
(2E,6Z)-farnesyl diphosphate + isopentenyl diphosphate
diphosphate + decaprenyl diphosphate
show the reaction diagram
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highest catalytic efficiency
plus smaller amounts of intermediiates with shorter chain length
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?
all-E-geranylgeranyl diphosphate + isopentenyl diphosphate
diphosphate + all-trans-decaprenyl diphosphate
show the reaction diagram
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74% of the activity with (2E,6E)-farnesyl diphosphate
plus minor amounts of undecaprenyl diphosphate
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?
dimethyl allyl diphosphate + isopentenyl diphosphate
diphosphate + ?
show the reaction diagram
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?
geranyl diphosphate + 6 isopentenyl diphosphate
diphosphate + all-trans-decaprenyl diphosphate
show the reaction diagram
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95% of the activity with E,E-farnesyl diphosphate
the relative amount of C50 and C55 products, i.e. decaprenyl diphosphate and undecaprenyl diphosphate, changes depending on the concentration of Mg2+. The ratio of the C50 and C55 product formed at 1 mM Mg2+ is 23:1
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?
geranyl diphosphate + 8 isopentenyl diphosphate
8 diphosphate + all-trans-decaprenyl diphosphate
show the reaction diagram
geranyl diphosphate + isopentenyl diphosphate
diphosphate + ?
show the reaction diagram
geranyl diphosphate + isopentenyl diphosphate
diphosphate + all-trans-decaprenyl diphosphate
show the reaction diagram
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-
-
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?
geranyl diphosphate + isopentenyl diphosphate
diphosphate + decaprenyl diphosphate
show the reaction diagram
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plus some farnesyl diphosphate
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?
geranylgeranyl diphosphate + 6 isopentenyl diphosphate
6 diphosphate + all-trans-decaprenyl diphosphate
show the reaction diagram
neryl diphosphate + isopentenyl diphosphate
diphosphate + nonaprenyl diphosphate
show the reaction diagram
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plus some farnesyl diphosphate
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?
additional information
?
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
(2E,6E)-farnesyl diphosphate + 7 isopentenyl diphosphate
7 diphosphate + all-trans-decaprenyl diphosphate
show the reaction diagram
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
KCl
removal of KCl from the reaction mixture results in a decrease of activity
MgCl2
essential for activity, highest enzyme activity with 5 mM MgCl2
additional information
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
dithiothreitol
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NH4+
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activation
Triton X-100
Tween 20
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0.2% significantly activates, detergent is required; hardly any activity in absence of detergent. 0.2% required for full activity
additional information
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00006 - 0.084
(2E,6E)-farnesyl diphosphate
0.00007 - 0.04
(2E,6E,10E)-geranylgeranyl diphosphate
0.29
(2E,6Z)-farnesyl diphosphate
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pH 7.9, 37C
0.0029
all-E-geranylgeranyl diphosphate
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pH 7.3, 37C
0.005 - 0.49
geranyl diphosphate
0.0115
geranyl geranyl diphosphate
pH 7.5, 37C
0.00007 - 0.00375
geranylgeranyl diphosphate
0.0138 - 0.089
isopentenyl diphosphate
0.029
neryl diphosphate
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pH 7.9, 37C
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.072 - 0.147
(2E,6E)-farnesyl diphosphate
0.03 - 0.058
(2E,6E,10E)-geranylgeranyl diphosphate
11.5
(2E,6Z)-farnesyl diphosphate
Mycobacterium tuberculosis
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pH 7.9, 37C
0.06 - 0.067
geranyl diphosphate
0.06
geranyl geranyl diphosphate
Rhodobacter sphaeroides
Q5I7E1
pH 7.5, 37C
0.08 - 0.143
isopentenyl diphosphate
0.052
neryl diphosphate
Mycobacterium tuberculosis
-
pH 7.9, 37C
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.86 - 11.22
(2E,6E)-farnesyl diphosphate
81
0.75 - 5.04
(2E,6E,10E)-geranylgeranyl diphosphate
3767
39.65
(2E,6Z)-farnesyl diphosphate
Mycobacterium tuberculosis
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pH 7.9, 37C
6369
0.122 - 3.62
geranyl diphosphate
175
5.2
geranyl geranyl diphosphate
Rhodobacter sphaeroides
Q5I7E1
pH 7.5, 37C
12858
0.89 - 10.77
isopentenyl diphosphate
113
1.79
neryl diphosphate
Mycobacterium tuberculosis
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pH 7.9, 37C
1451
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7
assay at; assay at
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
40 - 45
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; substrate: farnesyl diphosphate
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.16
calculated from sequence
6.28
sequence calculation
8.13
sequence calculation
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
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Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
additional information
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Gluconobacter oxydans decaprenyl diphosphate synthase is predominantly produced in the leaves and seeds of transgenic rice
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Manually annotated by BRENDA team
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
17500
gel filtration; gel filtration
32411
2 * 42047 (DSP1) + 2 * 32411 (DLP1), both DPS1 and DLPd1 are required for the enzymatic activity, calculated from sequence
33898
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x * 33898, calculated from sequence
36400
2 * 36400, calculated from sequence
37000
x * 37000, calculated from sequence
38100
x * 38100, calculated from sequence; x * 38100, SDS-PAGE and calculated
38900
x * 38900, calculated from sequence
38960
2 * 38960, calculated from sequence
41000
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x * 41000, SDS-PAGE of His-tagged recombinant protein
42047
2 * 42047 (DSP1) + 2 * 32411 (DLP1), both DPS1 and DLPd1 are required for the enzymatic activity, calculated from sequence
42700
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8 * 42700, SDS-PAGE and gel filtration
45443
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x * 45443, calculated
60000
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gel filtration
71000
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
heterodimer
1 * 46150, subunit 1/AgDPPS1 + 1 x 46740, subunit 2/AgDPPS2, sequence calculation; 1 * 46150, subunit 1/AgDPPS1 + 1 x 46740, subunit 2/AgDPPS2, sequence calculation
heterotetramer
homodimer
2 * 36400, calculated from sequence; 2 * 38960, calculated from sequence
octamer
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8 * 42700, SDS-PAGE and gel filtration
tetramer
additional information
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
enzyme shows high stability towards extreme pH values, sodium dodecyl sulfate and urea
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
His-tagged DdsA protein is purified; recombinant enzyme
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partial
recombinant GST-tagged enzyme from Escherichia coli strain BL21 by glutathione affinity chromatography and ultrafiltration, tag cleavage by Factor Xa, followed by again affinity chromatography and ultrafiltration
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
coexpression of decaprenyl diphosphate synthase and 1-deoxy-D-xylulose 5-phosphate synthase in Escherichia coli
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DdsA is expressed successfully in Escherichia coli. Recombinant Escherichia coli synthesizes UQ-10 in addition to the endogenous production UQ-8
efficient production of coenzyme Q10 in rice by introducing the gene for decaprenyl diphosphate synthase into rice sugary and shrunken mutants
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expressed under the control of an Escherichia coli constitutive promoter, CoQ10 rather than endogenous CoQ8 is biologically synthesized as the major coenzyme Q. Expression of the ddsA gene with low copy number leads to the accumulation of CoQ10 in batch fermentation. A high cell density in fed-batch fermentation of Escherichia coli BL21/pACDdsA increases the CoQ10 concentration
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expression in Escherichia coli
expression in Escherichia coli, detecting UQ-10 in addition to innate UQ-8 in Escherichia coli
expression in Escherichia coli. Escherichia coli JM109 harboring the dps gene produces ubiquinone-10 in addition to endogenous ubiquinone-8
expression in Escherichia coli; expression in Escherichia coli. Expression of the ddsA gene complements the lethality resulting from a defect in the octaprenyl diphosphate synthase gene of Escherichia coli and produces coenzyme Q10, indicating that coenzyme Q10 can substitute for the function of coenzyme Q8
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expression in Escherichia coli; expression in Escherichia coli. Wild-type Escherichia coli produces coenzyme Q8 and does not produce any coenzyme Q10. Recombinant Escherichia coli produces coenzyme Q10 in addition to coenzyme Q8
expression in Escherichia coli; expression in Escherichia coli; expression in Escherichia coli
for biotechnological production of coenzyme Q10 in recombinant Escherichia coli, three genetic manipulations are performed: heterologous expression of decaprenyl diphosphate synthase (Dps) from Agrobacterium tumefaciens, deletion of endogenous octaprenyl diphosphate synthase (IspB), and overexpression of 1-deoxy-D-xylulose synthase (Dxs). Expression of the dps gene and deletion of the ispB gene in Escherichia coli BL21(DE3) DELTAispB/pAP1 allows production of CoQ10 only. Coexpression of the dxs gene increases the specific content of CoQ10
