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Information on EC 2.5.1.90 - all-trans-octaprenyl-diphosphate synthase and Organism(s) Escherichia coli and UniProt Accession P0AD57
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2.5.1.90 all-trans-octaprenyl-diphosphate synthaseIUBMB Comments
This enzyme catalyses the condensation reactions resulting in the formation of all-trans-octaprenyl diphosphate, the isoprenoid side chain of ubiquinone-8 and menaquinone-8. The enzyme adds five isopentenyl diphosphate molecules sequentially to farnesyl diphosphate with trans stereochemistry
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Word Map
- 2.5.1.90
- ubiquinone
-
isoprenoids
-
polyprenyl
-
decaprenylation
- menaquinone
-
prenylates
- undecaprenyl
-
geranyl
- isoprene
-
hexaprenyl
-
farnesyl-pp
-
solanesyl
-
chain-length
-
ddxxd
- 4-hydroxybenzoate
- dolichols
- coq
-
polyisoprenoids
-
dimethylallyl
-
carbocation
- cis-prenyltransferase
The taxonomic range for the selected organisms is: Escherichia coli
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
Reaction Schemes
Synonyms
trans-prenyltransferase, octaprenyl diphosphate synthase, octaprenyl pyrophosphate synthase, octaprenyl pyrophosphate, opp synthetase, long-chain c40 octaprenyl diphosphate synthase, gbs1789, octaprenyl-diphosphate synthase, long-chain trans-prenyltransferase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
(2E,6E)-farnesyl diphosphate + 5 isopentenyl diphosphate = 5 diphosphate + all-trans-octaprenyl diphosphate
sequential mechanism
-
PATHWAY SOURCE
PATHWAYS
BRENDA
-
-
SYSTEMATIC NAME
IUBMB Comments
(2E,6E)-farnesyl-diphosphate:isopentenyl-diphosphate farnesyltranstransferase (adding 5 isopentenyl units)
This enzyme catalyses the condensation reactions resulting in the formation of all-trans-octaprenyl diphosphate, the isoprenoid side chain of ubiquinone-8 and menaquinone-8. The enzyme adds five isopentenyl diphosphate molecules sequentially to farnesyl diphosphate with trans stereochemistry
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
(2E,6E)-8-O-(N-methyl-2-aminobenzoyl)-3,7-dimethyl-2,6-octandien-1-diphosphate + 5 isopentenyl diphosphate
?
-
-
-
?
(2E,6E)-farnesyl diphosphate + 5 isopentenyl diphosphate
5 diphosphate + all-trans-octaprenyl diphosphate
dimethylallyl diphosphate + isopentenyl diphosphate
diphosphate + octaprenyl diphosphate + nonaprenyl diphosphate
0.7% activity compared to (2E,6E)-farnesyl diphosphate
-
-
?
geranyl diphosphate + isopentenyl diphosphate
?
5.3% activity compared to (2E,6E)-farnesyl diphosphate
-
-
?
geranylgeranyl diphosphate + isopentenyl diphosphate
?
53.4% activity compared to (2E,6E)-farnesyl diphosphate
-
-
?
(2E,6E)-farnesyl diphosphate + 3-bromo-3-butenyl diphosphate
diphosphate + ?
-
isopentenyl diphosphate analogue, showing a significantly reduced activity. Only two 3-bromo-3-butenyl diphosphate condensation reactions occurr in 24 h and the reaction products do not reach C40 and C55. Use results in trapping of farnesol in the reaction from radioloabeled farnesyl diphosphate under basic conditions, consistent with a sequential mechanism
-
-
?
(2E,6E)-farnesyl diphosphate + 5 isopentenyl diphosphate
5 diphosphate + all-trans-octaprenyl diphosphate
(2E,6E)-farnesyl diphosphate + 5 isopentenyl diphosphate
5 diphosphate + all-trans-octaprenyl diphosphate
-
-
-
?
(2E,6E)-farnesyl diphosphate + 5 isopentenyl diphosphate
5 diphosphate + all-trans-octaprenyl diphosphate
-
-
-
-
?
(2E,6E)-farnesyl diphosphate + 5 isopentenyl diphosphate
5 diphosphate + all-trans-octaprenyl diphosphate
-
-
-
?
(2E,6E)-farnesyl diphosphate + 5 isopentenyl diphosphate
5 diphosphate + all-trans-octaprenyl diphosphate
-
-
-
-
?
