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- PDB-8bc2: Ligand-Free Structure of the decameric sulfofructose transaldolas... -

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Basic information

Entry
Database: PDB / ID: 8bc2
TitleLigand-Free Structure of the decameric sulfofructose transaldolase BmSF-TAL
ComponentsTransaldolase
KeywordsTRANSFERASE / transaldolase / cryo-EM / decamer / sulfofructose
Function / homology
Function and homology information


6-deoxy-6-sulfo-D-fructose transaldolase / transaldolase activity / aldehyde-lyase activity / carbohydrate metabolic process
Similarity search - Function
Transaldolase/Fructose-6-phosphate aldolase, archaeal/bacterial / Transaldolase/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
6-deoxy-6-sulfo-D-fructose transaldolase
Similarity search - Component
Biological speciesBacillus aryabhattai (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsSnow, A.J.D. / Sharma, M. / Blaza, J. / Davies, G.J.
Funding support United Kingdom, 3items
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, 2022Deposition site: PDBE / Processing site: PDBE
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transaldolase
B: Transaldolase
C: Transaldolase
D: Transaldolase
E: Transaldolase
F: Transaldolase
G: Transaldolase
H: Transaldolase
I: Transaldolase
J: Transaldolase


Theoretical massNumber of molelcules
Total (without water)244,43510
Polymers244,43510
Non-polymers00
Water8,287460
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area39580 Å2
ΔGint-271 kcal/mol
Surface area69110 Å2

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Components

#1: Protein
Transaldolase


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 / water


Mass: 18.015 Da / Num. of mol.: 460 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Decameric complex of BmSF-TAL in a ligand-free state. / Type: CELL / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Priestia megaterium DSM 319 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
Details: Buffer was clarified in a 0.22um filter and used for final SEC polishing.
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTRISC4H11NO31
2200 mMNaClNaCl1
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 30 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage 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 scansWidth: 4096 / Height: 4096

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameCategory
2EPUimage acquisition
4RELIONCTF correction
8PHENIXmodel refinement
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 153063
SymmetryPoint symmetry: D5 (2x5 fold dihedral)
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 59063 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00415660
ELECTRON MICROSCOPYf_angle_d0.51421248
ELECTRON MICROSCOPYf_dihedral_angle_d4.1262300
ELECTRON MICROSCOPYf_chiral_restr0.0442580
ELECTRON MICROSCOPYf_plane_restr0.0042478

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