2PKQ

Crystal structure of the photosynthetic A2B2-glyceraldehyde-3-phosphate dehydrogenase, complexed with NADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.261 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Molecular mechanism of thioredoxin regulation in photosynthetic A2B2-glyceraldehyde-3-phosphate dehydrogenase.

Fermani, S.Sparla, F.Falini, G.Martelli, P.L.Casadio, R.Pupillo, P.Ripamonti, A.Trost, P.

(2007) Proc Natl Acad Sci U S A 104: 11109-11114

  • DOI: 10.1073/pnas.0611636104
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Chloroplast glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a light-regulated, NAD(P)H-dependent enzyme involved in plant photosynthetic carbon reduction. Unlike lower photosynthetic organisms, which only contain A(4)-GAPDH, the major GAPDH isofo ...

    Chloroplast glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a light-regulated, NAD(P)H-dependent enzyme involved in plant photosynthetic carbon reduction. Unlike lower photosynthetic organisms, which only contain A(4)-GAPDH, the major GAPDH isoform of land plants is made up of A and B subunits, the latter containing a C-terminal extension (CTE) with fundamental regulatory functions. Light-activation of AB-GAPDH depends on the redox state of a pair of cysteines of the CTE, which can form a disulfide bond under control of thioredoxin f, leading to specific inhibition of the NADPH-dependent activity. The tridimensional structure of A(2)B(2)-GAPDH from spinach chloroplasts, crystallized in the oxidized state, shows that each disulfide-containing CTE is docked into a deep cleft between a pair of A and B subunits. The structure of the CTE was derived from crystallographic data and computational modeling and confirmed by site-specific mutagenesis. Structural analysis of oxidized A(2)B(2)-GAPDH and chimeric mutant [A+CTE](4)-GAPDH revealed that Arg-77, which is essential for coenzyme specificity and high NADPH-dependent activity, fails to interact with NADP in these kinetically inhibited GAPDH tetramers and is attracted instead by negative residues of oxidized CTE. Other subtle changes in catalytic domains and overall conformation of the tetramers were noticed in oxidized A(2)B(2)-GAPDH and [A+CTE](4)-GAPDH, compared with fully active A(4)-GAPDH. The CTE is envisioned as a redox-sensitive regulatory domain that can force AB-GAPDH into a kinetically inhibited conformation under oxidizing conditions, which also occur during dark inactivation of the enzyme in vivo.


    Related Citations: 
    • Coenzyme Site-directed Mutants of Photosynthetic A4-GAPDH Show Selectively Reduced NADPH-dependent Catalysis, Similar to Regulatory AB-GAPDH Inhibited by Oxidized Thioredoxin
      Sparla, F., Fermani, S., Falini, G., Zaffagnini, M., Ripamonti, A., Sabatino, P., Pupillo, P., Trost, P.
      (2004) J Mol Biol 340: 1025
    • Dual Coenzyme Specificity of Photosynthetic Glyceraldehyde-3-phosphate Dehydrogenase Interpreted by the Crystal Structure of A4 Isoform Complexed with NAD
      Falini, G., Fermani, S., Ripamonti, A., Sabatino, P., Sparla, F., Pupillo, P., Trost, P.
      (2003) Biochemistry 42: 4631
    • Crystal structure of the non-regulatory A4 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

    Organizational Affiliation

    Department of Chemistry, University of Bologna, Via Selmi 2, 40126 Bologna, Italy.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glyceraldehyde-3-phosphate dehydrogenase BO, Q, T368Spinacia oleraceaMutation(s): 0 
Gene Names: GAPBGPB1
EC: 1.2.1.13
Find proteins for P12860 (Spinacia oleracea)
Explore P12860 
Go to UniProtKB:  P12860
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Glyceraldehyde-3-phosphate dehydrogenase AP, R, S337Spinacia oleraceaMutation(s): 0 
Gene Names: GAPAGPA1
EC: 1.2.1.13
Find proteins for P19866 (Spinacia oleracea)
Explore P19866 
Go to UniProtKB:  P19866
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download CCD File 
O, P, Q, R, S, T
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
O, P, Q, R, S, T
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.261 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 186.147α = 90
b = 215.687β = 102.52
c = 81.469γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-19
    Type: Initial release
  • Version 1.1: 2007-10-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2014-11-12
    Changes: Structure summary
  • Version 1.4: 2017-10-18
    Changes: Refinement description