3B1J

Crystal structure of Glyceraldehyde-3-Phosphate Dehydrogenase complexed with CP12 in the presence of copper from Synechococcus elongatus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structure Basis for the Regulation of Glyceraldehyde-3-Phosphate Dehydrogenase Activity via the Intrinsically Disordered Protein CP12.

Matsumura, H.Kai, A.Maeda, T.Tamoi, M.Satoh, A.Tamura, H.Hirose, M.Ogawa, T.Kizu, N.Wadano, A.Inoue, T.Shigeoka, S.

(2011) Structure 19: 1846-1854

  • DOI: https://doi.org/10.1016/j.str.2011.08.016
  • Primary Citation of Related Structures:  
    3B1J, 3B1K, 3B20

  • PubMed Abstract: 

    The reversible formation of a glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-CP12-phosphoribulokinase (PRK) supramolecular complex, identified in oxygenic photosynthetic organisms, provides light-dependent Calvin cycle regulation in a coordinated manner. An intrinsically disordered protein (IDP) CP12 acts as a linker to sequentially bind GAPDH and PRK to downregulate both enzymes. Here, we report the crystal structures of the ternary GAPDH-CP12-NAD and binary GAPDH-NAD complexes from Synechococcus elongates. The GAPDH-CP12 complex structure reveals that the oxidized CP12 becomes partially structured upon GAPDH binding. The C-terminus of CP12 is inserted into the active-site region of GAPDH, resulting in competitive inhibition of GAPDH. This study also provides insight into how the GAPDH-CP12 complex is dissociated by a high NADP(H)/NAD(H) ratio. An unexpected increase in negative charge potential that emerged upon CP12 binding highlights the biological function of CP12 in the sequential assembly of the supramolecular complex.


  • Organizational Affiliation

    Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan. matsumura@chem.eng.osaka-u.ac.jp


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glyceraldehyde 3-phosphate dehydrogenase (NADP+)
A, B
339Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
Gene Names: gap2Synpcc7942_1742
EC: 1.2.1.13 (PDB Primary Data), 1.2.1 (UniProt)
UniProt
Find proteins for Q9R6W2 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
Explore Q9R6W2 
Go to UniProtKB:  Q9R6W2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9R6W2
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CP12
C, D
25Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
Gene Names: cp12Synpcc7942_0361
UniProt
Find proteins for Q6BBK3 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
Explore Q6BBK3 
Go to UniProtKB:  Q6BBK3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6BBK3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.999α = 90
b = 161.603β = 90
c = 146.876γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-01-11
    Type: Initial release
  • Version 1.1: 2013-06-12
    Changes: Structure summary
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary