Information on EC 4.2.3.13 - (+)-delta-cadinene synthase

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The expected taxonomic range for this enzyme is: Eukaryota

EC NUMBER
COMMENTARY hide
4.2.3.13
-
RECOMMENDED NAME
GeneOntology No.
(+)-delta-cadinene synthase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
(2E,6E)-farnesyl diphosphate = (+)-delta-cadinene + diphosphate
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
cyclization
-
elimination of diphosphate
elimination of diphosphate
-
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Biosynthesis of secondary metabolites
-
-
gossypol biosynthesis
-
-
lacinilene C biosynthesis
-
-
Metabolic pathways
-
-
Sesquiterpenoid and triterpenoid biosynthesis
-
-
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 hide
166800-09-5
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
; isoform TPS2; cultivar HA300
UniProt
Manually annotated by BRENDA team
-
UniProt
Manually annotated by BRENDA team
-
UniProt
Manually annotated by BRENDA team
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(2E,6E)-farnesyl diphosphate
(+)-delta-cadinene + diphosphate
show the reaction diagram
-
products are about 60% (-)-alpha-copaene, 40% (+)-delta-cadinene
-
?
(2E,6E)-farnesyl diphosphate
delta-cadinene + diphosphate
show the reaction diagram
(2E,6E)-farnesyl diphosphate + H2O
delta-cadinene + diphosphate
show the reaction diagram
(2E,6Z)-farnesyl diphosphate
(+)-delta-cadinene + diphosphate
show the reaction diagram
-
-
-
?
2-trans,6-trans-farnesyl diphosphate
(+)-delta-cadinene + diphosphate
show the reaction diagram
nerolidyl diphosphate
(+)-delta-cadinene + alpha-bisabolol + beta-bisabolene + beta-farnesene + ?
show the reaction diagram
-
-
?
nerolidyl diphosphate
(+)-delta-cadinene + diphosphate
show the reaction diagram
-
-
-
?
additional information
?
-
-
products (in vivo expression in Saccharomyces cerevisiae): delta-cadinene and a compound with a cadinene skeleton, minor products: alpha-muurolene, beta-caryophyllene, alpha-humulene and alpha-copaene
-
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
2-trans,6-trans-farnesyl diphosphate
(+)-delta-cadinene + diphosphate
show the reaction diagram
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2-fluorofarnesyl diphosphate
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0048
(2E,6E)-farnesyl diphosphate
pH 7.5, 30C
0.0024 - 0.043
(2E,6Z)-farnesyl diphosphate
0.0017 - 0.0106
2-trans,6-trans-farnesyl diphosphate
0.00065
nerolidyl diphosphate
pH 7.5, 30C, recombinant CDN1-C1 enzyme
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.04
(2E,6E)-farnesyl diphosphate
Phyla dulcis
J7LP58
pH 7.5, 30C
0.01 - 0.043
(2E,6Z)-farnesyl diphosphate
0.033
2-trans,6-trans-farnesyl diphosphate
Gossypium arboreum
Q39760, Q39761
fusion protein composed of the pXC1-encoded protein and the histidine leader peptide derived from pET28, pH 7, 30C
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.03
2-fluorofarnesyl diphosphate
Gossypium arboreum
Q39761
0.01 mM farnesyl diphosphate
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.0000487
-
[3H] farnesyl diphosphate
0.000405
-
27 days postanthesis
0.0005
-
60 days postanthesis
0.000746
-
35 days postanthesis
0.000988
-
40 days postanthesis
0.021
-
CAD1-A isozyme, expressed in Escherichia coli
0.03
recombinant protein
0.036
-
CAD1-A isozyme, removal of 15 amino acids by thrombin cleavage
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7 - 7.5
-
enzyme form CAD1-C
8.7
-
enzyme form CAD1-A
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.8 - 8.7
-
62% of maximal activity at pH 6.8, enzyme form CAD1-A
7 - 8.7
-
60% of maximal activity at pH 8.7, enzyme form CAD1-C
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
time-dependent 10fold increase in mRNA in response to a challenge by preparation from Verticillium dahliae
Manually annotated by BRENDA team
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
45000
-
gel filtration
64000
-
SDS-PAGE
64060
-
calculated from DNA sequence, CAD1-A isozyme
64100
calculated from DNA sequence
64120
calculated from DNA sequence
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
x * 64200, calculated; x * 64200, calculated from amino acid sequence
monomer
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
hanging drop vapor diffusion method
modeled from amino acid sequence of CDN1-C1, in SWISS-MODEL automated homology modeling server
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
loss of activity during freezing and thawing is gradually restored during incubation at 0C, complete recovery after 4-5 h
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20C, stable for at least 1 year
-
-20C, stable for at least 4 weeks
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
affinity chromatography, chromatography on glutathione-Sepharose-4B column and anion-exchange column
CAD1-A isoenzyme
-
N-terminal fusion of 10x His-tag, purification by affinity chromatography under native and denaturing conditions
-
Ni-NTA affinity chromatography; Ni-NTA affinity column chromatography
purification of a recombinant enzyme using histidine affinity chromatography; purification of a recombinant enzyme using histidine affinity chromatography
slurry homogenization and centrifugation
-
soluble at pH 11.6, ion exchange chromatography (DEAE), gel filtration
to homogeneity, several chromatographic steps, including hydroxyapatite, phenyl-agarose and anion-exchange chromatography
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli
expressed in Escherichia coli; expressed in Escherichia coli BL21(DE3) cells
-
expressed in Saccharomyces cerevisiae strain EPY300 as a thioredoxin-fusion protein; thioredoxin-fusion protein expressed in Escherichia coli, expressed in Saccharomyces cerevisiae EPY300
expression in Escherichia coli
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 CDN1-C1
expression in Escherichia coli of the CAD1-A isoenzyme, 80% of homology with CAD1-C isoenzyme
-
expression in Saccharomyces cerevisiae and Escherichia coli
exprsssion in Escherichia coli and Saccharomyces cerevisiae
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D307A
aspartate-rich motif interacts with putative Mg2+
D308A
aspartate-rich motif interacts with putative Mg2+
D311A
aspartate-rich motif interacts with putative Mg2+
D451A
aspartate-rich motif interacts with putative Mg2+
D452A
aspartate-rich motif interacts with putative Mg2+
E455A
aspartate-rich motif interacts with putative Mg2+
L405H
-
mutation alters product selectivity from (+)-d-cadinene to germacrene D-4-ol (53%). Mutation improves the solubility of the enzyme
N403P
-
mutation significantly alters the product selectivity to germacrene D-4-ol (52%)
N403P/L405H
-
mutant maintains its specific activity and shows higher selectivity to germacrene D-4-ol in vivo (up to 93%)
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
agriculture
-
RNAi is used to disrupt gossypol biosynthesis in cotton seed tissue by interfering with the expression of the delta-cadinene synthase gene during seed development. It is possible to significantly reduce cottonseed-gossypol levels in a stable and heritable manner. The levels of gossypol and related terpenoids in the foliage and floral parts are not diminished, and thus their potential function in plant defense against insects and diseases remains untouched. A targeted genetic modification, applied to an underutilized agricultural byproduct, provides a mechanism to open up a new source of nutrition for hundreds of millions of people
synthesis
expression in Saccharomyces cerevisiae leads to a titer of (-)-alpha-copaene of 9 mg/l at 48 h and around 7 mg/l in Escherichia coli, and the titer of (+)-delta-cadinene is 6 mg/l in Saccharomyces cerevisiae and 3.5 mg/l in Escherichia coli