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Information on EC 4.2.3.128 - beta-cubebene synthase
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EC Tree
4.2.3.128 beta-cubebene synthaseIUBMB Comments
Isolated from the fungus Coprinus cinereus. The enzyme also forms (+)-delta-cadinene, beta-copaene, (+)-sativene and traces of several other sequiterpenoids [2-4]. It is found in many higher plants such as Magnolia grandiflora (Southern Magnolia) together with germacrene A . See EC 4.2.3.13, (+)-delta-cadinene synthase, EC 4.2.3.127, beta-copaene synthase, EC 4.2.3.129, (+)-sativene synthase, and EC 4.2.3.23, germacrene A synthase.
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The enzyme appears in viruses and cellular organisms
Synonyms
vvtps, caryophyllene/cubebene synthase, vvshiraztps-y2, 
more
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
Cop4
Mg25
Cop4
-
-
ambiguous
-
Mg25
-
-
-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
(2E,6E)-farnesyl diphosphate = beta-cubebene + diphosphate
-
-
-
-
(2E,6E)-farnesyl diphosphate = beta-cubebene + diphosphate
reaction mechanism, overview
(2E,6E)-farnesyl diphosphate = beta-cubebene + diphosphate
reaction mechanism, structure-function relationship, overview. The reaction mechanism for (E,E)-FPP cyclization by Cop4 involves the 1,10-cyclization of a cisoid neryl cation to form a (Z,E)-germacradienyl cation, which undergoes a 1,3-hydride shift to form an allylic carbocation that is either deprotonated to yield (-)-germacrene D, the major product of Cop4, or 1,6 cyclized to the bicyclic cadinyl cation
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PATHWAY SOURCE
PATHWAYS
-
-
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SYSTEMATIC NAME
IUBMB Comments
(2E,6E)-farnesyl-diphosphate diphosphate-lyase (cyclizing, beta-cubebene-forming)
Isolated from the fungus Coprinus cinereus. The enzyme also forms (+)-delta-cadinene, beta-copaene, (+)-sativene and traces of several other sequiterpenoids [2-4]. It is found in many higher plants such as Magnolia grandiflora (Southern Magnolia) together with germacrene A [1]. See EC 4.2.3.13, (+)-delta-cadinene synthase, EC 4.2.3.127, beta-copaene synthase, EC 4.2.3.129, (+)-sativene synthase, and EC 4.2.3.23, germacrene A synthase.
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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
(2Z,6E)-farnesyl diphosphate
beta-cubebene + diphosphate
conversion of (E,E)-farnesyl diphosphate proceeds via a (6S)-beta-bisabolene carbocation in the case of Cop4
-
-
?
(E)-geraniol diphosphate
?
Cop4 converts 30% of (E)-geraniol diphosphate into cyclic monoterpene products. Limonene is synthesized as the major cyclic monoterpene product. Limonene can be derived from either a cisoid, exo- or cisoid, endo-conformation of the initial geranyl cation of the initial geranyl cation. Exo-conformation yields (Z)-beta-ocimene and linalool, while the endoconformation would give (E)-beta-ocimene
-
-
?
(2E,6E)-farnesyl diphosphate
beta-cubebene + diphosphate
-
-
-
-
?
(2E,6E)-farnesyl diphosphate
beta-cubebene + diphosphate
-
-
-
?
(2E,6E)-farnesyl diphosphate
beta-cubebene + diphosphate
Cop4 synthesizes delta-cadinene as its major product, cf. EC 4.2.3.13
-
-
?
(2E,6E)-farnesyl diphosphate
beta-cubebene + diphosphate
conversion of (E,E)-farnesyl diphosphate proceeds via an (E,E)-germacradienyl carbocation in the case of Cop4
-
-
?
(2E,6E)-farnesyl diphosphate
beta-cubebene + diphosphate
-
-
-
?
(2E,6E)-farnesyl diphosphate
beta-cubebene + diphosphate
Cop4 synthesizes delta-cadinene as its major product, cf. EC 4.2.3.13
-
-
?
(2E,6E)-farnesyl diphosphate
beta-cubebene + diphosphate
Mg25 converts farnesyl diphosphate predominantly to beta-cubebene
-
-
?
additional information
?
-
-
enzyme CoTPS2 is multifunctional and a terpene synthase that catalyses the synthesis of three sesquiterpenes, beta-ylangene, beta-copaene, and beta-cubebene
-
-
?
additional information
?
-
Cop4 cultures produce several sesquiterpene compounds, e.g. beta-cubebene, sativene, beta-copaene, and cubebol
-
-
?
additional information
?
-
Cop4 is a catalytically promiscuous enzyme that cyclizes (2E,6E)-farnesyl diphosphate into multiple products, including (-)-germacrene D and cubebol. Cop 4 produces several volatile sesquiterpene products, including delta-cadinene as the major product, when expressed in Escherichia coli
-
-
?
additional information
?
-
Cop4 cultures produce several sesquiterpene compounds, e.g. beta-cubebene, sativene, beta-copaene, and cubebol
-
-
?
additional information
?
-
the dominant reaction products generated by Mg25 are beta-cubebene with 24.5%, alpha-muurolene with 19.3%, cf. EC 4.2.3.125, delta-cadinol with 18.6%, delta-elemene with 16.0%, tau-muurolene with 10.8%, and beta-elemene with 10.8%
-
-
?
additional information
?
-
-
the enzyme also forms beta-caryophyllene via (Z,E)-germacradienyl cation and (E,E)-humulyl cation intermediates. The product profile of the VvShirazTPS-Y2 reaction includes alpha- and beta-cubebene, alpha-copaene, isocaryophyllene, alpha-caryophyllene, (+)-delta-cadinene, cadina-1,4-diene, and caryophyllene oxide, overview. The major products are isocaryophyllene and beta-cubenene
-
-
?
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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
beta-cubebene + diphosphate
-
-
-
-
?
(2E,6E)-farnesyl diphosphate
beta-cubebene + diphosphate
-
-
-
?
(2E,6E)-farnesyl diphosphate
beta-cubebene + diphosphate
Cop4 synthesizes delta-cadinene as its major product, cf. EC 4.2.3.13
-
-
?
(2E,6E)-farnesyl diphosphate
beta-cubebene + diphosphate
Cop4 synthesizes delta-cadinene as its major product, cf. EC 4.2.3.13
-
-
?
(2E,6E)-farnesyl diphosphate
beta-cubebene + diphosphate
Mg25 converts farnesyl diphosphate predominantly to beta-cubebene
-
-
?
additional information
?
-
-
enzyme CoTPS2 is multifunctional and a terpene synthase that catalyses the synthesis of three sesquiterpenes, beta-ylangene, beta-copaene, and beta-cubebene
-
-
?
additional information
?
-
Cop4 cultures produce several sesquiterpene compounds, e.g. beta-cubebene, sativene, beta-copaene, and cubebol
-
-
?
additional information
?
-
Cop4 is a catalytically promiscuous enzyme that cyclizes (2E,6E)-farnesyl diphosphate into multiple products, including (-)-germacrene D and cubebol. Cop 4 produces several volatile sesquiterpene products, including delta-cadinene as the major product, when expressed in Escherichia coli
-
-
?
additional information
?
-
Cop4 cultures produce several sesquiterpene compounds, e.g. beta-cubebene, sativene, beta-copaene, and cubebol
-
-
?
additional information
?
-
the dominant reaction products generated by Mg25 are beta-cubebene with 24.5%, alpha-muurolene with 19.3%, cf. EC 4.2.3.125, delta-cadinol with 18.6%, delta-elemene with 16.0%, tau-muurolene with 10.8%, and beta-elemene with 10.8%
-
-
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
Mn2+
NaCl
does not affect the product specificity of Cop4 significantly at 1 M
additional information
the enzyme contains the metal-binding DDXXD motif
Mg2+
-
required, enzyme CoTPS2 has the conserved aspartate-rich motif (DDXXD) and NSE/DTE motifs that chelate divalent metal ions, typically Mg2+, in the C-terminal domain
Mg2+
required, substitution of Mg2+ with Mn2+ as the divalent metal ion shifts the product profile of Cop4 to germacrene D, disfavoring subsequent ring closures that produce the cadinyl cation and its tricyclic descendents. Two consensus sequences - an aspartate rich DDXXD/E and a NSE/DTE motif - located at the entrance of the active site coordinate a trinuclear Mg2+ cluster that ligands the diphosphate moiety of the isoprenoid substrate, positions the isoprenyl chain in the binding pocket and triggers closure of the active site along with diphosphate cleavage to generate an initial transoid, allylic carbocation
Mg2+
required, maximal activities at Mg2+ concentrations of 1 to 10 mM
Mn2+
substitution of Mg2+ with Mn2+ as the divalent metal ion shifts the product profile of Cop4 to germacrene D, disfavoring subsequent ring closures that produce the cadinyl cation and its tricyclic descendents
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
increasing the reaction temperature to 37°C decreases the fidelity of Cop4. At this temperature Cop4 generates a relative larger fraction of products beta-cubebene, sativene, delta-cadinene and beta-copaene, that are derived from a cadinyl cation intermediate
-
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
kinetic analysis, overview
-
0.011
(2E,6E)-farnesyl diphosphate
wild-type enzyme, and mutants H235P and N239L, pH 8.0, 30°C
0.048
(2E,6E)-farnesyl diphosphate
Cop6 loop graft mutant Cop6L4, pH 8.0, 30°C
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7.5
maximal activity at pH 7.5, dominated by four products: beta-cubebene, alpha-muurolene, delta-cadinol, and tau-muurolene
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
changing the pH of the reaction drastically alters the fidelity of Cop4 and makes it a highly selective enzyme. Increasing the reaction temperature to 37°C decreases the fidelity of Cop4. At this temperature Cop4 generates a relative larger fraction of products beta-cubebene, sativene, delta-cadinene and beta-copaene, that are derived from a cadinyl cation intermediate. The histidine side chain in the Cop4 loop, in particular, has a strong impact on the net charge of the loop at different pH values
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
i.e. Citrus aurantium var. sinensis, pineapple sweet orange
UniProt
brenda
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
-
CoTPS2 is highly expressed at the floral bud stage
brenda
additional information
Mg25 is much more evident in young developing leaf tissues than in older, more mature leaves
brenda
additional information
-
the enzyme expression increases from undeveloped small flowers to mature green flowers, is absent in mature yellow flowers, but very high in flower buds
brenda
additional information
in orange tissues, the sesquiterpene profile is qualitatively rich. Overall, up to 25 sesquiterpenes are identified in total, overview. Small amounts of beta-caryophyllene are detected in all samples, while alpha-copaene, beta-elemene, alpha-humulene, and alpha-selinene are emitted by all tissues except young leaves. Beside this, each tissue shows a characteristic sesquiterpene emission profile. Major sesquiterpenes emitted by adult leaves are beta-elemene and beta-caryophyllene, while flowers emitt nerolidol, absent from most tissues analyzed. In fruit tissues, valencene emission contributes greatly to total emitted volatiles, in much more extent in peel than in pulp
brenda
additional information
Mg25 transcript levels are low or below detection limits in tepal and carpel tissues
brenda
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
metabolism
physiological function
additional information
evolution
the terpene synthase Mg25 belongs to the angiosperm sesquiterpene synthase subclass TPS-a. The structural diversity observed in the three Magnolia terpene synthase genes have occurred either by a rapid loss of introns from a common ancestor TPS gene or by a gain of introns into an intron-deficient progenote TPS gene
evolution
-
the enzyme belongs to the terpene sythase superfamily, subfamily TPS-a. The arginine-tryptophan motif, R(R)X8W, present at the N terminus of most mono-TPS and in some sesqui-TPS and di-TPS, is found in CoTPS2. CoTPS2 does not contain a plastid Tp sequence
metabolism
-
the enzyme is part of the biosynthesis of volatile organic compounds in flowers
metabolism
-
the farnesyl cation can undergo either 1,10- or 1,11-cyclization, giving rise to either an (E,E)-germacradienyl cation or an (E,E)-humulyl cation, respectively
physiological function
the enzyme belongs to the sesquiterpene synthases that are responsible for the cyclization of farnesyl diphosphate into a myriad of structurally diverse compounds with various biological activities
physiological function
in sweet orange tissues sesquiterpene profile is qualitatively rich. Overall, up to 25 sesquiterpenes are identified in total. Enzyme CsSesquiTPS1 catalyzes formation of a 62:38% mixture of (Z)-beta-cubebene and alpha-copaene
physiological function
-
recombinant CoTPS2 catalysed the synthesis of three compounds, beta-ylangene, beta-copaene, and beta-cubebene, from farnesyl diphosphate. CoTPS2 is a multifunctional beta-ylangene/beta-copaene/beta-cubebene synthase capable of producing three sesquiterpenes, beta-ylangene, beta-copaene, and beta-cubebene. The enzyme is part of the biosynthesis of volatile organic compounds (VOCs) in flowers. Floral scents are a key factor in plant-insect interactions and are vital for successful pollination. The scented flowers of Cananga odorata var. fruticosa are analysed by GC-MS and a total of 49 VOCs are identified at four different stages of flower development. The bulk of these VOCs are terpenes, mainly sesquiterpenes. Enzyme CoTPS2 is a multifunctional terpene synthase that catalyses the synthesis of three sesquiterpenes, beta-ylangene, beta-copaene, and beta-cubebene
additional information
directed mutations of the H-alpha1 loop have a marked effect on the product profile Cop4, loop mutations in Cop4 also implicate specific residues responsible for the pH sensitivity of the enzyme. In vivo analysis of sesquiterpene product profiles of H-alpha1 loop mutants, overview. Mutation of K233, presumed to interact with the second Asp92 in the DDXXD motif of Cop4, does not significantly change the overall product promiscuity of Cop4, though beta-cubebene, with 27% of total sesquiterpene products, does become the major product
additional information
structural modeling, structure-function relationship, overview. Changing the pH of the reaction drastically alters the fidelity of Cop4 and makes it a highly selective enzyme
additional information
two terpenes dominate the plant sesquiterpene profile, with beta-cubebene accounting for 31.3% of the total and beta-elemene for 25.3%. The enzyme contains the conserved Asp-rich domain, DDXXD, that coordinates substrate binding via the formation of divalent cation salt bridges
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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). TPS2_CANOD
561
0
65255
Swiss-Prot
other Location (Reliability: 2)
BCUSY_MAGGA
550
0
63421
Swiss-Prot
other Location (Reliability: 3)
COP4_COPC7
Coprinopsis cinerea (strain Okayama-7 / 130 / ATCC MYA-4618 / FGSC 9003)
345
0
39693
Swiss-Prot
other Location (Reliability: 3)
STS10_POSPM
Postia placenta (strain ATCC 44394 / Madison 698-R)
336
0
38275
Swiss-Prot
other Location (Reliability: 4)
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
structural modeling, structure-function relationship, overview. Cop4 has a large binding pocket in the open conformation
additional information
structure comparison, homology structural modeling of Cop enzymes, overview. Cop4 has a large active site cavity that undergoes substantial conformational change in the model upon ligand binding
additional information
the enzyme contains the conserved Asp-rich domain, DDXXD, that coordinates substrate binding via the formation of divalent cation salt bridges
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
H235P
site-directed mutagenesis, the mutation converts Cop4 into a much more selective enzyme that produces (-)-germacrene D as the major cyclization product with 50% of total sesquiterpenes products. The mutant makes beta-ylangene, which is a diastereomer of beta-copaene and not synthesized by wild-type Cop4
K233I
site-directed mutagenesis, mutation of K233, interacting with the second Asp92 in the DDXXD motif of Cop4, does not significantly change the overall product promiscuity of Cop4, though beta-cubebene 4 does become the major product
N238L
site-directed mutagenesis, the mutant shows a altered product profile compared to the wild-type enzyme with a slight reduction in beta-cubebene synthesis. The mutant does no longer show production of cubebol and has reduced (-)-germacrene D synthesis activity compared to the wild-type enzyme, synthesis of beta-cubebene, beta-copaene, delta-cadinene, and alpha-cubebene
N239L
site-directed mutagenesis, no production of beta-cubebene, the mutation converts Cop4 into a much more selective enzyme that produces (-)-germacrene D as the major cyclization product with 50% of total sesquiterpenes products. The mutant makes beta-ylangene, which is a diastereomer of beta-copaene and not synthesized by wild-type Cop4
T236L
site-directed mutagenesis, the mutant shows a altered product profile compared to the wild-type enzyme with an increase in beta-cubebene synthesis. The mutant does no longer show production of cubebol and (-)-germacrene D compared to the wild-type enzyme
additional information
directed mutations of the H-alpha1 loop have a marked effect on the product profile Cop4, loop mutations in Cop4 also implicate specific residues responsible for the pH sensitivity of the enzyme. H-alpha1 loop swap between Cop4 and Cop6 shifts Cop4 to a germacrene D synthase
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3)pLysS by nickel affinity chromatography
-
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression of wild-type and mutant enzymes in Escherichia coli strain JM109
gene cop4, DNA and amino acid sequence determination and analysis, phylogenetic analysis, recombinant expression in Escherichia coli strain JM109
gene CsSesquiTPS1, DNA and amino acid sequence determination and analysis, sequence comparisons and phylogenetic analysis, the enzyme encoded by CsSesquiTPS1 produces a 62:38% mixture of (Z)-beta-cubebene and alpha-copaene
gene Mg25, DNA and amino acid sequence determination and analysis, Mg25 has one single intron located near the 5' terminus of the gene, expression analysis and phylogenetic analysis
gene TPS2, sequence comparisons and phylogenetic analysis and tree, quantitative real-time PCR enzyme expression analysis, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3)pLysS, transient and functional recombinant expression of YFP-tagged enzyme CoTPS2 in transgenic Nicotiana benthamiana leaves in cytosol under control of CaMV 35S promoter via Agrobacterium tumefaciens-mediated transfection method
-
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Agger, S.; Lopez-Gallego, F.; Schmidt-Dannert, C.
Diversity of sesquiterpene synthases in the basidiomycete Coprinus cinereus
Mol. Microbiol.
72
1181-1195
2009
Coprinopsis cinerea (A8NU13), Coprinopsis cinerea ATCC MYA-4618 (A8NU13)
brenda
Lopez-Gallego, F.; Wawrzyn, G.; Schmidt-Dannert, C.
Selectivity of fungal sesquiterpene synthases: Role of the active sites H-1alpha loop in catalysis
Appl. Environ. Microbiol.
76
7723-7733
2010
Coprinopsis cinerea (A8NU13)
brenda
Lopez-Gallego, F.; Agger, S.A.; Abate-Pella, D.; Distefano, M.D.; Schmidt-Dannert, C.
Sesquiterpene synthases Cop4 and Cop6 from Coprinus cinereus: catalytic promiscuity and cyclization of farnesyl pyrophosphate geometric isomers
ChemBioChem
11
1093-1106
2010
Coprinopsis cinerea (A8NU13)
brenda
Lee, S.; Chappell, J.
Biochemical and genomic characterization of terpene synthases in Magnolia grandiflora
Plant Physiol.
147
1017-1033
2008
Magnolia grandiflora (B3TPQ6)
brenda
Jin, J.; Kim, M.J.; Dhandapani, S.; Tjhang, J.G.; Yin, J.L.; Wong, L.; Sarojam, R.; Chua, N.H.; Jang, I.C.
The floral transcriptome of ylang ylang (Cananga odorata var. fruticosa) uncovers biosynthetic pathways for volatile organic compounds and a multifunctional and novel sesquiterpene synthase
J. Exp. Bot.
66
3959-3975
2015
Cananga odorata var. fruticosa
brenda
Alquezar, B.; Rodriguez, A.; de la Pena, M.; Pena, L.
Genomic analysis of terpene synthase family and functional characterization of seven sesquiterpene synthases from Citrus sinensis
Front. Plant Sci.
8
1481
2017
Citrus sinensis (D0UZK2)
brenda
Dueholm, B.; Drew, D.P.; Sweetman, C.; Simonsen, H.T.
In planta and in silico characterization of five sesquiterpene synthases from Vitis vinifera (cv. Shiraz) berries
Planta
249
59-70
2019
Vitis vinifera
brenda
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Release 2023.1 (January 2023)
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