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gene AgDPPS1, DNA and amino acid sequence determination and analysis, sequence comparisons, phylogenetic analysis, recombinant expression of N-terminally GST-tagged enzyme in Escherichia coli strain BL21, coexpression with gene AgDPPS2; gene AgDPPS2, DNA and amino acid sequence determination and analysis, sequence comparisons, phylogenetic analysis, recombinant expression of N-terminally GST-tagged enzyme in Escherichia coli strain BL21, coexpression with gene AgDPPS1
genetic engineering of rice to produce CoQ10 using the gene for decaprenyl diphosphate synthase from Gluconobacter suboxydans. The production of CoQ9 is almost completely replaced with that of CoQ10, despite the presence of endogenous CoQ9 synthesis. DdsA designed to express at the mitochondria increases accumulation of total CoQ amount in seeds
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the proteins Dps1 abd Dlp1 must be present simultaneously in Escherichia coli transformants before ubiquinone-10, which is produced by Schizosaccharomyces pombe but not by Escherichia coli, is generated. DLP1 and DPS1 form a heterotetramer in Escherichia coli
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
the recombinant enzyme is expressed with various concentrations of IPTG at various temperatures. A significant level of expression is observed when the enzyme is induced at 20C with 0.25 mM isopropyl-beta-D-thiogalactopyranoside
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D245E
significant decrease of activity
D245G
complete loss of activity
A197V
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mainly heptaprenyl diphosphate is produced with smaller amounts of octaprenyl diphosphate and solanesyl diphosphate. Compared to wild-type enzyme the KM- and Vmax-values are altered; main products all-E-octaprenyl diphosphate and heptaprenyl diphosphate
A70G
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a small amount of undecaprenyl diphosphate is produced with higher amounts of decaprenyl diphosphate. Compared to wild-type enzyme the KM- and Vmax-values are altered; main product is decaprenyl diphosphate with small amounts of undecaprenyl diphosphate
A70V
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mainly heptaprenyl diphosphate is produced with smaller amounts of octaprenyl diphosphate and solanesyl diphosphate. Compared to wild-type enzyme the KM- and Vmax-values are altered; main product is all-E-heptaprenyl diphosphate
A70Y
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complete loss of activity; mutation completely abolishes the decaprenyl diphosphate synthase function, indicating that Ala70 is important for enzyme activity and the determination of the chain-length properties of DdsA
C63A
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an even distribution in the amounts of the four products, heptaprenyl diphosphate, octaprenyl diphosphate, solanesyl diphosphate and decaprenyl diphosphate is observed. Compared to wild-type enzyme the KM- and Vmax-values are altered; main products all-E-octaprenyl diphosphate and all-E-solanesyl diphosphate
C63F
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main products all-E-octaprenyl diphosphate and all-E-geranylfarnesyl diphosphate; produces mostly geranylfarnesyl diphosphate and octaprenyl diphosphosphate. Compared to wild-type enzyme the KM- and Vmax-values are altered. Compared to wild-type enzyme the KM- and Vmax-values are altered
F190A
-
mainly heptaprenyl diphosphate is produced with smaller amounts of octaprenyl diphosphate and solanesyl diphosphate. Compared to wild-type enzyme the KM- and Vmax-values are altered; main product is all-E-heptaprenyl diphosphate
F190W
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mainly heptaprenyl diphosphate is produced with smaller amounts of octaprenyl diphosphate and solanesyl diphosphate. Compared to wild-type enzyme the KM- and Vmax-values are altered; main product is all-E-heptaprenyl diphosphate
N193A
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an even distribution in the amounts of the four products, heptaprenyl diphosphate, octaprenyl diphosphate, solanesyl diphosphate and decaprenyl diphosphate is observed. Compared to wild-type enzyme the KM- and Vmax-values are altered; main product is decaprenyl diphosphate
R321A
expression of Schizosaccharomyces pombe decaprenyl diphosphate synthase Dps1 or D-less polyprenyl diphosphate synthase Dlp1 recover the thermo-sensitive growth of an Escherichia coli ispB R321A mutant and restor IspB activity and production of coenzyme Q-8. IspB interacts with Dlp1 or Dps1, forming a high-molecular weight complex that stabilizes IspB, leading to full functionality
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
synthesis