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: 2.2 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1016/j.str.2011.08.016
  • Primary Citation of Related Structures:  

  • 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 m ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glyceraldehyde 3-phosphate dehydrogenase (NADP+)
A, B
339Synechococcus elongatus (strain PCC 7942)Mutation(s): 0 
Gene Names: gap2
EC: 1.2.1.-
Find proteins for Q9R6W2 (Synechococcus elongatus (strain PCC 7942))
Go to UniProtKB:  Q9R6W2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CP12
C, D
25Synechococcus elongatus (strain PCC 7942)Mutation(s): 0 
Gene Names: cp12
Find proteins for Q6BBK3 (Synechococcus elongatus (strain PCC 7942))
Go to UniProtKB:  Q6BBK3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
CU
Query on CU

Download SDF File 
Download CCD File 
A, B
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.230 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 69.999α = 90.00
b = 161.603β = 90.00
c = 146.876γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data collection
CNSphasing
HKL-2000data scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-01-11
    Type: Initial release
  • Version 1.1: 2013-06-12
    Type: Structure summary