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Enzyme Nomenclature
Information on EC 4.2.3.46 - alpha-farnesene synthase
for references in articles please use BRENDA:EC4.2.3.46
Word Map on EC 4.2.3.46
- 4.2.3.46
- apple
-
terpene
-
monoterpene
-
sesquiterpene
-
volatile
- salicylate
-
terpenoids
-
e-beta-ocimene
- jasmonate
-
herbivores
- linalool
-
conifer
- synthesis
- agriculture
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The enzyme appears in viruses and cellular organisms
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EC NUMBER 
COMMENTARY 
4.2.3.46
-
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RECOMMENDED NAME
GeneOntology No.
alpha-farnesene synthase
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
(2E,6E)-farnesyl diphosphate = (3E,6E)-alpha-farnesene + diphosphate
-
-
-
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
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SYSTEMATIC NAME
IUBMB Comments
(2E,6E)-farnesyl-diphosphate lyase [(3E,6E)-alpha-farnesene-forming]
-
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
genomic structure and sequence polymorphism of E,E-alpha farnesene synthase gene in Malus domestica; Borkh.; genomic structure and sequence polymorphism of E,E-alpha-farnesene synthase gene in Malus domestica; Borkh.
UniProt
The deduced amino acid sequence of this enzyme shares the greatest degree of homology with a variety of monoterpene synthases, including alpha-(-)beta-pinene synthase, a gamma-terpinene synthase, and a (+)-limonene synthase from Citrus limon, which have 41-42% amino acid identity. A geraniol synthase from Cinnamomum tenuipilum and an isoprene synthase from Populus tremuloides have 42% identity to AFS1. The closest homology is with a linalool/nerolidol synthase from Fragaria ananassa (35% identity) and a (+)-delta-cadinene synthase from Gossypium hirsutum (33% identity).; Malus domestica Borkh., cultivar Law Rome
UniProt
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
differences in the relative emissions of (E)-beta-ocimene and (E,E)-alpha-farnesene from accession Wassilewskija, a high-(E)-beta-ocimene emitter, and accession Columbia, a trace-(E)-beta-ocimene emitter, are attributed to allelic variation of closely related, tandem-duplicated terpene synthase genes, TPS02 and TPS03. The Wassilewskija genome contains a functional allele of TPS02 but not of TPS03, while the opposite is the case for Columbia. Recombinant proteins of the functional Wassilewskija TPS02 and Columbia TPS03 genes both show (E)-beta-ocimene and (E,E)-alpha-farnesene synthase activities. Differential subcellular compartmentalization of the two enzymes in plastids and the cytosol is responsible for the ecotype-specific differences in (E)-beta-ocimene/(E,E)-alpha-farnesene emission; differences in the relative emissions of (E)-beta-ocimene and (E,E)-alpha-farnesene from accession Wassilewskija, a high-(E)-beta-ocimene emitter, and accession Columbia, a trace-(E)-beta-ocimene emitter, are attributed to allelic variation of closely related, tandem-duplicated terpene synthase genes, TPS02 and TPS03. The Wassilewskija genome contains a functional allele of TPS02 but not of TPS03, while the opposite is the case for Columbia. Recombinant proteins of the functional Wassilewskija TPS02 and Columbia TPS03 genes both show (E)-beta-ocimene and (E,E)-alpha-farnesene synthase activities. Differential subcellular compartmentalization of the two enzymes in plastids and the cytosol is responsible for the ecotype-specific differences in (E)-beta-ocimene/(E,E)-alpha-farnesene emission
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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)-farnesyl diphosphate
(3E,6E)-alpha-farnesene + beta-farnesene + diphosphate
-
when farnesyl diphosphate, synthesised from 96% (E,E)-farnesol, is incubated with recombinant protein, (E,E)- and (Z,E)-alpha-farnesene are produced in a ratio of 96:4, respectively
-
-
?
