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Information on EC 4.2.1.125 - dammarenediol II synthase and Organism(s) Panax ginseng and UniProt Accession Q08IT1
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4.2.1.125 dammarenediol II synthaseIUBMB Comments
The reaction occurs in the reverse direction.
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Word Map
- 4.2.1.125
- panax
- ginsenosides
- ginseng
- saponin
-
epoxidase
- protopanaxadiol
-
triterpene
- jasmonate
-
triterpenoid
- 2,3-oxidosqualene
-
adventitious
-
tetracyclic
-
aglycone
-
dammarane-type
- notoginseng
- oxidosqualene
- elicitors
-
nadph-cytochrome
- quinquefolius
-
meyer
- beta-amyrin
-
sapogenins
- lanosterol
- udp-glycosyltransferase
- cycloartenol
-
chromatography-atmospheric
- synthesis
The taxonomic range for the selected organisms is: Panax ginseng
The expected taxonomic range for this enzyme is: Apiineae
The expected taxonomic range for this enzyme is: Apiineae
Synonyms
dammarenediol synthase, dammarenediol-ii synthase, pgdds, dammarenediol ii synthase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
dammarenediol-II synthase
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
dammarenediol II = (3S)-2,3-epoxy-2,3-dihydrosqualene + H2O
an unusually complex and flexible reaction mechanism generates this ring system. As a general mechanism, firstly (3S)-2,3-oxidosqualene adopts a preorganized chair-chair-chair conformation, and activated by cationic attack. Then the oxirane ring of (3S)-2,3-oxidosqualene opens, following with a cascade of cation-olefin cyclizations, and generates a cyclic C-20 dammarenyl cation
dammarenediol II = (3S)-2,3-epoxy-2,3-dihydrosqualene + H2O
cyclization initiated by protonation at the oxirane ring proceeds to form tetracycles. The resulting dammarenyl cation is trapped by stereospecific addition of water at C20 without further rearrangement
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PATHWAY SOURCE
PATHWAYS
BRENDA
-
-
SYSTEMATIC NAME
IUBMB Comments
(S)-squalene-2,3-epoxide hydro-lyase (dammarenediol-II forming)
The reaction occurs in the reverse direction.
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
(S)-2,3-oxidosqualene + H2O
(20S)-dammarenediol
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S-isomer is the sole product, water addition to the dammarenyl cation intermediate is stereospecific
-
?
(S)-2,3-oxidosqualene + H2O
(20S)-dammarenediol + hydroxydammarenone
-
-
-
?
(3S)-2,3-oxidosqualene + H2O
(20S)-dammarenediol
-
substrate is folded in a pre-chair-chair-chair conformation
-
-
?
(3S)-2,3-epoxy-2,3-dihydrosqualene + H2O
dammarenediol II
-
-
-
?
(3S)-2,3-epoxy-2,3-dihydrosqualene + H2O
dammarenediol II
-
-
-
r
(3S)-2,3-epoxy-2,3-dihydrosqualene + H2O
dammarenediol II
-
-
-
r
(3S)-2,3-epoxy-2,3-dihydrosqualene + H2O
dammarenediol II
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GC-MS product analysis
-
?
(3S)-2,3-epoxy-2,3-dihydrosqualene + H2O
dammarenediol II
dammarenediol-II is a ginsenoside precursor
-
-
?
additional information
?
-
LC-MS analysis of substrate and product amounts
-
-
?
additional information
?
-
-
LC-MS analysis of substrate and product amounts
-
-
?
additional information
?
-
dammarenediol-II synthase (DS) is a kind of 2,3-oxidosqualene-triterpene cyclase that catalyses 2,3-oxidosqualene to form dammarenediol-II. The substrate 2,3-oxidosqualene is cyclized by the enzyme at specific sites, and its particular 6-6-6-5 tetracyclic triterpenoid structure can be developed
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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
(3S)-2,3-epoxy-2,3-dihydrosqualene + H2O
dammarenediol II
-
-
-
?
(3S)-2,3-epoxy-2,3-dihydrosqualene + H2O
dammarenediol II
-
-
-
r
(3S)-2,3-epoxy-2,3-dihydrosqualene + H2O
dammarenediol II
-
-
-
r
(3S)-2,3-epoxy-2,3-dihydrosqualene + H2O
dammarenediol II
dammarenediol-II is a ginsenoside precursor
-
-
?
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
3-((3-cholamidopropyl)dimethylammonio)-1-propanesulfonate
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i.e. CHAPS, 0.1%, 30% residual activity
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
higher expression in flower bud compared with root, leaf and petiole
higher expression in flower bud compared with root, leaf and petiole
higher expression in flower bud compared with root, leaf and petiole
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
metabolism
physiological function
additional information
metabolism
the enzyme catalyzes the first step in biosynthetic pathway of ginsenosides, overview
metabolism
the enzyme catalyzes the first step in the biosynthetic pathway for ginsenosides in Panax ginseng, overview
metabolism
the enzyme catalyzes the first step in the synthesis of dammarane-type ginsenoside, the cyclization of 2,3-oxidosqualene to dammarenediol-II, overview
metabolism
the enzyme is involved in the ginsenoside biosynthetic pathway catalyzing the first committed step, the cyclization of 2,3-oxidosqualene to dammarenediol
physiological function
dammarenediol-II synthase catalyzes the cyclization of 2,3-oxidosqualene to dammarenediol-II, which is the basic triterpene skeleton in dammarene-type saponin (ginsenosides) in Panax ginseng. Dammarenediol-II is present in the roots of Panax ginseng in trace amounts because it is an intermediate product in triterpene biosynthesis
physiological function
dammarenediol synthase is a key enzyme in the biosynthetic process of ginsenosides
physiological function
dammarenediol-II synthase gene (PgDDS) from Panax ginseng is responsible for the cyclization of 2,3-oxidosqualene to dammarenediol-II, the nucleus of dammarane-type ginsenosides, which are a group of active triterpenoids exhibiting various pharmacological activities
additional information
close correlation of dammarenediol synthetase and saponin production in vitro
additional information
-
close correlation of dammarenediol synthetase and saponin production in vitro
additional information
determination of ginsenosides, i.e. Rg1, Re, F11, Rf, S-Rh1, Rg2, Rb1, R-Rh1, Rc, F1, R0, Rb2, Rb3, Rd, F2, S-Rg3, R1, and R-Rg3, in Panax ginseng cv. DAMAYA. The ginsenoside contents, of such as Rf, Rg1 and F1, change with the gene mutation
additional information
three-dimensional structure and catalytic active sites structures of dammarenediol-II synthase by homology modeling using human oxidosqualene cyclase 3D models (PDB IDs 1W6K and 1W6J) as templates and by molecular docking simulation between enzyme model and product dammarenediol-II, overview. Residues C568 and C264 play significant roles in the catalytic process of the enzyme. Active site residues are identified: Asp488 initiates the ring forming reaction by protonating the 2,3-oxirane ring, and is activated by strong polar amino acid Cys489 and Cys568. Aromatic residues Trp421, Phe477, Trp538, Tyr263 and Tyr732 may stabilize the intermediate conformation during the cyclization. Cys264, Tyr268 and Ile559 may have relation with a substrate channel that guides 2,3-oxidosqualene into the active site cavity
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). DADIS_PANGI
769
1
88343
Swiss-Prot
other Location (Reliability: 4)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
84600
x * 84600, about, sequence calculation, x * 89000, recombinant His-tagged enzyme, SDS-PAGE
89000
x * 84600, about, sequence calculation, x * 89000, recombinant His-tagged enzyme, SDS-PAGE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
three-dimensional structure and catalytic active sites structures of dammarenediol-II synthase, homology modelling, overview
?
x * 84600, about, sequence calculation, x * 89000, recombinant His-tagged enzyme, SDS-PAGE
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
C264A
site-directed mutagenesis, the mutant shows 53% decreased activity compared to the wild-type enzyme
C489A
site-directed mutagenesis, the mutant shows highly decreased activity compared to the wild-type enzyme
C568A
site-directed mutagenesis, the mutant shows slightly increased activity compared to the wild-type enzyme
D488A
site-directed mutagenesis, the mutant shows highly decreased activity compared to the wild-type enzyme
F477A
site-directed mutagenesis, the mutant shows highly decreased activity compared to the wild-type enzyme
I559A
site-directed mutagenesis, the mutant shows highly decreased activity compared to the wild-type enzyme
W421A
site-directed mutagenesis, the mutant shows highly decreased activity compared to the wild-type enzyme
W538A
site-directed mutagenesis, the mutant shows highly decreased activity compared to the wild-type enzyme
W616A
site-directed mutagenesis, the mutant shows highly decreased activity compared to the wild-type enzyme
Y263A
site-directed mutagenesis, the mutant shows highly decreased activity compared to the wild-type enzyme
Y268A
site-directed mutagenesis, the mutant shows highly decreased activity compared to the wild-type enzyme
Y732A
site-directed mutagenesis, the mutant shows highly decreased activity compared to the wild-type enzyme
additional information
additional information
expression in Saccharomyces cerevisiae mutant lacking lanosterol synthase results in production of dammarenediol and hydroxydammarenone. Silencing of gene expression by RNAi leads to a reduction of ginsenoide production to 84.5% in roots
additional information
-
expression in Saccharomyces cerevisiae mutant lacking lanosterol synthase results in production of dammarenediol and hydroxydammarenone. Silencing of gene expression by RNAi leads to a reduction of ginsenoide production to 84.5% in roots
additional information
establishment of dammarane-type ginsenosides synthesis from 2,3-oxidosqualene in Oryza sativa by expression of dammarenediol-II synthase from Panax ginseng resulting in a dammarane-type sapogenin 20(S)-protopanaxadiol (PPD) content of 0.35-0.59 mg/gdw and a dammarane-type sapogenin 20(S)-protopanaxatriol (PPT) content of 0.23-0.43 mg/g dry weight in the transgenic rice plants
additional information
-
establishment of dammarane-type ginsenosides synthesis from 2,3-oxidosqualene in Oryza sativa by expression of dammarenediol-II synthase from Panax ginseng resulting in a dammarane-type sapogenin 20(S)-protopanaxadiol (PPD) content of 0.35-0.59 mg/gdw and a dammarane-type sapogenin 20(S)-protopanaxatriol (PPT) content of 0.23-0.43 mg/g dry weight in the transgenic rice plants
additional information
heterologous biosynthesis of triterpenoid dammarenediol-II, the precursor of dammarane-type tetracyclic ginsenosides, in engineered Escherichia coli strain BL21(DE3) by expressing the enzyme, and coexpressing squalene synthase, squalene epoxidase, and NADPH-cytochrome P450 reductase from Saccharomyces cerevisiae, and squalene epoxidase from Methylococcus capsulatus, as well as NADPH-cytochrome P450 reductase from Arabidopsis thaliana, and thereby reconstituting the 2,3-oxidosqualene-derived triterpenoid biosynthetic pathway. Method evaluation and optimization, overview
additional information
identification of single nucleotide polymorphisms in different samples of Panax ginseng cultivar DAMAYA, specific single nucleotide polymorphisms (SNPs) of the DDS gene might be associated with the accumulation of some ginsenosides in DAMAYA ginseng and thus can be used for varietal characterization, molecular identification, qualitative evaluation of ginseng-type medicinal materials, or gene engineering and ginseng breeding. The ginsenoside contents, of such as Rf, Rg1 and F1, change with the gene mutation
additional information
