3BRK

Crystal Structure of ADP-Glucose Pyrophosphorylase from Agrobacterium tumefaciens


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1021/bi701933q

  • 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 i ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glucose-1-phosphate adenylyltransferase
X
420Rhizobium radiobacterMutation(s): 0 
Gene Names: glgC
EC: 2.7.7.27
Find proteins for P39669 (Rhizobium radiobacter)
Go to UniProtKB:  P39669
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
X
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
X
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.221 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 85.380α = 90.00
b = 93.793β = 90.00
c = 140.293γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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