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Yorodumi- PDB-8bc3: Cryo-EM Structure of a BmSF-TAL - Sulfofructose Schiff Base Complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bc3 | ||||||||||||
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Title | Cryo-EM Structure of a BmSF-TAL - Sulfofructose Schiff Base Complex | ||||||||||||
Components | BmSF-TAL | ||||||||||||
Keywords | TRANSFERASE / Transaldolase / sulfofructose / cryo-EM / decamer | ||||||||||||
Function / homology | Function and homology information 6-deoxy-6-sulfo-D-fructose transaldolase / transaldolase activity / aldehyde-lyase activity / carbohydrate metabolic process Similarity search - Function | ||||||||||||
Biological species | Bacillus aryabhattai (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.1 Å | ||||||||||||
Authors | Snow, A.J.D. / Sharma, M. / Blaza, J. / Davies, G.J. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Structure / Year: 2023 Title: Structure and mechanism of sulfofructose transaldolase, a key enzyme in sulfoquinovose metabolism. Authors: Alexander J D Snow / Mahima Sharma / Palika Abayakoon / Spencer J Williams / James N Blaza / Gideon J Davies / Abstract: Sulfoquinovose (SQ) is a key component of plant sulfolipids (sulfoquinovosyl diacylglycerols) and a major environmental reservoir of biological sulfur. Breakdown of SQ is achieved by bacteria through ...Sulfoquinovose (SQ) is a key component of plant sulfolipids (sulfoquinovosyl diacylglycerols) and a major environmental reservoir of biological sulfur. Breakdown of SQ is achieved by bacteria through the pathways of sulfoglycolysis. The sulfoglycolytic sulfofructose transaldolase (sulfo-SFT) pathway is used by gut-resident firmicutes and soil saprophytes. After isomerization of SQ to sulfofructose (SF), the namesake enzyme catalyzes the transaldol reaction of SF transferring dihydroxyacetone to 3C/4C acceptors to give sulfolactaldehyde and fructose-6-phosphate or sedoheptulose-7-phosphate. We report the 3D cryo-EM structure of SF transaldolase from Bacillus megaterium in apo and ligand bound forms, revealing a decameric structure formed from two pentameric rings of the protomer. We demonstrate a covalent "Schiff base" intermediate formed by reaction of SF with Lys89 within a conserved Asp-Lys-Glu catalytic triad and defined by an Arg-Trp-Arg sulfonate recognition triad. The structural characterization of the signature enzyme of the sulfo-SFT pathway provides key insights into molecular recognition of the sulfonate group of sulfosugars. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bc3.cif.gz | 364.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bc3.ent.gz | 285 KB | Display | PDB format |
PDBx/mmJSON format | 8bc3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bc3_validation.pdf.gz | 406.6 KB | Display | wwPDB validaton report |
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Full document | 8bc3_full_validation.pdf.gz | 517.2 KB | Display | |
Data in XML | 8bc3_validation.xml.gz | 46.4 KB | Display | |
Data in CIF | 8bc3_validation.cif.gz | 56.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/8bc3 ftp://data.pdbj.org/pub/pdb/validation_reports/bc/8bc3 | HTTPS FTP |
-Related structure data
Related structure data | 15961MC 8bc2C 8bc4C 8c4iC 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: 25311.557 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus aryabhattai (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7W3N5X5 #2: Chemical | ChemComp-QC9 / ( #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-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: Decameric complex of BmSF-TAL / Type: COMPLEX / Details: Solution decamer of BmSF-TAL / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.25 MDa / Experimental value: YES |
Source (natural) | Organism: Priestia megaterium DSM 319 (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: monodisperse sample with acceptable range of orientations; ice was of good quality |
Specimen support | Details: 20 mAmp, 10 s hold time / Grid material: GOLD / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: -10 blot force, 6 second blot time |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 310000 X / Nominal defocus max: 1000 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 30 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 3.39 sec. / Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1842 |
Image scans | Width: 4096 / Height: 4096 |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 77489 | ||||||||||||||||||||||||
Symmetry | Point symmetry: D5 (2x5 fold dihedral) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53450 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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