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Information on EC 4.2.3.20 - (R)-limonene synthase
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EC Tree
4.2.3.20 (R)-limonene synthaseIUBMB Comments
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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Word Map
- 4.2.3.20
-
monoterpene
- citrus
-
terpene
- orange
- peel
-
+-limonene
- linalool
- gpp
-
schizonepeta
- tenuifolia
-
mentha
- digitatum
- beta-pinene
-
lavandula
- angustifolia
- spicata
-
frugivores
- labiatae
-
neryl
- lavender
- gamma-terpinene
- isoprene
- drug development
The enzyme appears in viruses and cellular organisms
Synonyms
d-limonene synthase, (+)-limonene synthase, citmtse1, cl(+)lims2, lalims, (+)-ls, cl(+)lims1, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
(+)-limonene synthase
(+)-LS
CitMTSE1
Cl(+)LIMS1
Cl(+)LIMS2
-
-
-
-
d-limonene synthase
dLMS
-
-
-
-
limonene synthase
(+)-limonene synthase
-
-
-
-
Cl(+)LIMS1
-
-
-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
geranyl diphosphate = (R)-limonene + diphosphate
requires a divalent metal ion (preferably Mn2+) for catalysis
geranyl diphosphate = (R)-limonene + diphosphate
forms the first step of carvone biosynthesis in caraway
-
geranyl diphosphate = (R)-limonene + diphosphate
-
-
-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
cyclization
cyclization
-
-
-
-
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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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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
-
-
-
?
geranyl diphosphate
D-limonene + diphosphate
Nepeta tenuifolia
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
-
?
geranyl diphosphate
(+)-(R)-limonene + diphosphate
-
-
high stereoselectivity, 98.4% of (+)-product
?
geranyl diphosphate
(+)-(R)-limonene + diphosphate
-
product is exclusively R-(+)-limonene
?
geranyl diphosphate
(R)-limonene + diphosphate
-
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+
-
?
additional information
?
-
no substrates: farnesyl diphosphate, geranylgeranyl diphosphate
-
-
?
additional information
?
-
-
no substrates: farnesyl diphosphate, geranylgeranyl diphosphate
-
-
?
additional information
?
-
Nepeta tenuifolia
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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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
geranyl diphosphate
D-limonene + diphosphate
Nepeta tenuifolia
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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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
Mn2+
additional information
Mg2+
may replace Mn2+ but with much lower efficiency (maximum activity at 20 mM)
Mn2+
the proportions of the products change significantly when Mn2+ is supplied instead of Mg2+
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+
additional information
DDxxD motif, binding site for substrate-divalent metal cation complex
additional information
-
DDxxD motif, binding site for substrate-divalent metal cation complex
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INHIBITOR
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
Mn2+
the enzyme is strongly inhibited at concentrations of more than 1 mM
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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DISEASE
TITLE OF PUBLICATION
LINK TO PUBMED
Infections
Terpene down-regulation triggers defense responses in transgenic orange leading to resistance against fungal pathogens.
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0131
geranyl diphosphate
at pH 8.0, temperature not specified in the publication
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.00054
2-Fluorogeranyl diphosphate
-
pH and temperature not specified in the publication
0.00024
2-fluoroneryl diphosphate
-
pH and temperature not specified in the publication
0.186
geranyl diphosphate
at pH 8.0, temperature not specified in the publication
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0024
2-Fluorogeranyl diphosphate
-
pH and temperature not specified in the publication
0.0395
2-fluoroneryl diphosphate
-
pH and temperature not specified in the publication
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7.5
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Nepeta tenuifolia
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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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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
malfunction
-
Drastic down-regulation of D-limonene synthase gene expression in the peel of transgenic oranges leads to fruit resistance against Penicillium digitatum, Xanthomonas citri subsp. citri and other specialized pathogens
malfunction
-
enzyme down-regulation in orange fruit induces resistance against the fungus Phyllosticta citricarpa through enhanced accumulation of monoterpene alcohols and activation of defence
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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). RLC1_CITLI
606
0
70348
Swiss-Prot
Chloroplast (Reliability: 5)
RLC1_CITSI
607
0
70354
Swiss-Prot
Chloroplast (Reliability: 2)
BCGS_ORIVU
555
0
64443
Swiss-Prot
other Location (Reliability: 2)
LALIM_LAVAN
602
0
70345
Swiss-Prot
Chloroplast (Reliability: 3)
TPS1_TOOSI
595
0
68911
Swiss-Prot
Chloroplast (Reliability: 4)
A0A2G9GEG6_9LAMI
606
0
70951
TrEMBL
other Location (Reliability: 4)
B9S893_RICCO
250
0
28930
TrEMBL
other Location (Reliability: 4)
B9RXW6_RICCO
180
0
20877
TrEMBL
Mitochondrion (Reliability: 4)
A0A2G9GQ38_9LAMI
606
0
70759
TrEMBL
Mitochondrion (Reliability: 4)
A0A2G9HPL8_9LAMI
607
0
70197
TrEMBL
Chloroplast (Reliability: 2)
B9TL72_RICCO
143
0
17319
TrEMBL
other Location (Reliability: 2)
B9S899_RICCO
226
0
26444
TrEMBL
other Location (Reliability: 3)
B9S898_RICCO
192
0
22128
TrEMBL
other Location (Reliability: 4)
A0A7C8YC60_OPUST
Opuntia cardona
289
0
33062
TrEMBL
other Location (Reliability: 3)
A0A7C8YC60_OPUST
289
0
33062
TrEMBL
other Location (Reliability: 3)
B9S897_RICCO
123
0
14157
TrEMBL
other Location (Reliability: 3)
B9S8A3_RICCO
222
0
26283
TrEMBL
other Location (Reliability: 4)
A0A7C9E4H7_OPUST
248
0
28453
TrEMBL
other Location (Reliability: 2)
B9RH09_RICCO
599
0
69129
TrEMBL
Chloroplast (Reliability: 4)
B9T537_RICCO
257
0
29569
TrEMBL
other Location (Reliability: 1)
A0A6M9BIX0_9ROSI
399
0
46453
TrEMBL
Chloroplast (Reliability: 2)
B9SXQ2_RICCO
351
0
40294
TrEMBL
other Location (Reliability: 3)
B9RPM0_RICCO
596
0
68363
TrEMBL
Chloroplast (Reliability: 2)
B9RPN5_RICCO
288
0
32558
TrEMBL
Secretory Pathway (Reliability: 5)
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
70000
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
monomer
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
apoenzyme, sitting drop vapor diffusion method, using 12-16% (w/v) PEG 8000 as precipitant
in complex with 2-fluorogeranyl diphosphate or 2-fluoroneryl diphosphate, vapor diffusion method
-
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE