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- PDB-8io6: Cryo-EM structure of phosphoketolase from Bifidobacterium longum ... -

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Basic information

Entry
Database: PDB / ID: 8io6
TitleCryo-EM structure of phosphoketolase from Bifidobacterium longum in octameric assembly
ComponentsXylulose5phosphatefructose6phosphate phosphoketolase
KeywordsCYTOSOLIC PROTEIN / Carbon metabolism / TPP-dependent enzyme
Function / homology
Function and homology information


aldehyde-lyase activity / carbohydrate metabolic process
Similarity search - Function
Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, C-terminal / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, N-terminal / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, thiamine diphosphate binding site / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, conserved site / D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase / XFP C-terminal domain / XFP N-terminal domain / Phosphoketolase signature 1. / Phosphoketolase signature 2. ...Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, C-terminal / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, N-terminal / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, thiamine diphosphate binding site / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, conserved site / D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase / XFP C-terminal domain / XFP N-terminal domain / Phosphoketolase signature 1. / Phosphoketolase signature 2. / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate-binding fold
Similarity search - Domain/homology
THIAMINE DIPHOSPHATE / Xylulose5phosphatefructose6phosphate phosphoketolase
Similarity search - Component
Biological speciesBifidobacterium longum subsp. longum F8 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsChang, C.-W. / Tsai, M.-D.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)Grant No. AS-CFII-108-110 Taiwan
Academia Sinica (Taiwan)Grant No. AS-KPQ-109-TPP2 Taiwan
CitationJournal: Nat Metab / Year: 2023
Title: An ATP-sensitive phosphoketolase regulates carbon fixation in cyanobacteria.
Authors: Kuan-Jen Lu / Chiung-Wen Chang / Chun-Hsiung Wang / Frederic Y-H Chen / Irene Y Huang / Pin-Hsuan Huang / Cheng-Han Yang / Hsiang-Yi Wu / Wen-Jin Wu / Kai-Cheng Hsu / Meng-Chiao Ho / Ming- ...Authors: Kuan-Jen Lu / Chiung-Wen Chang / Chun-Hsiung Wang / Frederic Y-H Chen / Irene Y Huang / Pin-Hsuan Huang / Cheng-Han Yang / Hsiang-Yi Wu / Wen-Jin Wu / Kai-Cheng Hsu / Meng-Chiao Ho / Ming-Daw Tsai / James C Liao /
Abstract: Regulation of CO fixation in cyanobacteria is important both for the organism and global carbon balance. Here we show that phosphoketolase in Synechococcus elongatus PCC7942 (SeXPK) possesses a ...Regulation of CO fixation in cyanobacteria is important both for the organism and global carbon balance. Here we show that phosphoketolase in Synechococcus elongatus PCC7942 (SeXPK) possesses a distinct ATP-sensing mechanism, where a drop in ATP level allows SeXPK to divert precursors of the RuBisCO substrate away from the Calvin-Benson-Bassham cycle. Deleting the SeXPK gene increased CO fixation particularly during light-dark transitions. In high-density cultures, the Δxpk strain showed a 60% increase in carbon fixation and unexpectedly resulted in sucrose secretion without any pathway engineering. Using cryo-EM analysis, we discovered that these functions were enabled by a unique allosteric regulatory site involving two subunits jointly binding two ATP, which constantly suppresses the activity of SeXPK until the ATP level drops. This magnesium-independent ATP allosteric site is present in many species across all three domains of life, where it may also play important regulatory functions.
History
DepositionMar 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed
Revision 1.2Aug 2, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 15, 2023Group: Data collection / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / entity_src_gen
Item: _em_3d_fitting_list.initial_refinement_model_id / _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: Xylulose5phosphatefructose6phosphate phosphoketolase
B: Xylulose5phosphatefructose6phosphate phosphoketolase
C: Xylulose5phosphatefructose6phosphate phosphoketolase
D: Xylulose5phosphatefructose6phosphate phosphoketolase
E: Xylulose5phosphatefructose6phosphate phosphoketolase
F: Xylulose5phosphatefructose6phosphate phosphoketolase
G: Xylulose5phosphatefructose6phosphate phosphoketolase
H: Xylulose5phosphatefructose6phosphate phosphoketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)744,56624
Polymers740,9698
Non-polymers3,59716
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Xylulose5phosphatefructose6phosphate phosphoketolase


Mass: 92621.125 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum subsp. longum F8 (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: S6CP45
#2: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
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: Bifidobacterium longum XFPK in complex with TPP/Mg2+ / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.75 MDa / Experimental value: NO
Source (natural)Organism: Bifidobacteriaceae bacterium (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.2
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.5 sec. / Electron dose: 42 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6289
Image scansMovie frames/image: 40

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Processing

EM software
IDNameVersionCategory
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
13cryoSPARC23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 590627 / Num. of class averages: 3 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 3AI7

3ai7


Accession code: 3AI7 / Source name: PDB / Type: experimental model

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