Crystal structure of Glyceraldehyde-3-Phosphate Dehydrogenase complexed with NADfrom Synechococcus elongatus"

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

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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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glyceraldehyde 3-phosphate dehydrogenase (NADP+)339Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
Gene Names: gap2Synpcc7942_1742
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
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAD

Download Ideal Coordinates CCD File 
I [auth A]
L [auth B]
R [auth P]
U [auth Q]
I [auth A],
L [auth B],
R [auth P],
U [auth Q],
X [auth R]
C21 H27 N7 O14 P2
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
J [auth B]
K [auth B]
M [auth O]
G [auth A],
H [auth A],
J [auth B],
K [auth B],
M [auth O],
N [auth O],
Q [auth P],
S [auth Q],
T [auth Q],
V [auth R],
W [auth R]
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.589α = 90
b = 79.847β = 101.65
c = 206.794γ = 90
Software Package:
Software NamePurpose
DNAdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

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: 2024-03-13
    Changes: Data collection, Database references, Derived calculations