metabolic engineering of Pichia pastoris strain GS115 for the high yield production of dammarenediol-II, based on the native triterpene synthetic pathway, a dammarenediol-II synthetic pathway is established in Pichia pastoris by introducing a dammarenediol-II synthase gene (PgDDS) from Panax ginseng. To increase the supply of 2,3-oxidosqualene, the ERG1 gene, which is responsible for 2,3-oxidosqualene synthesis, is coexpressed. And to reduce competition for 2,3-oxidosqualene from ergosterol biosynthesis without affecting the normal growth of Pichia pastoris, the ERG7gene, which is responsible for conversion of 2,3-oxidosqualene to lanosterol, is downregulated by replacing its native promoter with a thiamine-repressible promoter, using a marker-recycling and gene-targeting Cre- lox71/66 system, developed for Pichia pastoris. Method evaluation and optimization, overview
additional information
-
metabolic engineering of Pichia pastoris strain GS115 for the high yield production of dammarenediol-II, based on the native triterpene synthetic pathway, a dammarenediol-II synthetic pathway is established in Pichia pastoris by introducing a dammarenediol-II synthase gene (PgDDS) from Panax ginseng. To increase the supply of 2,3-oxidosqualene, the ERG1 gene, which is responsible for 2,3-oxidosqualene synthesis, is coexpressed. And to reduce competition for 2,3-oxidosqualene from ergosterol biosynthesis without affecting the normal growth of Pichia pastoris, the ERG7gene, which is responsible for conversion of 2,3-oxidosqualene to lanosterol, is downregulated by replacing its native promoter with a thiamine-repressible promoter, using a marker-recycling and gene-targeting Cre- lox71/66 system, developed for Pichia pastoris. Method evaluation and optimization, overview
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged enzyme from Escherichia coli strains Origami B (DE3) amd Rosetta (DE3) by nickel affinity chromatography
recombinnat enzyme from Saccharomyces cerevisiae strain 31147 lipid particles, solubilization by Triton X-100
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
DNA and amino acid sequence determination and analysis, recombinant expression of functional His-tagged enzyme in Escherichia coli strains Origami B (DE3) amd Rosetta (DE3)
expression in an engineered strain of Saccharomyces cerevisiae strain 31147 from vector pAUR123, the enzyme is contained in microsomes, lipid particles, and total yeast homogenate
gene DDS, functional recombinant overexpression in Oryza sativa cv. Shuhui 527 plants using the Agrbacterium tumefaciens transfection method, transfer-DNA (T-DNA) insertion sites in homozygous lines of the T2 generation are determined by using high-efficiency thermal asymmetric interlaced PCR (hiTAIL-PCR), quantitative RT-PCR expression analysis
gene DDS, genotyping of cv. DAMAYA, identification of single nucleotide polymorphisms
gene DDS, recombinant expression in Pichia pastoris using the promoter of the AOX1 gene, coexpression with an ERG1 gene and an ERG7 gene
gene DDS, recombinant expression in Saccharomyces cerevisiae strain WTE (strain W303-1a integrated with pRS304-tHMG1 and pRS405-ERG20) from TEF1p-DS-ADH3t vector
gene PgDDS, functional expression in Nicotiana tabacum cv. Xanthi leaves using Agrobacterium strain GV3101, the heterologous expression confers resistance to Tobacco mosaic virus. Expression profile of PgDDS trangenic tobacco plants, overview. Production of dammarenediol-II in transgenic tobacco stimulates the expression of tobacco pathogenesis-related genes (PR1 and PR2) under both virus-untreated and -treated conditions
gene PNA, recombinant expression in Escherichia coli strain BL21(DE3), coexpression of squalene synthase (UniProt ID P29704), squalene epoxidase (UniProt ID P32476), and NADPH-cytochrome P450 reductase (UniProt ID P16603) from Saccharomyces cerevisiae, and squalene epoxidase (UniProt ID Q603D5) from Methylococcus capsulatus, as well as NADPH-cytochrome P450 reductase from Arabidopsis thaliana (UniProt ID Q9SB48)
recombinant expression in Nicotiana tabacum cv. Xanthi leaves using transfection via Agrobacterium tumefaciens strain LBA4404, accumulation of dammarenediol-II in transgenic tobacco plants occurred in an organ-specific manner in descending order: roots, stems, leaves, flower buds, and transgenic cell suspension line 14 exhibits a high amount, overview
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
synthesis
the production of dammarenediol-II in a cell suspension culture of transgenic tobacco can be applied to the large-scale production of this compound and utilized as a source of pharmacologically active medicinal materials
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Kushiro, T.; Ohno, Y.; Shibuya, M.; Ebizuka, Y.
In vitro conversion of 2,3-oxidosqualene into dammarenediol by Panax ginseng microsomes
Biol. Pharm. Bull.
20
292-294
1997
Panax ginseng
Tansakul, P.; Shibuya, M.; Kushiro, T.; Ebizuka, Y.
Dammarenediol-II synthase, the first dedicated enzyme for ginsenoside biosynthesis, in Panax ginseng
FEBS Lett.
580
5143-5149
2006
Panax ginseng (Q08IT1), Panax ginseng
Han, J.Y.; Kwon, Y.S.; Yang, D.C.; Jung, Y.R.; Choi, Y.E.
Expression and RNA interference-induced silencing of the dammarenediol synthase gene in Panax ginseng
Plant Cell Physiol.
47
1653-1662
2006
Panax ginseng (Q08IT1), Panax ginseng
Hu, W.; Liu, N.; Tian, Y.; Zhang, L.
Molecular cloning, expression, purification, and functional characterization of dammarenediol synthase from Panax ginseng
BioMed Res. Int.
2013
285740
2013
Panax ginseng (Q08IT1), Panax ginseng
Liang, Y.; Zhao, S.; Xu, L.; Zhang, X.
Heterologous expression of dammarenediol synthase gene in an engineered Saccharomyces cerevisiae
Lett. Appl. Microbiol.
55
323-329
2012
Panax ginseng (Q08IT1), Panax ginseng
Lee, M.H.; Han, J.Y.; Kim, H.J.; Kim, Y.S.; Huh, G.H.; Choi, Y.E.
Dammarenediol-II production confers TMV tolerance in transgenic tobacco expressing Panax ginseng dammarenediol-II synthase
Plant Cell Physiol.
53
173-182
2012
Panax ginseng (Q08IT1), Panax ginseng
Han, J.Y.; Wang, H.Y.; Choi, Y.E.
Production of dammarenediol-II triterpene in a cell suspension culture of transgenic tobacco
Plant Cell Rep.
33
225-233
2014
Panax ginseng (Q08IT1), Panax ginseng
Li, D.; Zhang, Q.; Zhou, Z.; Zhao, F.; Lu, W.
Heterologous biosynthesis of triterpenoid dammarenediol-II in engineered Escherichia coli
Biotechnol. Lett.
38
603-609
2016
Panax ginseng (Q08IT1)
Liu, T.; Zhang, X.; Zhao, F.; Lu, W.
Molecular simulation and catalytic active sites identification of dammarenediol-II synthase
J. Beijing Inst. Technol.
26
563-570
2017
Panax ginseng (Q08IT1)
-
Liu, X.B.; Liu, M.; Tao, X.Y.; Zhang, Z.X.; Wang, F.Q.; Wei, D.Z.
Metabolic engineering of Pichia pastoris for the production of dammarenediol-II
J. Biotechnol.
216
47-55
2015
Panax ginseng (Q08IT1), Panax ginseng
Cheng, C.; Wu, W.; Huang, B.; Liu, L.; Luo, P.; Zhou, H.
SNPs of dammarenediol synthase gene were associated with the accumulation of ginsenosides in DAMAYA ginseng, a cultivar of Panax ginseng C. A. Mey
Phytochem. Lett.
17
194-200
2016
Panax ginseng (Q08IT1)
-
Huang, Z.; Lin, J.; Cheng, Z.; Xu, M.; Huang, X.; Yang, Z.; Zheng, J.
Production of dammarane-type sapogenins in rice by expressing the dammarenediol-II synthase gene from Panax ginseng C.A. Mey
Plant Sci.
239
106-114
2015
no activity in Oryza sativa, Panax ginseng (Q08IT1), Panax ginseng
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