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- PDB-8ioe: Cryo-EM structure of cyanobacteria phosphoketolase in dodecameric... -

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Basic information

Entry
Database: PDB / ID: 8ioe
TitleCryo-EM structure of cyanobacteria phosphoketolase in dodecameric assembly
ComponentsProbable phosphoketolase
KeywordsCYTOSOLIC PROTEIN / Carbon metabolism / TPP-dependent enzyme
Function / homologyTHIAMINE DIPHOSPHATE / :
Function and homology information
Biological speciesSynechococcus elongatus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 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 11, 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.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.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _entity_src_gen.gene_src_strain / _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: Probable phosphoketolase
B: Probable phosphoketolase
C: Probable phosphoketolase
D: Probable phosphoketolase
E: Probable phosphoketolase
F: Probable phosphoketolase
G: Probable phosphoketolase
H: Probable phosphoketolase
I: Probable phosphoketolase
J: Probable phosphoketolase
K: Probable phosphoketolase
L: Probable phosphoketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,074,99436
Polymers1,069,59912
Non-polymers5,39524
Water00
1


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

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Components

#1: Protein
Probable phosphoketolase


Mass: 89133.211 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805) (bacteria)
Strain: ATCC 33912 / PCC 7942 / FACHB-805 / Gene: xfp / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8T9U4A0
#2: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / 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: Cyanobacteria XPK complexed with TPP/Mg2+ / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.89 MDa / Experimental value: NO
Source (natural)Organism: Synechococcus (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 FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 4.5 sec. / Electron dose: 59 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 3983
Image scansMovie frames/image: 60

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Processing

SoftwareName: PHENIX / Version: 1.19_4092: / Classification: refinement
EM software
IDNameVersionCategory
7UCSF Chimeramodel fitting
12cryoSPARC23D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30649 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 8IO8

8io8


Accession code: 8IO8 / Details: cyanobacteria holo-XPK dimer form / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00377574
ELECTRON MICROSCOPYf_angle_d0.465105908
ELECTRON MICROSCOPYf_dihedral_angle_d10.48627940
ELECTRON MICROSCOPYf_chiral_restr0.04211324
ELECTRON MICROSCOPYf_plane_restr0.00513940

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