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- EMDB-15961: Cryo-EM Structure of a BmSF-TAL - Sulfofructose Schiff Base Complex -
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Open data
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Basic information
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Title | Cryo-EM Structure of a BmSF-TAL - Sulfofructose Schiff Base Complex | ||||||||||||
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![]() | Transaldolase / sulfofructose / cryo-EM / decamer / TRANSFERASE | ||||||||||||
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![]() | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.1 Å | ||||||||||||
![]() | Snow AJD / Sharma M / Blaza J / Davies GJ | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 10.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.3 KB 17.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.8 KB | Display | ![]() |
Images | ![]() | 134.5 KB | ||
Masks | ![]() | 144.7 MB | ![]() | |
Filedesc metadata | ![]() | 6.2 KB | ||
Others | ![]() ![]() | 114.1 MB 114.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 189.8 KB | Display | ![]() |
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Full document | ![]() | 189.4 KB | Display | |
Data in XML | ![]() | 502 B | Display | |
Data in CIF | ![]() | 373 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8bc3MC ![]() 8bc2C ![]() 8bc4C ![]() 8c4iC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 0.9 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Half map: #2
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Density Histograms |
-Half map: #1
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Density Histograms |
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Sample components
-Entire : Decameric complex of BmSF-TAL
Entire | Name: Decameric complex of BmSF-TAL |
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Components |
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-Supramolecule #1: Decameric complex of BmSF-TAL
Supramolecule | Name: Decameric complex of BmSF-TAL / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Solution decamer of BmSF-TAL |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 250 KDa |
-Macromolecule #1: BmSF-TAL
Macromolecule | Name: BmSF-TAL / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 25.311557 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MKYFLDSAIL EEIRYAYENW AIDGVTTNPR HIMNSGKPFL TVLDEFASEF KGVENFPISV EINPHLDNAK DMVEEGTKIA KLSSNFVIK IPCTEPGLIA AKEFEKQGIS TNVTLVFSPS QALQPARIGA KFVSPFVGWK ENSGDDTTQY IQDIVNIYKN Y NYNTEIIV ...String: MKYFLDSAIL EEIRYAYENW AIDGVTTNPR HIMNSGKPFL TVLDEFASEF KGVENFPISV EINPHLDNAK DMVEEGTKIA KLSSNFVIK IPCTEPGLIA AKEFEKQGIS TNVTLVFSPS QALQPARIGA KFVSPFVGWK ENSGDDTTQY IQDIVNIYKN Y NYNTEIIV AALRNGKQIV DAAKAGAHIV TCGFDVYKES FQHAFTDYGL NKFRNAWDNT VTEAPVLK UniProtKB: 6-deoxy-6-sulfo-D-fructose transaldolase |
-Macromolecule #2: (2~{R},3~{S},4~{S})-2,3,4,6-tetrakis(oxidanyl)hexane-1-sulfonic acid
Macromolecule | Name: (2~{R},3~{S},4~{S})-2,3,4,6-tetrakis(oxidanyl)hexane-1-sulfonic acid type: ligand / ID: 2 / Number of copies: 10 / Formula: QC9 |
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Molecular weight | Theoretical: 230.236 Da |
Chemical component information | ![]() ChemComp-QC9: |
-Macromolecule #3: water
Macromolecule | Name: water / type: ligand / ID: 3 / Number of copies: 500 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2.5 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Quantifoil R2/2 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 180 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 38.0 kPa / Details: 20 mAmp, 10 s hold time |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: -10 blot force, 6 second blot time. |
Details | monodisperse sample with acceptable range of orientations; ice was of good quality |
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Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 1842 / Average exposure time: 3.39 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 30.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 310000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |