1JN0

Crystal structure of the non-regulatory A4 isoform of spinach chloroplast glyceraldehyde-3-phosphate dehydrogenase complexed with NADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the non-regulatory A(4 )isoform of spinach chloroplast glyceraldehyde-3-phosphate dehydrogenase complexed with NADP.

Fermani, S.Ripamonti, A.Sabatino, P.Zanotti, G.Scagliarini, S.Sparla, F.Trost, P.Pupillo, P.

(2001) J.Mol.Biol. 314: 527-542

  • DOI: 10.1006/jmbi.2001.5172

  • PubMed Abstract: 
  • Here, we report the first crystal structure of a photosynthetic glyceraldehyde-3-phosphate dehydrogenase (GAPDH) complexed with NADP. The enzyme, purified from spinach chloroplasts, is constituted of a single type of subunit (A) arranged in homotetra ...

    Here, we report the first crystal structure of a photosynthetic glyceraldehyde-3-phosphate dehydrogenase (GAPDH) complexed with NADP. The enzyme, purified from spinach chloroplasts, is constituted of a single type of subunit (A) arranged in homotetramers. It shows non-regulated NADP-dependent and NAD-dependent activities, with a preference for NADP. The structure has been solved to 3.0 A resolution by molecular replacement. The crystals belong to space group C222 with three monomers in the asymmetric unit. One of the three monomers generates a tetramer using the space group 222 point symmetry and a very similar tetramer is generated by the other two monomers, related by a non-crystallographic symmetry, using a crystallographic 2-fold axis. The protein reveals a large structural homology with known GAPDHs both in the cofactor-binding domain and in regions of the catalytic domain. Like all other GAPDHs investigated so far, the A(4)-GAPDH belongs to the Rossmann fold family of dehydrogenases. However, unlike most dehydrogenases of this family, the adenosine 2'-phosphate group of NADP does not form a salt-bridge with any positively charged residue in its surroundings, being instead set in place by hydrogen bonds with a threonine residue belonging to the Rossmann fold and a serine residue located in the S-loop of a symmetry-related monomer. While increasing our knowledge of an important photosynthetic enzyme, these results contribute to a general understanding of NADP versus NAD recognition in pyridine nucleotide-dependent enzymes. Although the overall structure of A(4)-GAPDH is similar to that of the cytosolic GAPDH from bacteria and eukaryotes, the chloroplast tetramer is peculiar, in that it can actually be considered a dimer of dimers, since monomers are bound in pairs by a disulphide bridge formed across Cys200 residues. This bridge is not found in other cytosolic or chloroplast GAPDHs from animals, bacteria, or plants other than spinach.


    Related Citations: 
    • The non-regulatory isoform of NADP(H)-glyceraldehyde-3-phosphate dehydrogenase from spinach chloroplasts
      Scagliarini, S.,Trost, P.,Pupillo, P.
      (1998) J.Exp.Bot. 49: 1307
    • Chloroplast glyceraldehyde-3-phosphate dehydrogenase (NADP): amino acid sequence of the subunits from isoenzyme I and structural relationship with isoenzyme II.
      Ferri, G.,Stoppini, M.,Meloni, M.,Zapponi, M.C.,Iadarola, P.
      (1990) Biochim.Biophys.Acta 1041: 36
    • Crystallization and preliminary X-ray study of chloroplast glyceraldehyde-3-phosphate dehydrogenase
      Sabatino, P.,Fermani, S.,Ripamonti, A.,Cassetta, A.,Scagliarini, S.,Trost, P.
      (1999) Acta Crystallogr.,Sect.D 55: 566


    Organizational Affiliation

    Dipartimento di Chimica "G. Ciamician", Università di Bologna, via Selmi 2, Bologna, 40126, Italia. fermani@ciam.unibo.it




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE A
O, A, B
335Spinacia oleraceaMutation(s): 0 
Gene Names: GAPA (GPA1)
EC: 1.2.1.13
Find proteins for P19866 (Spinacia oleracea)
Go to UniProtKB:  P19866
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, O
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NDP
Query on NDP

Download SDF File 
Download CCD File 
A, B, O
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.213 
  • Space Group: C 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 146.249α = 90.00
b = 182.184β = 90.00
c = 106.026γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
AMoREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-11-30
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2014-11-12
    Type: Structure summary