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Information on EC 4.2.3.13 - (+)-delta-cadinene synthase and Organism(s) Gossypium arboreum and UniProt Accession Q39760
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4.2.3.13 (+)-delta-cadinene synthaseIUBMB Comments
The sesquiterpenoid (+)-delta-cadinene is an intermediate in phytoalexin biosynthesis. Mg2+ is required for activity.
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Word Map
- 4.2.3.13
- synthases
-
terpenoids
- sesquiterpenoids
- germacrene
-
geranyl
- linalool
- arboreum
-
+-delta-cadinene
- lavandula
- beta-caryophyllene
-
multiproduct
-
fragrant
- alpha-humulene
-
agarwood
-
e,e-farnesyl
-
e-beta-farnesene
- amorpha-4,11-diene
-
ddxxd
- aquilaria
- 5-epi-aristolochene
- synthesis
- agriculture
The taxonomic range for the selected organisms is: Gossypium arboreum
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Synonyms
sesquiterpene synthase, (+)-delta-cadinene synthase, cdn1-c1, cadinene synthase, delta-cadinene synthase, pntps2, cadinol/cadinene synthase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
2-trans,6-trans-farnesyl-diphosphate diphosphate-lyase (cyclizing, (+)-alpha-cadinene-forming)
-
-
-
-
cyclase, delta-cadinene
-
-
-
-
delta-cadinene cyclase
-
-
-
-
delta-cadinene synthase
farnesyl diphosphate-delta-cadinene cyclase
-
-
-
-
delta-cadinene synthase
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
(2E,6E)-farnesyl diphosphate = (+)-delta-cadinene + diphosphate
catalytic mechanism, overview
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
elimination of diphosphate
-
-
-
-
PATHWAY SOURCE
PATHWAYS
-
-, -
SYSTEMATIC NAME
IUBMB Comments
(2E,6E)-farnesyl diphosphate diphosphate-lyase (cyclizing, (+)-delta-cadinene-forming)
The sesquiterpenoid (+)-delta-cadinene is an intermediate in phytoalexin biosynthesis. Mg2+ is required for activity.
CAS REGISTRY NUMBER
COMMENTARY
166800-09-5
-
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
(+)-delta-cadinene + diphosphate
-
-
-
?
(2E,6E)-farnesyl diphosphate
(+)-delta-cadinene + germacradien-4-ol + diphosphate
-
-
-
?
(2E,6Z)-farnesyl diphosphate
(+)-delta-cadinene + diphosphate
-
-
-
?
nerolidyl diphosphate
(+)-delta-cadinene + alpha-bisabolol + beta-bisabolene + beta-farnesene + ?
-
-
?
additional information
?
-
delta-cadinene synthase is a sesquiterpene cyclase that utilises the universal achiral precursor farnesyl diphosphate (FDP) to generate predominantly the bicyclic sesquiterpene delta-cadinene and about 2% germacradien-4-ol
-
-
?
2-trans,6-trans-farnesyl diphosphate
(+)-delta-cadinene + diphosphate
-
-
?
2-trans,6-trans-farnesyl diphosphate
(+)-delta-cadinene + diphosphate
the fungal-elicited production of a (+)-delta-cadinene synthase is consistent with a role for this enzyme as the first committed step in the pathways leading to the related phytoalexins gossypol and lacinilene C in cotton
-
-
?
2-trans,6-trans-farnesyl diphosphate
(+)-delta-cadinene + diphosphate
-
-
-
?
2-trans,6-trans-farnesyl diphosphate
(+)-delta-cadinene + diphosphate
-
-
?
2-trans,6-trans-farnesyl diphosphate
(+)-delta-cadinene + diphosphate
-
-
?
2-trans,6-trans-farnesyl diphosphate
(+)-delta-cadinene + diphosphate
the fungal-elicited production of a (+)-delta-cadinene synthase is consistent with a role for this enzyme as the first committed step in the pathways leading to the related phytoalexins gossypol and lacinilene C in cotton
-
-
?
2-trans,6-trans-farnesyl diphosphate
(+)-delta-cadinene + diphosphate
-
amount of enzyme does not increase significantly in stems treated with Verticillium dahliae due to a high basal level of enzyme in untreated stems
-
?