(2E,6E)-farnesyl diphosphate + 5 isopentenyl diphosphate
5 diphosphate + all-trans-octaprenyl diphosphate
-
-
-
?
(2E,6E)-farnesyl diphosphate + 5 isopentenyl diphosphate
5 diphosphate + all-trans-octaprenyl diphosphate
-
-
-
-
?
(2E,6E)-farnesyl diphosphate + 5 isopentenyl diphosphate
5 diphosphate + all-trans-octaprenyl diphosphate
the enzyme catalyzes the successive condensation of farnesyl diphosphate with five isopentenyl pyrophosphate molecules to form trans-C40-octaprenyl diphosphate
-
-
?
(2E,6E)-farnesyl diphosphate + 5 isopentenyl diphosphate
5 diphosphate + all-trans-octaprenyl diphosphate
(2E,6E)-farnesyl diphosphate is the most effective substrate
-
-
?
(2E,6E)-farnesyl diphosphate + 5 isopentenyl diphosphate
5 diphosphate + all-trans-octaprenyl diphosphate
-
-
-
-
?
(2E,6E)-farnesyl diphosphate + 5 isopentenyl diphosphate
5 diphosphate + all-trans-octaprenyl diphosphate
-
-
80% all-trans-octaprenyl diphosphate, 20% nonaprenyl diphosphate in presence of 0.01 mM enzyme, 0.0001 mM farnesyl diphosphate, 0.001 mM isopentenyl diphosphate. Variation of concentrations and conditions allows for synthesis of products with chain length C20 to C60
-
?
additional information
?
-
at the bottom of the active-site tunnel, residues M123 and M135 act in concert to form a wall which determines the final chain length, substrate binding and enzyme-ligand structure analysis, overview
-
-
?
additional information
?
-
-
at the bottom of the active-site tunnel, residues M123 and M135 act in concert to form a wall which determines the final chain length, substrate binding and enzyme-ligand structure analysis, overview
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
(2E,6E)-farnesyl diphosphate + 5 isopentenyl diphosphate
5 diphosphate + all-trans-octaprenyl diphosphate
(2E,6E)-farnesyl diphosphate + 5 isopentenyl diphosphate
5 diphosphate + all-trans-octaprenyl diphosphate
-
-
-
-
?
(2E,6E)-farnesyl diphosphate + 5 isopentenyl diphosphate
5 diphosphate + all-trans-octaprenyl diphosphate
-
-
-
?
(2E,6E)-farnesyl diphosphate + 5 isopentenyl diphosphate
5 diphosphate + all-trans-octaprenyl diphosphate
-
-
-
-
?
(2E,6E)-farnesyl diphosphate + 5 isopentenyl diphosphate
5 diphosphate + all-trans-octaprenyl diphosphate
the enzyme catalyzes the successive condensation of farnesyl diphosphate with five isopentenyl pyrophosphate molecules to form trans-C40-octaprenyl diphosphate
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0008
(2E,6E)-8-O-(N-methyl-2-aminobenzoyl)-3,7-dimethyl-2,6-octandien-1-diphosphate
at pH 7.5, temperature not specified in the publication
0.0015
(2E,6E)-farnesyl diphosphate
at pH 7.5, temperature not specified in the publication
0.004
isopentenyl diphosphate
with (2R,6E)-farnesyl diphosphate as cosubstrate, at pH 7.5, temperature not specified in the publication
0.0069
isopentenyl diphosphate
with (2E,6E)-8-O-(N-methyl-2-aminobenzoyl)-3,7-dimethyl-2,6-octandien-1-diphosphate as cosubstrate, at pH 7.5, temperature not specified in the publication
0.34
isopentenyl diphosphate
with dimethylallyl diphosphate as cosubstrate, at pH 7.5 and 30°C
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.055
(2E,6E)-8-O-(N-methyl-2-aminobenzoyl)-3,7-dimethyl-2,6-octandien-1-diphosphate
at pH 7.5, temperature not specified in the publication
0.06
(2E,6E)-farnesyl diphosphate
at pH 7.5, temperature not specified in the publication
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.00022
zoledronate
Escherichia coli
at pH 7.5, temperature not specified in the publication
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
31000
with geranylgeranyl diphosphate as substrate, at pH 7.5 and 30°C
58000
with (2E,6E)-farnesyl diphosphate as substrate, at pH 7.5 and 30°C
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
malfunction
-
it is impossible to obtain an ispB deletion mutant unless the ispB gene or its homolog is supplied on a plasmid. The ispB gene is essential for the normal growth of Escherichia coli
physiological function
additional information
evolution
octaprenyl diphosphate synthase, OPP, belongs to the trans-prenyltransferase class of protein
physiological function
-
octaprenyl diphosphate synthase is responsible for the synthesis of the side chain of isoprenoid quinones
physiological function
the enzyme catalyzes consecutive condensation reactions of one allylic substrate farnesyl diphosphate and five homoallylic substrate isopentenyl diphosphate molecules to form a C40 long-chain product octaprenyl diphosphate, which serves as a side chain of ubiquinone and menaquinone
physiological function
the enzyme is essential for the biosynthesis of bacterial ubiquinone or menaquinone side chains, which play an important role in the electron-transport system
additional information
enzyme homology modeling, overview. (2E,6E)-Farnesyl diphosphate is bound to the first DDXXD motif, and isopentenyl diphosphate is bound to several cationic residues (e.g. Arg, Lys, and His) via diphosphate, but not to the second DDXXD motif. The enzyme contains an elongated tunnel-shaped crevice as the active site to accommodate its reactants and product
additional information
-
enzyme homology modeling, overview. (2E,6E)-Farnesyl diphosphate is bound to the first DDXXD motif, and isopentenyl diphosphate is bound to several cationic residues (e.g. Arg, Lys, and His) via diphosphate, but not to the second DDXXD motif. The enzyme contains an elongated tunnel-shaped crevice as the active site to accommodate its reactants and product
additional information
enzyme structure modelling using the structure of Rhodobacter capsulatus decaprenyl diphosphate synthase, PDB ID 3mzv, as a template model
additional information
-
enzyme structure modelling using the structure of Rhodobacter capsulatus decaprenyl diphosphate synthase, PDB ID 3mzv, as a template model
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant enzyme, crystallization method screening, sitting drop vapour diffusion method, mixing of 0.002 ml of 3 mg/ml protein in 25 mM Tris-HCl, 150 mM NaCl, pH 7.5, with 0.002 ml of crystallization solution containing 0.3 M magnesium chloride hexahydrate, 0.1 M Tris-HCl, pH 8.5, 24% w/v PEG 3350, 3-4 days, X-ray diffraction structure determination and analysis at 2.2 A resolution, molecular replacement, the crystal contains one homodimer per asymmetric unit, structure modelling
purified recombinant His-tagged enzyme in apo-form and in complexes with isopentenyl diphosphate and a farnesyl diphosphate thio-analogue, FsPP, sitting drop vapor diffusion method, mixing of 0.002 ml of 3 mg/ml protein in 25 mM Tris-HCl, pH 7.5, and 150 mM NaCl, with 0.002 ml of reservoir solution containing 0.3 M magnesium chloride, 0.1 M Tris-HCl, pH 8.5, and 24% w/v PEG 3350, and equilibration against 0.3 ml of reservori solution, 22°C, 3-4 days, X-ray diffraction structure determination and analysis at resolutions of 2.2-2.6 A
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
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
additional information
-
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
additional information
residue D85 is the most important residue in the first DDXXD motif for both farnesyl diphosphate and isopentenyl diphosphate binding through an H-bond network involving R93 and R94, respectively, whereas R94, K45, R48, and H77 are responsible for isopentenyl binding by providing H-bonds and ionic interactions. K170 and T171 may stabilize the farnesyl carbocation intermediate to facilitate the reaction, whereas R93 and K225 may stabilize the catalytic base for HR proton abstraction after isopentenyl diphosphate condensation. K225 and K235 in a flexible loop may interact with farnesyl diphosphate when the enzyme becomes a closed conformation, which is therefore crucial for catalysis. Q208 is near the hydrophobic part of isopentenyl diphosphate and is important for isopentenyl diphosphate binding and catalysis
additional information
-
residue D85 is the most important residue in the first DDXXD motif for both farnesyl diphosphate and isopentenyl diphosphate binding through an H-bond network involving R93 and R94, respectively, whereas R94, K45, R48, and H77 are responsible for isopentenyl binding by providing H-bonds and ionic interactions. K170 and T171 may stabilize the farnesyl carbocation intermediate to facilitate the reaction, whereas R93 and K225 may stabilize the catalytic base for HR proton abstraction after isopentenyl diphosphate condensation. K225 and K235 in a flexible loop may interact with farnesyl diphosphate when the enzyme becomes a closed conformation, which is therefore crucial for catalysis. Q208 is near the hydrophobic part of isopentenyl diphosphate and is important for isopentenyl diphosphate binding and catalysis
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged enzyme from Escherichia coli strain BL21trxB (DE3) by nickel affinity and anion exchange chromatography, dialysis, and ultrafiltration
recombinant His-tagged enzyme from Escherichia coli strain BL21trxB (DE3) by nickel affinity and anion exchange chromatography, followed by dialysis
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
amino acid sequence comparison, recombinant cloning into vector pET46 Ek/LIC and expression of His-tagged enzyme in Escherichia coli strain BL21trxB (DE3)
recombinant expression of His-tagged enzyme in Escherichia coli strain BL21trxB (DE3) from vector pET46 Ek/LIC
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Asai, K.; Fujisaki, S.; Nishimura, Y.; Nishino, T.; Okada, K.; Nakagawa, T.; Kawamukai, M.; Matsuda, H.
The identification of Escherichia coli ispB (cel) gene encoding the octaprenyl diphosphate synthase
Biochem. Biophys. Res. Commun.
202
340-345
1994
Escherichia coli
Choi, J.-H.; Ryu, Y.-W.; Park, Y.-C.; Seo, J.-H.
Synergistic effects of chromosomal ispB deletion and dxs overexpression on coenzyme Q10 production in recombinant Escherichia coli expressing Agrobacterium tumefaciens dps gene
J. Biotechnol.
144
64-69
2009
Escherichia coli (P0AD57), Escherichia coli
Lu, Y.P.; Liu, H.G.; Liang, P.H.
Different reaction mechanisms for cis- and trans-prenyltransferases
Biochem. Biophys. Res. Commun.
379
351-355
2009
Escherichia coli
Pan, J.-J.; Kuo, T.-H.; Chen, Y.-K.; Yang, L.-W.; Liang, P.-H.
Insight into the activation mechanism of Escherichia coli octaprenyl pyrophosphate synthase derived from pre-steady-state kinetic analysis
Biochim. Biophys. Acta
1594
64-73
2002
Escherichia coli
Chang, K.; Chen, S.; Kuo, C.; Chang, C.; Guo, R.; Yang, J.; Liang, P.
Roles of amino acids in the Escherichia coli octaprenyl diphosphate synthase active site probed by structure-guided site-directed mutagenesis
Biochemistry
51
3412-3419
2012
Escherichia coli (P0AD57), Escherichia coli
Li, X.; Han, X.; Ko, T.P.; Chen, C.C.; Zhu, Z.; Hua, E.; Guo, R.T.; Huang, C.H.
Preliminary X-ray diffraction analysis of octaprenyl pyrophosphate synthase from Escherichia coli
Acta Crystallogr. Sect. F
69
328-331
2013
Escherichia coli (P0AD57), Escherichia coli
Han, X.; Chen, C.C.; Kuo, C.J.; Huang, C.H.; Zheng, Y.; Ko, T.P.; Zhu, Z.; Feng, X.; Wang, K.; Oldfield, E.; Wang, A.H.; Liang, P.H.; Guo, R.T.; Ma, Y.
Crystal structures of ligand-bound octaprenyl pyrophosphate synthase from Escherichia coli reveal the catalytic and chain-length determining mechanisms
Proteins
83
37-45
2015
Escherichia coli (P0AD57), Escherichia coli
Teng, K.H.; Hsu, E.T.; Chang, Y.H.; Lin, S.W.; Liang, P.H.
Fluorescent farnesyl diphosphate analogue A probe to validate trans-prenyltransferase inhibitors
Biochemistry
55
4366-4374
2016
Escherichia coli (P0AD57)
Takahashi, H.; Aihara, Y.; Ogawa, Y.; Murata, Y.; Nakajima, K.I.; Iida, M.; Shirai, M.; Fujisaki, S.
Suppression of phenotype of Escherichia coli mutant defective in farnesyl diphosphate synthase by overexpression of gene for octaprenyl diphosphate synthase
Biosci. Biotechnol. Biochem.
82
1003-1010
2018
Escherichia coli (P0AD57), Escherichia coli, Escherichia coli K12 (P0AD57)
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