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Yorodumi- PDB-9f2k: Myo-inositol-1-phosphate synthase from Thermochaetoides thermophi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9f2k | |||||||||||||||
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Title | Myo-inositol-1-phosphate synthase from Thermochaetoides thermophila in complex with NAD | |||||||||||||||
Components | inositol-3-phosphate synthase | |||||||||||||||
Keywords | ISOMERASE / inositol metabolism / endogenous / conformational selection | |||||||||||||||
Function / homology | Function and homology information inositol-3-phosphate synthase / inositol-3-phosphate synthase activity / inositol biosynthetic process / phospholipid biosynthetic process / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Thermochaetoides thermophila DSM 1495 (fungus) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.48 Å | |||||||||||||||
Authors | Traeger, T.K. / Kyrilis, F.L. / Hamdi, F. / Kastritis, P.L. | |||||||||||||||
Funding support | European Union, Germany, 4items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2024 Title: Disorder-to-order active site capping regulates the rate-limiting step of the inositol pathway. Authors: Toni K Träger / Fotis L Kyrilis / Farzad Hamdi / Christian Tüting / Marie Alfes / Tommy Hofmann / Carla Schmidt / Panagiotis L Kastritis / Abstract: Myo-inositol-1-phosphate synthase (MIPS) catalyzes the NAD-dependent isomerization of glucose-6-phosphate (G6P) into inositol-1-phosphate (IMP), controlling the rate-limiting step of the inositol ...Myo-inositol-1-phosphate synthase (MIPS) catalyzes the NAD-dependent isomerization of glucose-6-phosphate (G6P) into inositol-1-phosphate (IMP), controlling the rate-limiting step of the inositol pathway. Previous structural studies focused on the detailed molecular mechanism, neglecting large-scale conformational changes that drive the function of this 240 kDa homotetrameric complex. In this study, we identified the active, endogenous MIPS in cell extracts from the thermophilic fungus . By resolving the native structure at 2.48 Å (FSC = 0.143), we revealed a fully populated active site. Utilizing 3D variability analysis, we uncovered conformational states of MIPS, enabling us to directly visualize an order-to-disorder transition at its catalytic center. An acyclic intermediate of G6P occupied the active site in two out of the three conformational states, indicating a catalytic mechanism where electrostatic stabilization of high-energy intermediates plays a crucial role. Examination of all isomerases with known structures revealed similar fluctuations in secondary structure within their active sites. Based on these findings, we established a conformational selection model that governs substrate binding and eventually inositol availability. In particular, the ground state of MIPS demonstrates structural configurations regardless of substrate binding, a pattern observed across various isomerases. These findings contribute to the understanding of MIPS structure-based function, serving as a template for future studies targeting regulation and potential therapeutic applications. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9f2k.cif.gz | 113.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9f2k.ent.gz | 84.7 KB | Display | PDB format |
PDBx/mmJSON format | 9f2k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9f2k_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 9f2k_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 9f2k_validation.xml.gz | 40.5 KB | Display | |
Data in CIF | 9f2k_validation.cif.gz | 56.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f2/9f2k ftp://data.pdbj.org/pub/pdb/validation_reports/f2/9f2k | HTTPS FTP |
-Related structure data
Related structure data | 50149MC M: map data used to model this data 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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-Components
#1: Protein | Mass: 56735.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) References: UniProt: G0SDP4, inositol-3-phosphate synthase |
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#2: Chemical | ChemComp-NAD / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Native homotetramer of the Myo-inositol-1-phosphate synthase Type: COMPLEX / Entity ID: #1 / Source: NATURAL | ||||||||||||||||||||||||||||
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Molecular weight | Value: 0.24 MDa / Experimental value: NO | ||||||||||||||||||||||||||||
Source (natural) | Organism: Thermochaetoides thermophila DSM 1495 (fungus) | ||||||||||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||
Specimen support | Details: 15 mA / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 | ||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: 6 s blot time with a blot force of -1 |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 240000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: OTHER / Temperature (max): 103.15 K / Temperature (min): 77.15 K |
Image recording | Electron dose: 28 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 6261 |
Image scans | Width: 4000 / Height: 4000 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 309043 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: D2 (2x2 fold dihedral) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 255354 / Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Atomic model building |
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