Crystal Structure of ADP-Glucose Pyrophosphorylase from Agrobacterium tumefaciens

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.225 

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Structural analysis of ADP-glucose pyrophosphorylase from the bacterium Agrobacterium tumefaciens.

Cupp-Vickery, J.R.Igarashi, R.Y.Perez, M.Poland, M.Meyer, C.R.

(2008) Biochemistry 47: 4439-4451

  • DOI: https://doi.org/10.1021/bi701933q
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    ADP-glucose pyrophosphorylase (ADPGlc PPase) catalyzes the conversion of glucose 1-phosphate and ATP to ADP-glucose and pyrophosphate. As a key step in glucan synthesis, the ADPGlc PPases are highly regulated by allosteric activators and inhibitors in accord with the carbon metabolism pathways of the organism. Crystals of Agrobacterium tumefaciens ADPGlc PPase were obtained using lithium sulfate as a precipitant. A complete anomalous selenomethionyl derivative X-ray diffraction data set was collected with unit cell dimensions a = 85.38 A, b = 93.79 A, and c = 140.29 A (alpha = beta = gamma = 90 degrees ) and space group I 222. The A. tumefaciens ADPGlc PPase model was refined to 2.1 A with an R factor = 22% and R free = 26.6%. The model consists of two domains: an N-terminal alphabetaalpha sandwich and a C-terminal parallel beta-helix. ATP and glucose 1-phosphate were successfully modeled in the proposed active site, and site-directed mutagenesis of conserved glycines in this region (G20, G21, and G23) resulted in substantial loss of activity. The interface between the N- and the C-terminal domains harbors a strong sulfate-binding site, and kinetic studies revealed that sulfate is a competitive inhibitor for the allosteric activator fructose 6-phosphate. These results suggest that the interface between the N- and C-terminal domains binds the allosteric regulator, and fructose 6-phosphate was modeled into this region. The A. tumefaciens ADPGlc PPase/fructose 6-phosphate structural model along with sequence alignment analysis was used to design mutagenesis experiments to expand the activator specificity to include fructose 1,6-bisphosphate. The H379R and H379K enzymes were found to be activated by fructose 1,6-bisphosphate.

  • Organizational Affiliation

    Department of Physiology and Biophysics, University of California, Irvine, California 92697, USA. jvickery@uci.edu

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glucose-1-phosphate adenylyltransferaseA [auth X]420Agrobacterium tumefaciensMutation(s): 0 
Gene Names: glgC
Find proteins for P39669 (Rhizobium radiobacter)
Explore P39669 
Go to UniProtKB:  P39669
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39669
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.225 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.38α = 90
b = 93.793β = 90
c = 140.293γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description