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Yorodumi- PDB-7vtb: Partially closed conformation of talaropentaene synthase cyclase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vtb | ||||||
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Title | Partially closed conformation of talaropentaene synthase cyclase domain | ||||||
Components | TvTS cyclase domain | ||||||
Keywords | TRANSFERASE / Talaromyces verruculosus / talaropentaene synthase / triterpene | ||||||
Function / homology | NICKEL (II) ION Function and homology information | ||||||
Biological species | Talaromyces verruculosus (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Hui, T. / Mori, T. / Abe, I. | ||||||
Funding support | 1items
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Citation | Journal: Nature / Year: 2022 Title: Discovery of non-squalene triterpenes. Authors: Hui Tao / Lukas Lauterbach / Guangkai Bian / Rong Chen / Anwei Hou / Takahiro Mori / Shu Cheng / Ben Hu / Li Lu / Xin Mu / Min Li / Naruhiko Adachi / Masato Kawasaki / Toshio Moriya / ...Authors: Hui Tao / Lukas Lauterbach / Guangkai Bian / Rong Chen / Anwei Hou / Takahiro Mori / Shu Cheng / Ben Hu / Li Lu / Xin Mu / Min Li / Naruhiko Adachi / Masato Kawasaki / Toshio Moriya / Toshiya Senda / Xinghuan Wang / Zixin Deng / Ikuro Abe / Jeroen S Dickschat / Tiangang Liu / Abstract: All known triterpenes are generated by triterpene synthases (TrTSs) from squalene or oxidosqualene. This approach is fundamentally different from the biosynthesis of short-chain (C-C) terpenes that ...All known triterpenes are generated by triterpene synthases (TrTSs) from squalene or oxidosqualene. This approach is fundamentally different from the biosynthesis of short-chain (C-C) terpenes that are formed from polyisoprenyl diphosphates. In this study, two fungal chimeric class I TrTSs, Talaromyces verruculosus talaropentaene synthase (TvTS) and Macrophomina phaseolina macrophomene synthase (MpMS), were characterized. Both enzymes use dimethylallyl diphosphate and isopentenyl diphosphate or hexaprenyl diphosphate as substrates, representing the first examples, to our knowledge, of non-squalene-dependent triterpene biosynthesis. The cyclization mechanisms of TvTS and MpMS and the absolute configurations of their products were investigated in isotopic labelling experiments. Structural analyses of the terpene cyclase domain of TvTS and full-length MpMS provide detailed insights into their catalytic mechanisms. An AlphaFold2-based screening platform was developed to mine a third TrTS, Colletotrichum gloeosporioides colleterpenol synthase (CgCS). Our findings identify a new enzymatic mechanism for the biosynthesis of triterpenes and enhance understanding of terpene biosynthesis in nature. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vtb.cif.gz | 89.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vtb.ent.gz | 53.1 KB | Display | PDB format |
PDBx/mmJSON format | 7vtb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vt/7vtb ftp://data.pdbj.org/pub/pdb/validation_reports/vt/7vtb | HTTPS FTP |
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-Related structure data
Related structure data | 7vtaSC 7wijC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36987.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Talaromyces verruculosus (fungus) / Production host: Escherichia coli (E. coli) |
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#2: Chemical | ChemComp-NI / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris-Cl pH 8.5, 0.1 M MgCl2, 30% PEG 4000, 0.2 M NDSB-211 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 19, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2→47.2 Å / Num. obs: 22448 / % possible obs: 98.1 % / Redundancy: 3.6 % / Biso Wilson estimate: 22.52 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 1621 / CC1/2: 0.927 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7VTA Resolution: 2→47.2 Å / SU ML: 0.1731 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.1294 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.81 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→47.2 Å
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Refine LS restraints |
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LS refinement shell |
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