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Information on EC 4.2.3.20 - (R)-limonene synthase and Organism(s) Citrus sinensis and UniProt Accession A0A1C9J6A7

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EC Tree
     4 Lyases
         4.2 Carbon-oxygen lyases
             4.2.3 Acting on phosphates
                4.2.3.20 (R)-limonene synthase
IUBMB 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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Citrus sinensis
UNIPROT: A0A1C9J6A7
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The taxonomic range for the selected organisms is: Citrus sinensis
The enzyme appears in selected viruses and cellular organisms
Synonyms
d-limonene synthase, (+)-limonene synthase, citmtse1, cl(+)lims2, lalims, (+)-ls, cl(+)lims1, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
(+)-limonene synthase
-
(+)-limonene synthase
(+)-LS
-
-
Cl(+)LIMS1
-
-
-
-
Cl(+)LIMS2
-
-
-
-
d-limonene synthase
-
-
dLMS
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
cyclization
-
-
-
-
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.
CAS REGISTRY NUMBER
COMMENTARY hide
155807-65-1
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
geranyl diphosphate
(R)-limonene + diphosphate
show the reaction diagram
-
-
-
?
2-fluorogeranyl diphosphate
?
show the reaction diagram
-
-
-
-
?
2-fluoroneryl diphosphate
?
show the reaction diagram
-
-
-
-
?
geranyl diphosphate
(D)-limonene + diphosphate
show the reaction diagram
-
-
-
-
?
geranyl diphosphate
(R)-limonene + diphosphate
show the reaction diagram
-
-
-
-
?
geranyl diphosphate
(S)-limonene + diphosphate
show the reaction diagram
-
-
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
geranyl diphosphate
(R)-limonene + diphosphate
show the reaction diagram
-
-
-
?
geranyl diphosphate
(D)-limonene + diphosphate
show the reaction diagram
-
-
-
-
?
geranyl diphosphate
(R)-limonene + diphosphate
show the reaction diagram
-
-
-
-
?
geranyl diphosphate
(S)-limonene + diphosphate
show the reaction diagram
-
-
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mg2+
may replace Mn2+ but with much lower efficiency (maximum activity at 20 mM)
Mn2+
required for activity, 0.4 mM used in assay conditions
additional information
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Mn2+
the enzyme is strongly inhibited at concentrations of more than 1 mM
2-Fluorogeranyl diphosphate
-
competitive inhibitor
2-fluoroneryl diphosphate
-
competitive inhibitor
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0131
geranyl diphosphate
at pH 8.0, temperature not specified in the publication
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.186
geranyl diphosphate
at pH 8.0, temperature not specified in the publication
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
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
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
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
navel orange
UniProt
Manually annotated by BRENDA team
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
RLC1_CITSI
607
0
70354
Swiss-Prot
Chloroplast (Reliability: 2)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
70000
gel filtration
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
monomer
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
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
Ni-Sepharose column chromatography
Ni2+-affinity column chromatography
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21-CodonPlus(DE3)-RIL cells
expressed in Escherichia coli BL21-CodonPlus(DE3)-RIL cells
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Morehouse, B.R.; Kumar, R.P.; Matos, J.O.; Olsen, S.N.; Entova, S.; Oprian, D.D.
Functional and structural characterization of a (+)-limonene synthase from Citrus sinensis
Biochemistry
56
1706-1715
2017
Citrus sinensis (A0A1C9J6A7), Citrus sinensis
Manually annotated by BRENDA team
Kumar, R.P.; Morehouse, B.R.; Matos, J.O.; Malik, K.; Lin, H.; Krauss, I.J.; Oprian, D.D.
Structural characterization of early Michaelis complexes in the reaction catalyzed by (+)-limonene synthase from Citrus sinensis using fluorinated substrate analogues
Biochemistry
56
1716-1725
2017
Citrus sinensis
Manually annotated by BRENDA team
Rodriguez, A.; Peris, J.E.; Redondo, A.; Shimada, T.; Pena, L.
Principal component analysis (PCA) of volatile terpene compounds dataset emitted by genetically modified sweet orange fruits and juices in which a D-limonene synthase was either up- or down-regulated vs. empty vector controls
Data Brief
9
355-361
2016
Citrus sinensis
Manually annotated by BRENDA team
Rodriguez, A.; Peris, J.E.; Redondo, A.; Shimada, T.; Costell, E.; Carbonell, I.; Rojas, C.; Pena, L.
Impact of D-limonene synthase up- or down-regulation on sweet orange fruit and juice odor perception
Food Chem.
217
139-150
2017
Citrus sinensis
Manually annotated by BRENDA team
Rodriguez, A.; Kava, V.; Latorre-Garcia, L.; da Silva, G.J.; Pereira, R.G.; Glienke, C.; Ferreira-Maba, L.S.; Vicent, A.; Shimada, T.; Pena, L.
Engineering D-limonene synthase down-regulation in orange fruit induces resistance against the fungus Phyllosticta citricarpa through enhanced accumulation of monoterpene alcohols and activation of defence
Mol. Plant Pathol.
19
2077-2093
2018
Citrus sinensis
Manually annotated by BRENDA team
Rodriguez, A.; Shimada, T.; Cervera, M.; Redondo, A.; Alquezar, B.; Rodrigo, M.J.; Zacarias, L.; Palou, L.; Lopez, M.M.; Pena, L.
Resistance to pathogens in terpene down-regulated orange fruits inversely correlates with the accumulation of D-limonene in peel oil glands
Plant Signal. Behav.
10
e1028704
2015
Citrus sinensis
Manually annotated by BRENDA team