(2E,6E)-farnesyl diphosphate + H2O
(3E,6E)-alpha-farnesene + diphosphate
-
-
about 95% of total product, plus trace amounts of beta-farnesene
-
?
farnesyl diphosphate
(E,E)-alpha-farnesene + diphosphate
sesquiterpene synthase activity
-
-
?
farnesyl diphosphate
(Z,E)-alpha-farnesene + diphosphate
isomers of farnesene produced in apple fruit are (E,E)-alpha and (Z,E)-alpha are in a ratio of 300:1
trace amounts
-
?
geranyl diphosphate
(E)-beta-ocimene + beta-myrcene
poor substrate
-
-
?
geranyl diphosphate
(Z)-beta-ocimene + diphosphate
monoterpene synthase activity
-
-
?
geranyl diphosphate
linalool + (Z)-beta-ocimene + (E)-beta-ocimene + beta-myrcene
-
at 18% of the optimised rate for alpha-farnesene synthesis from farnesyl diphosphate
-
-
?
(2E,6E)-farnesyl diphosphate
(3E,6E)-alpha-farnesene + diphosphate
the product consists primarily of (E,E)-alpha-farnesene (more than 95%) with trace amounts of (Z,E)-alpha-farnesene
-
-
?
(2E,6E)-farnesyl diphosphate
(3E,6E)-alpha-farnesene + diphosphate
-
-
-
?
(2E,6E)-farnesyl diphosphate
(3E,6E)-alpha-farnesene + diphosphate
-
-
-
?
(2E,6E)-farnesyl diphosphate
(3E,6E)-alpha-farnesene + diphosphate
commentary
-
-
?
(2E,6E)-farnesyl diphosphate
(3E,6E)-alpha-farnesene + diphosphate
alpha-farnesene synthase is a key enzyme in the pathway of alpha-farnesene synthesis
-
-
?
(2E,6E)-farnesyl diphosphate
(3E,6E)-alpha-farnesene + diphosphate
apha-farnesene synthase is a key enzyme in the pathway of alpha-farnesene synthesis
-
-
?
(2E,6E)-farnesyl diphosphate
(3E,6E)-alpha-farnesene + diphosphate
-
sole product
-
?
(2E,6E)-farnesyl diphosphate
alpha-farnesene + diphosphate
Cucumis melo variety Noy Yizre'el
-
-
-
-
?
geranyl diphosphate
(E)-beta-ocimene + diphosphate
AdAFS1 can function as a bifunctional enzyme possessing both sesquiterpene and monoterpene synthase activities. Exhibits significant monoterpene synthase activity, producing exclusively (E)-beta-ocimene. kcat/Km is about 5fold lower than kcat/Km for farnesyl diphosphate
-
-
?
geranyl diphosphate
(E)-beta-ocimene + diphosphate
in monoterpene synthase assays, only (E)-beta-ocimene is produced at much reduced levels
-
-
?
additional information
?
-
enzyme shows both (E)-beta-ocimene and (E,E)-alpha-farnesene synthase activities
-
-
-
additional information
?
-
enzyme shows both (E)-beta-ocimene and (E,E)-alpha-farnesene synthase activities
-
-
-
additional information
?
-
other sesquiterpenes identified in trace amounts are (E)-nerolidol and beta-farnesene
-
-
-
additional information
?
-
the monoterpene synthase ((E)-beta-ocimene and beta-myrcene) and sesquiterpene synthase (alpha-farnesene) products produced by the mutated and wild-type enzymes are identical, there are no significant alterations in the ratios of the alpha-farnesene isomers produced
-
-
-
additional information
?
-
-
the monoterpene synthase ((E)-beta-ocimene and beta-myrcene) and sesquiterpene synthase (alpha-farnesene) products produced by the mutated and wild-type enzymes are identical, there are no significant alterations in the ratios of the alpha-farnesene isomers produced
-
-
-
additional information
?
-
the monoterpene synthase ((E)-beta-ocimene and beta-myrcene) and sesquiterpene synthase (alpha-farnesene) products produced by the mutated and wild-type enzymes are identical, there are no significant alterations in the ratios of the alpha-farnesene isomers produced
-
-
-
additional information
?
-
-
although (E,E)-farnesyl diphosphate is the preferred substrate, the enzyme accepts all four isomeric forms of the farnesyl diphosphate precursor. Both isomers of beta-farnesene are also synthesised by the enzyme presumably from a specific farnesene isomer. The enzyme also produces alpha-farnesene by a reaction involving coupling of geranyl diphosphate and isoprenyl diphosphate but at less than 1% of the rate with farnesyl diphosphate
-
-
-
additional information
?
-
-
Populus trichocarpa Pts2 also acceepts geranyl diphosphate to produce small amounts of (E)-beta-ocimene
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-
-
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NATURAL SUBSTRATES
NATURAL PRODUCTS
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
farnesyl diphosphate
(E,E)-alpha-farnesene + diphosphate
Q84LB2
sesquiterpene synthase activity
-
-
?
farnesyl diphosphate
(Z,E)-alpha-farnesene + diphosphate
Q84LB2
isomers of farnesene produced in apple fruit are (E,E)-alpha and (Z,E)-alpha are in a ratio of 300:1
trace amounts
-
?
geranyl diphosphate
(E)-beta-ocimene + diphosphate
Q84LB2
in monoterpene synthase assays, only (E)-beta-ocimene is produced at much reduced levels
-
-
?
geranyl diphosphate
(Z)-beta-ocimene + diphosphate
Q84LB2
monoterpene synthase activity
-
-
?
(2E,6E)-farnesyl diphosphate
(3E,6E)-alpha-farnesene + diphosphate
B2ZZ11, Q84LB2
commentary
-
-
?
(2E,6E)-farnesyl diphosphate
(3E,6E)-alpha-farnesene + diphosphate
Q84LB2
alpha-farnesene synthase is a key enzyme in the pathway of alpha-farnesene synthesis
-
-
?
(2E,6E)-farnesyl diphosphate
(3E,6E)-alpha-farnesene + diphosphate
Q84LB2
apha-farnesene synthase is a key enzyme in the pathway of alpha-farnesene synthesis
-
-
?
additional information
?
-
Q84LB2
other sesquiterpenes identified in trace amounts are (E)-nerolidol and beta-farnesene
-
-
-
additional information
?
-
B2ZZ11
the monoterpene synthase ((E)-beta-ocimene and beta-myrcene) and sesquiterpene synthase (alpha-farnesene) products produced by the mutated and wild-type enzymes are identical, there are no significant alterations in the ratios of the alpha-farnesene isomers produced
-
-
-
additional information
?
-
-
the monoterpene synthase ((E)-beta-ocimene and beta-myrcene) and sesquiterpene synthase (alpha-farnesene) products produced by the mutated and wild-type enzymes are identical, there are no significant alterations in the ratios of the alpha-farnesene isomers produced
-
-
-
additional information
?
-
Q84LB2
the monoterpene synthase ((E)-beta-ocimene and beta-myrcene) and sesquiterpene synthase (alpha-farnesene) products produced by the mutated and wild-type enzymes are identical, there are no significant alterations in the ratios of the alpha-farnesene isomers produced
-
-
-
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
K+
Mg2+
Mn2+
K+
-
activity is dependent on K+, the potassium binding region is defined; MdAFS1 retains up to 12% of its activity in the absence of K+, enzyme contains K+ binding region, MdAFS1 exhibits a type II K+ response, MdAFS1 is not absolutely dependent upon M+ its unequivocal classification as type I or type II K+ activated, or that of any other terpene synthases, will not be possibl, then type I enzymes can exhibit type II kinetics and vice versa.
K+
-
30-50 mM, enhances activity 5fold. Km: 3 mM. Addition of K+ reduces monoterpene synthase activity
K+
-
in presence of 50 mM potassium, the enzyme activity increases 15fold as compared to the activity in an assay devoid of potassium
Mg2+
Km: 0.248 mM, divalent cation required, preference for Mg2+. Maximal velocities with Mn2+ is about 50% of that with Mg2+
Mn2+
KM: about 0.02 mM, divalent cation required, preference for Mg2+. Maximal velocities with Mn2+ is about 50% of that with Mg2+
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
1-methylcyclopropene
after treatment of fruits at harvest with a blocker of ethylene action, AFS1 mRNA declines sharply over the initial 4 weeks of cold storage, and falls to nearly undetectable levels by 8 weeks
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0026
(2E,6E)-farnesyl diphosphate
accession Columbia, 30°C, pH not specified in the publication
0.004
(2E,6E)-farnesyl diphosphate
accession Wassilewskija, 30°C, pH not specified in the publication
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0045
(2E,6E)-farnesyl diphosphate
accession Wassilewskija, 30°C, pH not specified in the publication
0.0048
(2E,6E)-farnesyl diphosphate
accession Columbia, 30°C, pH not specified in the publication
0.022
farnesyl diphosphate
-
without K+, sesquiterpene synthase activity in mutant S487K is independent of K+
0.000005
geranyl diphosphate
-
mutant S487A; pH 7.5, 30°C, mutant enzyme S487A
0.000034
geranyl diphosphate
-
mutant D484A; pH 7.5, 30°C, mutant enzyme D484A
0.000052
geranyl diphosphate
-
mutant S488A; pH 7.5, 30°C, mutant enzyme S488A
0.000588
geranyl diphosphate
-
mutant S485A; pH 7.5, 30°C, mutant enzyme S485A
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
1.12
(2E,6E)-farnesyl diphosphate
accession Wassilewskija, 30°C, pH not specified in the publication
1.82
(2E,6E)-farnesyl diphosphate
accession Columbia, 30°C, pH not specified in the publication
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
-
S487K mutant has 35-45% of the wild-type activity with farnesyl diphosphate with no significant alterations in the alpha-farnesene isomer ratios produced and a small decrease in catalytic efficiency (wild-type and S487K respective kcat/Km values of 17.5 and 13.3 mM/s)
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7.5
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
production of (E,E)-alpha-farnesene occurs in the epidermal (peel tissue) or adjacent hypodermal cell layers and the sesquiterpene can accumulate to high levels in the natural epicuticular coating of scald-susceptible apples during the first weeks of storage
within floral tissues, expression is highest in petals and stamens
within floral tissues, expression is highest in petals and stamens
expression of AdAFS1 is significantly higher in flowers than in leaf tissue. Within floral tissues, expression is highest in petals and stamens. AdAFS1 expression is low in sepals in both sexes and also in ‘Hayward’ pistils. AdAFS1 expression in ‘Hayward’ is co-ordinated with anthesis, with low levels of expression in unopened flower buds and high levels detected in open flowers. The temporal accumulation patterns of AdAFS1 mRNA is constitutive. No difference in expression between male and female flowers
expression occurs constitutively in floral tissues; expression occurs constitutively in floral tissues
CmTpsDul expression is specific to ’Dulce’ rind. CmTpsDul is not expressed in either the rind or flesh of ‘Noy Yizre’el’ melons at any developmental stage
Cucumis melo variety Noy Yizre'el
-
CmTpsDul expression is specific to ’Dulce’ rind. CmTpsDul is not expressed in either the rind or flesh of ‘Noy Yizre’el’ melons at any developmental stage
-
expression of AdAFS1 is significantly higher in flowers than in leaf tissue. AdAFS1 expression is similar in leaves of both cultivars ‘Chieftain’ and ‘Hayward’
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
plastidial transit peptide of 25 amino acids, and fluoresence studies using GPF-fusion protein, accession Wassilewskija
additional information
AdAFS1 protein sequences lacks predicted N-terminal transit peptide-like sequences for chloroplast targeting
-
The encoded protein appears to lack approximately 20 amino acids that are present in the N-terminal chloroplast-targeting region of monoterpene synthases. Thus, the product of this TS gene is most likely localized in the cytosol.
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
sesquiterpene synthase activity declined below pH 7.0 and at pH 5.0-5.5, it is reduced more than 50%
694765
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
AFS1 transcript increases about 4fold in peel tissue of apple fruit during the first 4 weeks of storage at 0.5°C
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
After screening a cDNA library generated from the peel tissue mRNA, a full-length terpene synthase cDNA 1931 nucleotides long is isolated (hot phenol RNA extraction protocol is used). The 1728-bp open reading frame encodes the 576 amino acid protein. Expression of the apple gene in Escherichia coli.
expression in Escherichia coli
mutated enzymes are generated using the QuickChange II site-directed mutagenesis kit. The PCR-based mutagenesis protocol is performed using pET-30a harbouring the MdAFS1 cDNAs as template. The single-site mutant enzymes overexpressed in Escherichia coli.