2-trans,6-trans-farnesyl diphosphate
(+)-delta-cadinene + diphosphate
-
the enzyme is encoded by a complex gene family that based on homology can be divided into two subfamilies, cad1-A and cad1-C
-
?
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
2-trans,6-trans-farnesyl diphosphate
(+)-delta-cadinene + diphosphate
the fungal-elicited production of a (+)-delta-cadinene synthase is consistent with a role for this enzyme as the first committed step in the pathways leading to the related phytoalexins gossypol and lacinilene C in cotton
-
-
?
(2E,6E)-farnesyl diphosphate
(+)-delta-cadinene + diphosphate
-
-
-
?
(2E,6E)-farnesyl diphosphate
(+)-delta-cadinene + germacradien-4-ol + diphosphate
-
-
-
?
additional information
?
-
delta-cadinene synthase is a sesquiterpene cyclase that utilises the universal achiral precursor farnesyl diphosphate (FDP) to generate predominantly the bicyclic sesquiterpene delta-cadinene and about 2% germacradien-4-ol
-
-
?
2-trans,6-trans-farnesyl diphosphate
(+)-delta-cadinene + diphosphate
-
-
?
2-trans,6-trans-farnesyl diphosphate
(+)-delta-cadinene + diphosphate
the fungal-elicited production of a (+)-delta-cadinene synthase is consistent with a role for this enzyme as the first committed step in the pathways leading to the related phytoalexins gossypol and lacinilene C in cotton
-
-
?
2-trans,6-trans-farnesyl diphosphate
(+)-delta-cadinene + diphosphate
-
amount of enzyme does not increase significantly in stems treated with Verticillium dahliae due to a high basal level of enzyme in untreated stems
-
?
2-trans,6-trans-farnesyl diphosphate
(+)-delta-cadinene + diphosphate
-
the enzyme is encoded by a complex gene family that based on homology can be divided into two subfamilies, cad1-A and cad1-C
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0017
2-trans,6-trans-farnesyl diphosphate
pH 7, 30°C, fusion protein composed of the pXC1-encoded protein and the histidine leader peptide derived from pET28
0.00065
nerolidyl diphosphate
pH 7.5, 30ºC, recombinant CDN1-C1 enzyme
additional information
additional information
Michaelis-Menten steady-state kinetics, overview
-
0.00058
(2E,6E)-farnesyl diphosphate
wild type enzyme, at pH 7.5 and 25°C
0.00058
(2E,6E)-farnesyl diphosphate
recombinant His6-tagged wild-type enzyme, pH 7.5, 25°C
0.00145
(2E,6E)-farnesyl diphosphate
mutant enzyme W279E, at pH 7.5 and 25°C
0.00145
(2E,6E)-farnesyl diphosphate
recombinant mutant W279E, pH 7.5, 25°C
0.0019
(2E,6E)-farnesyl diphosphate
mutant enzyme W279M, at pH 7.5 and 25°C
0.0019
(2E,6E)-farnesyl diphosphate
recombinant mutant W279M, pH 7.5, 25°C
0.0022
(2E,6E)-farnesyl diphosphate
recombinant mutant W279A, pH 7.5, 25°C
0.00223
(2E,6E)-farnesyl diphosphate
mutant enzyme W279A, at pH 7.5 and 25°C
0.0032
(2E,6E)-farnesyl diphosphate
wild type enzyme, at pH 8.0 and 30°C
0.0032
(2E,6E)-farnesyl diphosphate
wild type enzyme, at pH 7.5 and 25°C
0.00428
(2E,6E)-farnesyl diphosphate
mutant enzyme W279Y, at pH 7.5 and 25°C
0.0043
(2E,6E)-farnesyl diphosphate
recombinant mutant W279Y, pH 7.5, 25°C
0.008
(2E,6E)-farnesyl diphosphate
mutant enzyme W279Q, at pH 7.5 and 25°C
0.008
(2E,6E)-farnesyl diphosphate
recombinant mutant W279Q, pH 7.5, 25°C
0.0092
(2E,6E)-farnesyl diphosphate
recombinant mutant W279D, pH 7.5, 25°C
0.00924
(2E,6E)-farnesyl diphosphate
mutant enzyme W279D, at pH 7.5 and 25°C
0.00945
(2E,6E)-farnesyl diphosphate
mutant enzyme W279L, at pH 7.5 and 25°C
0.0095
(2E,6E)-farnesyl diphosphate
recombinant mutant W279L, pH 7.5, 25°C
0.00605
2-trans,6-trans-farnesyl diphosphate
pH 7.5, 30ºC, recombinant CDN1-C1 enzyme
