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- PDB-8bc3: Cryo-EM Structure of a BmSF-TAL - Sulfofructose Schiff Base Complex -

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Basic information

Entry
Database: PDB / ID: 8bc3
TitleCryo-EM Structure of a BmSF-TAL - Sulfofructose Schiff Base Complex
ComponentsBmSF-TAL
KeywordsTRANSFERASE / 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
Transaldolase/Fructose-6-phosphate aldolase, archaeal/bacterial / Transaldolase/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase / Aldolase-type TIM barrel
Similarity search - Domain/homology
Chem-QC9 / 6-deoxy-6-sulfo-D-fructose transaldolase
Similarity search - Component
Biological speciesBacillus aryabhattai (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.1 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
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 15, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Nov 15, 2023Group: Data collection / Source and taxonomy / Category: chem_comp_atom / chem_comp_bond / entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BmSF-TAL
H: BmSF-TAL
B: BmSF-TAL
C: BmSF-TAL
D: BmSF-TAL
E: BmSF-TAL
F: BmSF-TAL
G: BmSF-TAL
I: BmSF-TAL
J: BmSF-TAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,41820
Polymers253,11610
Non-polymers2,30210
Water9,008500
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area39520 Å2
ΔGint-272 kcal/mol
Surface area68530 Å2

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Components

#1: Protein
BmSF-TAL


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


Mass: 230.236 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H14O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 500 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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 / Type: COMPLEX / Details: Solution decamer of BmSF-TAL / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.25 MDa / Experimental value: YES
Source (natural)Organism: Priestia megaterium DSM 319 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenConc.: 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 supportDetails: 20 mAmp, 10 s hold time / Grid material: GOLD / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: -10 blot force, 6 second blot time

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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 FIELDBright-field microscopy / Nominal magnification: 310000 X / Nominal defocus max: 1000 nm / Nominal defocus min: 2000 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: 3.39 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 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
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 77489
SymmetryPoint symmetry: D5 (2x5 fold dihedral)
3D reconstructionResolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53450 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00716420
ELECTRON MICROSCOPYf_angle_d0.94122460
ELECTRON MICROSCOPYf_dihedral_angle_d6.5422290
ELECTRON MICROSCOPYf_chiral_restr0.1292620
ELECTRON MICROSCOPYf_plane_restr0.0072870

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