-
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
expression is induced in leaves by elicitor and insect treatment; expression is induced in leaves by elicitor and insect treatment
expression of AdAFS1 is significantly higher in flowers than in leaf tissue. Within floral tissues, expression is highest in petals and stamens. AdAFS1 expression is low in sepals in both sexes and also in ‘Hayward’ pistils. AdAFS1 expression in ‘Hayward’ is co-ordinated with anthesis, with low levels of expression in unopened flower buds and high levels detected in open flowers. The temporal accumulation patterns of AdAFS1 mRNA is constitutive. No difference in expression between male and female flowers. AdAFS1 expression is similar in leaves of both cultivars ‘Chieftain’ and ‘Hayward’
expression of pMdAFS1 is repressed by 1-methylcyclopropene treatment, pMdAFS1 expression is controlled by ethylene
-
induced by Lymantria dispar feeding, up to 136fold increase in transcript abundance
-
MdAFS1 transcript abundance increases rapidly in untreated Cortland and Law Rome fruit, reaching close to maximal values after 2 weeks of storage, whereas in Idared controls it increases through 4 weeks, declines slightly, and then increases to a maximum by 10 weeks. 1-Methylcyclopropene treatment initially suppresses MdAFS1 expression in all three cultivars. However, Cortland and Law Rome escape from this suppression after 10-15 weeks, with MdAFS1 transcript abundance increasing to maximal control levels by 15-20 weeks. In Cortland, but not in Law Rome, this delayed increase in expression occurrs sooner in green than in red tissue. MdAFS1 transcript levels increase gradually in 1-methylcyclopropene-treated Idared fruit, but throughout storage remains much lower than the maximum levels in untreated fruit
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D326A
-
alpha-farnesene synthase, monoterpene synthase and prenyltransferase activities are lost in the mutant
D326A/D330A
-
alpha-farnesene synthase, monoterpene synthase and prenyltransferase activities are lost in the mutant
D484A
-
85% loss of sesquiterpene synthase activity compared with wild-type enzyme. Little change in K+-independent activity; 85% loss of sesquiterpene synthase activity compared with wild-type enzyme when K+ is present
S485A
-
exhibits marginally increased sesquiterpene synthase activities, and an approximate 2fold increase in monoterpene synthase activity compared with the wild-type enzyme; mutant exhibits marginally increased sesquiterpene synthase activities, and an approximate 2fold increase in monoterpene synthase activity compared with the wild-type enzyme
S487A
-
95% decrease in sesquiterpene synthase activity compared with wild-type enzyme. Little change in K+-independent activity; 95% decrease in sesquiterpene synthase activity compared with wild-type enzyme when K+ is present
S487K
-
mutant has 35–45% of the wild-type activity with farnesyl diphosphate, with no significant alterations in the alpha-farnesene isomer ratios produced and a small decrease in catalytic efficiency; The S487K mutant has 35-45% of the wild-type activity with farnesyl diphosphate, with no significant alterations in the alpha-farnesene isomer ratios produced and a small decrease in catalytic efficiency
S488A
-
mutant shows decreases in both sesqui- and monoterpene synthase activities compared with the WT enzyme, with mono-TPS activity being reduced more than sesquiterpene synthase activity. Sesquiterpene synthase (alpha-farnesene) products produced by the mutated and wild-type enzymes are identical, there are no significant alterations in the ratios of the alpha-farnesene isomers produced.; mutant shows decreases in both sesqui- and mono-terpene synthases activities, compared with the wild-type enzyme, with mono-terpene synthases activity being reduced more than sesqui-terpene synthases activity
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Renatured/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
myc-tagged and untagged AFS1 expressed protein in bacterial inclusion-body fractions is urea-denatured, purified and renatured prior to assay of enzymatic activity.
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
agriculture
Because diphenylamine treatment leaves unwanted chemical residues on the fruit, restricts export markets, and creates environmental concerns, a long-range molecular genetic strategy for control of scald by reduction of (E,E)-alpha-farnesene synthesis in scald-susceptible apples is searched. The success of this strategy will rely on our ability to identify, clone, and characterize key genes involved in alpha-farnesene biosynthesis and its regulation by ethylene.
synthesis
expression in Sacchaomyces cerevisiae leads to a titer of (-)-alpha-copaene of 9 mg/l at 48 h and around 7 mg/l in Eschrichia coli, and the titer of (+)-delta-cadinene is 6 mg/l in Saccharomyces cerevisiae and 3.5 mg/l in Escherichia coli
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