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Yorodumi- PDB-8bc2: Ligand-Free Structure of the decameric sulfofructose transaldolas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bc2 | ||||||||||||
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Title | Ligand-Free Structure of the decameric sulfofructose transaldolase BmSF-TAL | ||||||||||||
Components | Transaldolase | ||||||||||||
Keywords | TRANSFERASE / transaldolase / cryo-EM / decamer / sulfofructose | ||||||||||||
Function / homology | 6-deoxy-6-sulfo-D-fructose transaldolase / Transaldolase/Fructose-6-phosphate aldolase, archaeal/bacterial / transaldolase activity / Transaldolase/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase / aldehyde-lyase activity / Aldolase-type TIM barrel / carbohydrate metabolic process / 6-deoxy-6-sulfo-D-fructose transaldolase Function and homology information | ||||||||||||
Biological species | Bacillus aryabhattai (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 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 | 8bc2.cif.gz | 407.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bc2.ent.gz | 330.1 KB | Display | PDB format |
PDBx/mmJSON format | 8bc2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bc2_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8bc2_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8bc2_validation.xml.gz | 68 KB | Display | |
Data in CIF | 8bc2_validation.cif.gz | 95.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/8bc2 ftp://data.pdbj.org/pub/pdb/validation_reports/bc/8bc2 | HTTPS FTP |
-Related structure data
Related structure data | 15960MC 8bc3C 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: 24443.545 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus aryabhattai (bacteria) / Gene: HNP21_000079 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7W3N5X5, transaldolase #2: Water | ChemComp-HOH / | |
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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 in a ligand-free state. / Type: CELL / Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||
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Source (natural) | Organism: Priestia megaterium DSM 319 (bacteria) | |||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | |||||||||||||||
Buffer solution | pH: 7.4 Details: Buffer was clarified in a 0.22um filter and used for final SEC polishing. | |||||||||||||||
Buffer component |
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Specimen | Conc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid material: GOLD / Grid type: Quantifoil | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
-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 defocus max: 2000 nm / Nominal defocus min: 1000 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: 3.68 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: 4690 |
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: 153063 | ||||||||||||||||||||||||
Symmetry | Point symmetry: D5 (2x5 fold dihedral) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 59063 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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