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 8IO7 | pdb_00008io7

Cryo-EM structure of phosphoketolase from Bifidobacterium longum in dimeric assembly


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.62 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8IO7

This is version 1.3 of the entry. See complete history. 

Literature

An ATP-sensitive phosphoketolase regulates carbon fixation in cyanobacteria.

Lu, K.J., Chang, C.W., Wang, C.H., Chen, F.Y., Huang, I.Y., Huang, P.H., Yang, C.H., Wu, H.Y., Wu, W.J., Hsu, K.C., Ho, M.C., Tsai, M.D., Liao, J.C.

(2023) Nat Metab 5: 1111-1126

  • DOI: https://doi.org/10.1038/s42255-023-00831-w
  • Primary Citation Related Structures: 
    8IO6, 8IO7, 8IO8, 8IO9, 8IOA, 8IOE

  • PubMed Abstract: 

    Regulation of CO 2 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 2 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.


  • Organizational Affiliation: 
    • Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.

Macromolecule Content 

  • Total Structure Weight: 186.14 kDa 
  • Atom Count: 12,876 
  • Modeled Residue Count: 1,612 
  • Deposited Residue Count: 1,650 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Xylulose5phosphatefructose6phosphate phosphoketolase
A, B
825Bifidobacterium longum subsp. longum F8Mutation(s): 0 
UniProt
Find proteins for A0ACD7UJP1 (Bifidobacterium longum subsp. longum (strain ATCC 15707 / DSM 20219 / JCM 1217 / NCTC 11818 / E194b))
Explore A0ACD7UJP1 
Go to UniProtKB:  A0ACD7UJP1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD7UJP1
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.62 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC2.0

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academia Sinica (Taiwan)TaiwanGrant No. AS-CFII-108-110
Academia Sinica (Taiwan)TaiwanGrant No. AS-KPQ-109-TPP2

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-28
    Type: Initial release
  • Version 1.1: 2023-07-05
    Changes: Database references
  • Version 1.2: 2023-08-02
    Changes: Database references
  • Version 1.3: 2023-11-15
    Changes: Data collection, Refinement description, Source and taxonomy