6KEV

Reduced phosphoribulokinase from Synechococcus elongatus PCC 7942 complexed with adenosine diphosphate and glucose 6-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

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This is version 1.2 of the entry. See complete history


Literature

Photosynthetic Phosphoribulokinase Structures: Enzymatic Mechanisms and the Redox Regulation of the Calvin-Benson-Bassham Cycle.

Yu, A.Xie, Y.Pan, X.Zhang, H.Cao, P.Su, X.Chang, W.Li, M.

(2020) Plant Cell 32: 1556-1573

  • DOI: https://doi.org/10.1105/tpc.19.00642
  • Primary Citation of Related Structures:  
    6KEV, 6KEW, 6KEX, 6KEZ

  • PubMed Abstract: 

    The Calvin-Benson-Bassham (CBB) cycle is responsible for CO 2 assimilation and carbohydrate production in oxyphototrophs. Phosphoribulokinase (PRK) is an essential enzyme of the CBB cycle in photosynthesis, catalyzing ATP-dependent conversion of ribulose-5-phosphate (Ru5P) to ribulose-1,5-bisphosphate. The oxyphototrophic PRK is redox-regulated and can be further regulated by reversible association with both glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and oxidized chloroplast protein CP12. The resulting GAPDH/CP12/PRK complex is central in the regulation of the CBB cycle; however, the PRK-CP12 interface in the recently reported cyanobacterial GAPDH/CP12/PRK structure was not well resolved, and the detailed binding mode of PRK with ATP and Ru5P remains undetermined, as only apo-form structures of PRK are currently available. Here, we report the crystal structures of cyanobacterial ( Synechococcus elongatus ) PRK in complex with ADP and glucose-6-phosphate and of the Arabidopsis ( Arabidopsis thaliana ) GAPDH/CP12/PRK complex, providing detailed information regarding the active site of PRK and the key elements essential for PRK-CP12 interaction. Our structural and biochemical results together reveal that the ATP binding site is disrupted in the oxidized PRK, whereas the Ru5P binding site is occupied by oxidized CP12 in the GAPDH/CP12/PRK complex. This structure-function study greatly advances the understanding of the reaction mechanism of PRK and the subtle regulations of redox signaling for the CBB cycle.


  • Organizational Affiliation

    National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoribulokinase343Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
Gene Names: Synpcc7942_0977
EC: 2.7.1.19
UniProt
Find proteins for Q31PL2 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
Explore Q31PL2 
Go to UniProtKB:  Q31PL2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ31PL2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.415α = 90
b = 77.104β = 90
c = 94.405γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31770778

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-13
    Type: Initial release
  • Version 1.1: 2020-05-20
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary