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- EMDB-15961: Cryo-EM Structure of a BmSF-TAL - Sulfofructose Schiff Base Complex -

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Basic information

Entry
Database: EMDB / ID: EMD-15961
TitleCryo-EM Structure of a BmSF-TAL - Sulfofructose Schiff Base Complex
Map data
Sample
  • Complex: Decameric complex of BmSF-TAL
    • Protein or peptide: BmSF-TAL
  • Ligand: (2~{R},3~{S},4~{S})-2,3,4,6-tetrakis(oxidanyl)hexane-1-sulfonic acid
  • Ligand: water
KeywordsTransaldolase / sulfofructose / cryo-EM / decamer / TRANSFERASE
Function / homology6-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 speciesPriestia megaterium DSM 319 (bacteria) / Bacillus aryabhattai (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsSnow AJD / Sharma M / Blaza J / Davies GJ
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Leverhulme TrustRPG-2017-190 United Kingdom
Wellcome Trust206161/Z/17/Z United Kingdom
UK Research and Innovation (UKRI)MR/T040742/1 United Kingdom
CitationJournal: 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
DepositionOct 14, 2022-
Header (metadata) releaseJan 18, 2023-
Map releaseJan 18, 2023-
UpdateNov 15, 2023-
Current statusNov 15, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15961.png

Downloads & links

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Map

FileDownload / File: emd_15961.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.9 Å/pix.
x 336 pix.
= 302.4 Å		0.9 Å/pix.
x 336 pix.
= 302.4 Å		0.9 Å/pix.
x 336 pix.
= 302.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0259
Minimum - Maximum-0.083276354 - 0.15821606
Average (Standard dev.)0.00006434572 (±0.0035263447)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 302.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15961_msk_1.map
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Half map: #2

Fileemd_15961_half_map_1.map
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Half map: #1

Fileemd_15961_half_map_2.map
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Sample components

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Entire : Decameric complex of BmSF-TAL

EntireName: Decameric complex of BmSF-TAL
Components
  • Complex: Decameric complex of BmSF-TAL
    • Protein or peptide: BmSF-TAL
  • Ligand: (2~{R},3~{S},4~{S})-2,3,4,6-tetrakis(oxidanyl)hexane-1-sulfonic acid
  • Ligand: water

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Supramolecule #1: Decameric complex of BmSF-TAL

SupramoleculeName: Decameric complex of BmSF-TAL / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Solution decamer of BmSF-TAL
Source (natural)Organism: Priestia megaterium DSM 319 (bacteria)
Molecular weightTheoretical: 250 KDa

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Macromolecule #1: BmSF-TAL

MacromoleculeName: BmSF-TAL / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Bacillus aryabhattai (bacteria)
Molecular weightTheoretical: 25.311557 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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Macromolecule #2: (2~{R},3~{S},4~{S})-2,3,4,6-tetrakis(oxidanyl)hexane-1-sulfonic acid

MacromoleculeName: (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
Molecular weightTheoretical: 230.236 Da
Chemical component information

ChemComp-QC9:
(2~{R},3~{S},4~{S})-2,3,4,6-tetrakis(oxidanyl)hexane-1-sulfonic acid

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 500 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.5 mg/mL
BufferpH: 7.4
GridModel: 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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: -10 blot force, 6 second blot time.
Detailsmonodisperse sample with acceptable range of orientations; ice was of good quality

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 310000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm 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

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Image processing

Particle selectionNumber selected: 77489
Startup modelType of model: OTHER
Details: Structure of ligand-free BmSF-TAL, processed immediately prior to this collection
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 4 / Avg.num./class: 19372
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: D5 (2x5 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 53450
FSC plot (resolution estimation)

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