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Enzyme Nomenclature
Information on EC 4.2.3.20 - (R)-limonene synthase
for references in articles please use BRENDA:EC4.2.3.20
Word Map on EC 4.2.3.20
- 4.2.3.20
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monoterpene
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terpene
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volatile
- citrus
- orange
- peel
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+-limonene
- linalool
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schizonepeta
- tenuifolia
- digitatum
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frugivores
- beta-pinene
- lavender
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mentha
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lavandula
- labiatae
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repelling
- angustifolia
- gpp
- isoprene
- plastidial
- gamma-terpinene
- drug development
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The enzyme appears in viruses and cellular organisms
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EC NUMBER 
COMMENTARY 
4.2.3.20
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RECOMMENDED NAME
GeneOntology No.
(R)-limonene synthase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
geranyl diphosphate = (R)-limonene + diphosphate
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geranyl diphosphate = (R)-limonene + diphosphate
forms the first step of carvone biosynthesis in caraway
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geranyl diphosphate = (R)-limonene + diphosphate
requires a divalent metal ion (preferably Mn2+) for catalysis
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
cyclization
cyclization
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-
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-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
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SYSTEMATIC NAME
IUBMB Comments
geranyl-diphosphate diphosphate-lyase [cyclizing, (+)-(4R)-limonene-forming]
Forms the first step of carvone biosynthesis in caraway. The enzyme from Carum carvi (caraway) seeds requires a divalent metal ion (preferably Mn2+) for catalysis. This enzyme occurs in Citrus, Carum (caraway) and Anethum (dill); (-)-limonene, however, is made in the fir, Abies, and mint, Mentha, by EC 4.2.3.16, (4S)-limonene synthase.
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CAS REGISTRY NUMBER
COMMENTARY
155807-65-1
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
; production of the monoterpene limonene and modulation of apoptosis-related proteins in embryonic-mouse NIH 3T3 fibroblast cells by introduction of the limonene synthase gene isolated from japanese catnip
SwissProt
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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
geranyl diphosphate
(1R,5R)-(+)-alpha-pinene + diphosphate
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geranyl diphosphate
(R)-limonene
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products are 39% (R)-limonene, 22% terpinolene, 16% (1R,5S)-camphene, 14% (1R,5R)-(+)-alpha-pinene, 8% betamyrcene and traces of alpha-phellandrene. Product pattern changes markedly to 46% limonene, 9% terpinolene, 23% alpha-pinene, 5% beta-myrcene and 4% alpha-phellandrene, when Mn2+ is supplied instead of Mg2+
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?
geranyl diphosphate
D-limonene + diphosphate
single step in plants
D-limonene shows cancer preventative and cancer therapeutic activities in vitro and in vivo, its modulates apoptosis-related genes and proteins in cultured cells
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?
geranyl diphosphate
(+)-(R)-limonene + diphosphate
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high stereoselectivity, 98.4% of (+)-product
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geranyl diphosphate
(+)-(R)-limonene + diphosphate
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product is exclusively R-(+)-limonene
?
additional information
?
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no substrates: farnesyl diphosphate, geranylgeranyl diphosphate
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additional information
?
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a concomitant increase in the level of apoptosis-related protein B-cell lymphoma protein 2 and decreases in the levels of Bcl-2 antagonist of cell death and phosphorylated c-Jun N-terminal kinase are observed in limonene-producing cells
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additional information
?
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limonene can be synthesized in animal cells using their own mevalonate pathway and limonene-producing cells may provide a new system for the elucidation of limonene function
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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
geranyl diphosphate
D-limonene + diphosphate
Q9FUW5
single step in plants
D-limonene shows cancer preventative and cancer therapeutic activities in vitro and in vivo, its modulates apoptosis-related genes and proteins in cultured cells
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?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
Mn2+
additional information
Mn2+
or Mg2+, required. Optimum concentration 0.2 mM, 68% of the efficieny with Mg2+. Product pattern changes markedly to 46% limonene, 9% terpinolene, 23% alpha-pinene, 5% beta-myrcene and 4% alpha-phellandrene, when Mn2+ is supplied instead of Mg2+; the proportions of the products change significantly when Mn2+ is supplied instead of Mg2+
additional information
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DDxxD motif, binding site for substrate-divalent metal cation complex
additional information
DDxxD motif, binding site for substrate-divalent metal cation complex
additional information
divalent metal ion required, probably Mn2+; divalent metal ion required, probably Mn2+
additional information
divalent metal ion required, probably Mn2+; divalent metal ion required, probably Mn2+
additional information
DDxxD motif, binding site for substrate-divalent metal cation complex
additional information
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DDxxD motif, binding site for substrate-divalent metal cation complex
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
geranyl diphosphate
substrate inhibition above 0.01 mM; substrate inhibition above 0.01 mM
K+
maximum inhibition above 100 mM; maximum inhibition above 100 mM
Mn2+
above 0.6 mM, activation below; above 0.6 mM, activation below
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
Mn2+
inhibition above 0.6 mM, activation below; inhibition above 0.6 mM, activation below
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0474
geranyl diphosphate
LaLIMS_RR, truncated protein; pH 7.0, 30°C
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7.5
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
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PDB
SCOP
CATH
ORGANISM
UNIPROT
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
62000
x * 62000, SDS-PAGE, x * 64000, deduced from gene sequence
64000
x * 62000, SDS-PAGE, x * 64000, deduced from gene sequence
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SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in NIH 3T3 cell; The cDNA of D-limonene synthase obtained from Japanese catnip, modified by deletion of the transit peptide sequence and addition of a new ATG initiation codon, is cloned. Establishment of transgenic mouse embryonic NIH 3T3 fibroblast cells that produce limonene by introducing the D-limonene synthase gene. Apoptosis is not observed in the limonene-producing cells.
expression in Escherichia coli; into the pGEM-T vector for sequencing and into the pGEX-T-1 vector for expression in Escherichia coli cells
introduction of limonene synthase cDNA with three different sorting signals (to localize either in cytosol or the endoplasmic reticulum) in Nicotiana tabacum. Full-length and modified enzyme are subcloned in a binary vector under the El2 promoter, which is a strong constitutive promoter, to yield pBin-FullLC1, pBin-DEltaLC1 and pBin.ERLC1 to plastidial, cytosolic and endoplasmic localization, respectively. These plasmids are introduced via Agrobacterium tumefaciens into tobacco. More than 10 transgenic tobacco plants for each construct, i.e. 15 plastid localization, 17 cytosol localization, 11 endoplasmic reticulum localization are established
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limonene cyclase enzyme Cl(+)LIMS2 produced exclusively (+)-limonene as the major product of the enzymatic catalysis. In a chimeric enzyme, substitution of ClgammaTS domain III and domain IV by their counterparts from Cl(+)LIMS2 changed product specificity to that of Cl(+)LIMS2, (+)-limonene being the major product formed
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
drug development
D-limonene is effective in cancer prevention in animal cancer models, some clinical applications have been performed
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LINKS TO OTHER DATABASES (specific for EC-Number 4.2.3.20)
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