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Literature summary extracted from
- Molecular simulation and catalytic active sites identification of dammarenediol-II synthase (2017), J. Beijing Inst. Technol., 26, 563-570 .
No PubMed abstract available
Cloned(Commentary)
| EC Number | Cloned (Comment) | Organism |
|---|---|---|
| 4.2.1.125 | gene DDS, recombinant expression in Saccharomyces cerevisiae strain WTE (strain W303-1a integrated with pRS304-tHMG1 and pRS405-ERG20) from TEF1p-DS-ADH3t vector | Panax ginseng |
Protein Variants
| EC Number | Protein Variants | Comment | Organism |
|---|---|---|---|
| 4.2.1.125 | C264A | site-directed mutagenesis, the mutant shows 53% decreased activity compared to the wild-type enzyme | Panax ginseng |
| 4.2.1.125 | C489A | site-directed mutagenesis, the mutant shows highly decreased activity compared to the wild-type enzyme | Panax ginseng |
| 4.2.1.125 | C568A | site-directed mutagenesis, the mutant shows slightly increased activity compared to the wild-type enzyme | Panax ginseng |
| 4.2.1.125 | D488A | site-directed mutagenesis, the mutant shows highly decreased activity compared to the wild-type enzyme | Panax ginseng |
| 4.2.1.125 | F477A | site-directed mutagenesis, the mutant shows highly decreased activity compared to the wild-type enzyme | Panax ginseng |
| 4.2.1.125 | I559A | site-directed mutagenesis, the mutant shows highly decreased activity compared to the wild-type enzyme | Panax ginseng |
| 4.2.1.125 | W421A | site-directed mutagenesis, the mutant shows highly decreased activity compared to the wild-type enzyme | Panax ginseng |
| 4.2.1.125 | W538A | site-directed mutagenesis, the mutant shows highly decreased activity compared to the wild-type enzyme | Panax ginseng |
| 4.2.1.125 | W616A | site-directed mutagenesis, the mutant shows highly decreased activity compared to the wild-type enzyme | Panax ginseng |
| 4.2.1.125 | Y263A | site-directed mutagenesis, the mutant shows highly decreased activity compared to the wild-type enzyme | Panax ginseng |
| 4.2.1.125 | Y268A | site-directed mutagenesis, the mutant shows highly decreased activity compared to the wild-type enzyme | Panax ginseng |
| 4.2.1.125 | Y732A | site-directed mutagenesis, the mutant shows highly decreased activity compared to the wild-type enzyme | Panax ginseng |
Natural Substrates/ Products (Substrates)
| EC Number | Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 4.2.1.125 | (3S)-2,3-epoxy-2,3-dihydrosqualene + H2O | Panax ginseng | - |
dammarenediol II | - |
r |  |
Organism
| EC Number | Organism | UniProt | Comment | Textmining |
|---|---|---|---|---|
| 4.2.1.125 | Panax ginseng | Q08IT1 | - |
- |
Reaction
| EC Number | Reaction | Comment | Organism | Reaction ID |
|---|---|---|---|---|
| 4.2.1.125 | 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 | Panax ginseng |
Substrates and Products (Substrate)
| EC Number | Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 4.2.1.125 | (3S)-2,3-epoxy-2,3-dihydrosqualene + H2O | - |
Panax ginseng | dammarenediol II | - |
r | |
| 4.2.1.125 | 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 | Panax ginseng | ? | - |
? | |
Subunits
| EC Number | Subunits | Comment | Organism |
|---|---|---|---|
| 4.2.1.125 | More | three-dimensional structure and catalytic active sites structures of dammarenediol-II synthase, homology modelling, overview | Panax ginseng |
Synonyms
| EC Number | Synonyms | Comment | Organism |
|---|---|---|---|
| 4.2.1.125 | dammarenediol-II synthase | - |
Panax ginseng |
| 4.2.1.125 | DDS | - |
Panax ginseng |
General Information
| EC Number | General Information | Comment | Organism |
|---|---|---|---|
| 4.2.1.125 | 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 | Panax ginseng |
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