Skip to main content

 8IOA | pdb_00008ioa

Cryo-EM structure of cyanobacteria phosphoketolase


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.63 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8IOA

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: 179.17 kDa 
  • Atom Count: 12,570 
  • Modeled Residue Count: 1,576 
  • Deposited Residue Count: 1,592 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable phosphoketolase
A, B
796Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
Gene Names: xfp
EC: 4.1.2
UniProt
Find proteins for Q31LF9 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
Explore Q31LF9 
Go to UniProtKB:  Q31LF9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ31LF9
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.63 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2.0
MODEL REFINEMENTPHENIX

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