0.007
2-trans,6-trans-farnesyl diphosphate
-
isoenzyme CAD1-A, pH 8.7, 30°C
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.033
2-trans,6-trans-farnesyl diphosphate
fusion protein composed of the pXC1-encoded protein and the histidine leader peptide derived from pET28, pH 7, 30°C
0.00059
(2E,6E)-farnesyl diphosphate
mutant enzyme W279E, at pH 7.5 and 25°C
0.00059
(2E,6E)-farnesyl diphosphate
recombinant mutant W279E, pH 7.5, 25°C
0.00067
(2E,6E)-farnesyl diphosphate
mutant enzyme W279D, at pH 7.5 and 25°C
0.00067
(2E,6E)-farnesyl diphosphate
recombinant mutant W279D, pH 7.5, 25°C
0.00073
(2E,6E)-farnesyl diphosphate
mutant enzyme W279Y, at pH 7.5 and 25°C
0.00073
(2E,6E)-farnesyl diphosphate
recombinant mutant W279Y, pH 7.5, 25°C
0.001
(2E,6E)-farnesyl diphosphate
wild type enzyme, at pH 7.5 and 25°C
0.00109
(2E,6E)-farnesyl diphosphate
mutant enzyme W279M, at pH 7.5 and 25°C
0.0011
(2E,6E)-farnesyl diphosphate
recombinant mutant W279M, pH 7.5, 25°C
0.00127
(2E,6E)-farnesyl diphosphate
His-tagged recombinant enzyme, at pH 7.5 and 25°C
0.00127
(2E,6E)-farnesyl diphosphate
recombinant His6-tagged wild-type enzyme, pH 7.5, 25°C
0.003
(2E,6E)-farnesyl diphosphate
mutant enzyme W279Q, at pH 7.5 and 25°C
0.003
(2E,6E)-farnesyl diphosphate
recombinant mutant W279Q, pH 7.5, 25°C
0.0031
(2E,6E)-farnesyl diphosphate
recombinant mutant W279A, pH 7.5, 25°C
0.00312
(2E,6E)-farnesyl diphosphate
mutant enzyme W279A, at pH 7.5 and 25°C
0.0038
(2E,6E)-farnesyl diphosphate
mutant enzyme W279L, at pH 7.5 and 25°C
0.0038
(2E,6E)-farnesyl diphosphate
recombinant mutant W279L, pH 7.5, 25°C
0.01
(2E,6E)-farnesyl diphosphate
wild type enzyme, at pH 8.0 and 30°C
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.073
(2E,6E)-farnesyl diphosphate
recombinant mutant W279D, pH 7.5, 25°C
0.17
(2E,6E)-farnesyl diphosphate
recombinant mutant W279Y, pH 7.5, 25°C
0.38
(2E,6E)-farnesyl diphosphate
recombinant mutant W279Q, pH 7.5, 25°C
0.4
(2E,6E)-farnesyl diphosphate
recombinant mutant W279L, pH 7.5, 25°C
0.41
(2E,6E)-farnesyl diphosphate
recombinant mutant W279E, pH 7.5, 25°C
0.58
(2E,6E)-farnesyl diphosphate
recombinant mutant W279M, pH 7.5, 25°C
0.7
(2E,6E)-farnesyl diphosphate
mutant enzyme W279D, at pH 7.5 and 25°C
1.41
(2E,6E)-farnesyl diphosphate
recombinant mutant W279A, pH 7.5, 25°C
1.7
(2E,6E)-farnesyl diphosphate
mutant enzyme W279Y, at pH 7.5 and 25°C
2.2
(2E,6E)-farnesyl diphosphate
recombinant His6-tagged wild-type enzyme, pH 7.5, 25°C
2.5
(2E,6E)-farnesyl diphosphate
mutant enzyme W279Q, at pH 7.5 and 25°C
3.1
(2E,6E)-farnesyl diphosphate
wild type enzyme, at pH 8.0 and 30°C
4
(2E,6E)-farnesyl diphosphate
mutant enzyme W279L, at pH 7.5 and 25°C
4.1
(2E,6E)-farnesyl diphosphate
mutant enzyme W279E, at pH 7.5 and 25°C
5.7
(2E,6E)-farnesyl diphosphate
mutant enzyme W279M, at pH 7.5 and 25°C
14
(2E,6E)-farnesyl diphosphate
mutant enzyme W279A, at pH 7.5 and 25°C
21.7
(2E,6E)-farnesyl diphosphate
wild type enzyme, at pH 7.5 and 25°C
31
(2E,6E)-farnesyl diphosphate
wild type enzyme, at pH 7.5 and 25°C
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
specific activity of the enzyme increases concomitantly with the cad1 transcripts in developing cottonseeds
additional information
-
specific activity of the enzyme increases concomitantly with the cad1 transcripts in developing cottonseeds
additional information
-
in roots the activity increases on day 7 post germination. In cotyledons and hypocotyls the activity decreases on day 7 post germination
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
time-dependent 10fold increase in mRNA in response to a challenge by preparation from Verticillium dahliae
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
if W279 in delta-cadinene synthase is replaced with various smaller amino acids, the ratio of alcohol versus hydrocarbon product is directly proportional to the van der Waals volume of the amino acid side chain. Mutant DCS-W279A is a catalytically highly efficient germacradien-4-ol synthase that produces predominantly germacradien-4-ol in addition to 11% delta-cadinene
physiological function
enzyme DCS from Gossypium arboreum produces (+)-delta-cadinene in the first committed step of the biosynthetic pathway to the phytoalexin gossypol
additional information
catalytic mechanisms of (+)-delta-cadinene synthase (DCS) and germacradien-4-ol synthase (GdolS) catalysed conversions of (2E,6E)-farnesyl diphosphate to of (+)-delta-cadinene and germacradien-4-ol, analysis of the mechanism by which sesquiterpene synthases discriminate between deprotonation and reaction with a nucleophilic water molecule, molecular dynamics simulations, overview. Enzyme active site structure with bound Mg2+ ions
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). DCS2_GOSAR
554
0
64159
Swiss-Prot
Chloroplast (Reliability: 5)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
modeled from amino acid sequence of CDN1-C1, in SWISS-MODEL automated homology modeling server
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
N403P/L405H
W279A
W279D
W279E
W279L
W279M
W279Q
W279Y
additional information
if W279 in delta-cadinene synthase is replaced with various smaller amino acids, the ratio of alcohol versus hydrocarbon product is directly proportional to the van der Waals volume of the amino acid side chain
N403P/L405H
the double-mutant DCS converts farnesyl diphosphate into germacradien-4-ol (93%) and an additional unidentified cyclic sesquiterpene alcohol. The catalytic activity of DCS mutant N403P/L405H is severely compromised relative to that of the wild-type enzyme
N403P/L405H
the mutant enzyme converts (2E,6E)-farnesyl diphosphate into germacradien-4-ol (93%) and an additional unidentified cyclic sesquiterpene alcohol.However, the catalytic activity of the mutant is severely compromised relative to that of the wild type enzyme
W279A
site-directed mutagenesis, the mutant is a catalytically highly efficient germacradien-4-ol synthase that produces predominantly germacradien-4-ol in addition to 11% delta-cadinene
W279A
the mutant is a catalytically highly efficient germacradien-4-ol synthase that produces predominantly germacradien-4-ol (89%) in addition to 11% (+)-delta-cadinene
W279D
site-directed mutagenesis, the mutant shows altered substrate specificity and increased germacradien-4-ol synthase activity compared to the wild-type enzyme
W279D
the mutant produces 60% germacradien-4-ol and 40% (+)-delta-cadinene from (2E,6E)-farnesyl diphosphate
W279E
site-directed mutagenesis, the mutant shows altered substrate specificity and increased germacradien-4-ol synthase activity compared to the wild-type enzyme
W279E
the mutant produces 50% germacradien-4-ol and 50% (+)-delta-cadinene from (2E,6E)-farnesyl diphosphate
W279L
site-directed mutagenesis, the mutant shows altered substrate specificity and increased germacradien-4-ol synthase activity compared to the wild-type enzyme
W279L
the mutant produces 32% germacradien-4-ol and 68% (+)-delta-cadinene from (2E,6E)-farnesyl diphosphate
W279M
site-directed mutagenesis, the mutant shows altered substrate specificity and increased germacradien-4-ol synthase activity compared to the wild-type enzyme
W279M
the mutant produces 35% germacradien-4-ol and 65% (+)-delta-cadinene from (2E,6E)-farnesyl diphosphate
W279Q
site-directed mutagenesis, the mutant shows altered substrate specificity and increased germacradien-4-ol synthase activity compared to the wild-type enzyme
W279Q
the mutant produces 40% germacradien-4-ol and 60% (+)-delta-cadinene from (2E,6E)-farnesyl diphosphate
W279Y
site-directed mutagenesis, the mutant shows altered substrate specificity and increased germacradien-4-ol synthase activity compared to the wild-type enzyme
W279Y
the mutant produces 17% germacradien-4-ol and 83% (+)-delta-cadinene from (2E,6E)-farnesyl diphosphate
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purification of a recombinant enzyme using histidine affinity chromatography
affinity chromatography, chromatography on glutathione-Sepharose-4B column and anion-exchange column
purification of a recombinant enzyme using histidine affinity chromatography
recombinant His6-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, diaylsis, and ultrafiltration
soluble at pH 11.6, ion exchange chromatography (DEAE), gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli of a cDNA isolated and amplified from a cell culture infected with Verticillium dahliae
expression in Escherichia coli of a cDNA isolated and amplified from a cell culture infected with Verticillium dahliae
expression in Escherichia coli of the CAD1-A isoenzyme, 80% of homology with CAD1-C isoenzyme
-
recombinant expression of His6-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Chen, X.Y.; Wang, M.; Chen, Y.; Davisson, V.J.; Heinstein, P.
Cloning and heterologous expression of a second (+)-delta-cadinene synthase from Gossypium arboreum
J. Nat. Prod.
59
944-951
1996
Gossypium arboreum
Chen, X.Y.; Chen, Y.; Heinstein, P.; Davisson, V.J.
Cloning, expression, and characterization of (+)-delta-cadinene synthase: a catalyst for cotton phytoalexin biosynthesis
Arch. Biochem. Biophys.
324
255-266
1995
Gossypium arboreum (Q39760), Gossypium arboreum (Q39761), Gossypium arboreum
Benedict, C.R.; Lu, J.L.; Pettigrew, D.W.; Liu, J.; Stipanovic, R.D.; Williams, H.J.
The cyclization of farnesyl diphosphate and nerolidyl diphosphate by a purified recombinant delta-cadinene synthase
Plant Physiol.
125
1754-1765
2001
Gossypium barbadense, Gossypium arboreum (Q39761), Gossypium arboreum
Tan, X.P.; Liang, W.Q.; Liu, C.J.; Luo, P.; Heinstein, P.; Chen, X.Y.
Expression pattern of (+)-delta-cadinene synthase genes and biosynthesis of sesquiterpene aldehydes in plants of Gossypium arboreum L
Planta
210
644-651
2000
Gossypium arboreum, Gossypium hirsutum
Meng, Y.L.; Jia, J.W.; Liu, C.J.; Liang, W.Q.; Heinstein, P.; Chen, X.Y.
Coordinated accumulation of (+)-delta-cadinene synthase mRNAs and gossypol in developing seeds of Gossypium hirsutum and a new member of the cad1 family from G. arboreum
J. Nat. Prod.
62
248-252
1999
Gossypium hirsutum, Gossypium arboreum (O49853), Gossypium arboreum
ennadios, H.A.; Gonzalez, V.; Di Costanzo, L.; Li, A.; Yu, F.; Miller, D.J.; Allemann, R.K.; Christianson, D.W.
Crystal structure of (+)-delta-cadinene synthase from Gossypium arboreum and evolutionary divergence of metal binding motifs for catalysis
Biochemistry
48
6175-6183
2009
Gossypium arboreum (Q39761), Gossypium arboreum
Loizzi, M.; Gonzalez, V.; Miller, D.J.; Allemann, R.K.
Nucleophilic water capture or proton loss single amino acid switch converts delta-cadinene synthase into germacradien-4-ol synthase
ChemBioChem
19
100-105
2018
Gossypium arboreum (Q39761)
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