4GPB

COMPARISON OF THE BINDING OF GLUCOSE AND GLUCOSE-1-PHOSPHATE DERIVATIVES TO T-STATE GLYCOGEN PHOSPHORYLASE B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Comparison of the binding of glucose and glucose 1-phosphate derivatives to T-state glycogen phosphorylase b.

Martin, J.L.Johnson, L.N.Withers, S.G.

(1990) Biochemistry 29: 10745-10757

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The binding of T-state- and R-state-stabilizing ligands to the catalytic C site of T-state glycogen phosphorylase b has been investigated by crystallographic methods to study the interactions made and the conformational changes that occur at the C si ...

    The binding of T-state- and R-state-stabilizing ligands to the catalytic C site of T-state glycogen phosphorylase b has been investigated by crystallographic methods to study the interactions made and the conformational changes that occur at the C site. The compounds studied were alpha-D-glucose, 1, a T-state-stabilizing inhibitor of the enzyme, and the R-state-stabilizing phosphorylated ligands alpha-D-glucose 1-phosphate (2), 2-deoxy-2-fluoro-alpha-D-glucose 1-phosphate (3), and alpha-D-glucose 1-methylenephosphonate (4). The complexes have been refined, giving crystallographic R factors of less than 19%, for data between 8 and 2.3 A. Analysis of the refined structures shows that the glucosyl portions of the phosphorylated ligands bind in the same orientation as glucose and retain most of the interactions formed between glucose and the enzyme. However, the phosphates of the phosphorylated ligands adopt different conformations in each case; the stability of these conformations have been studied by using computational methods to rationalize the different binding modes. Binding of the phosphorylated ligands is accompanied by movement of C-site residues, most notably a shift of a loop out of the C site and toward the exterior of the protein. The C-site alterations do not include movement of Arg569, which has been observed in both the refined complex with 1-deoxy-D-gluco-heptulose 2-phosphate (5) [Johnson, L. N., et al (1990) J. Mol. Biol. 211, 645-661] and in the R-state enzyme [Barford, D. & Johnson, L. N. (1989) Nature 340, 609-616]. Refinement of the ligand complexes has also led to the observation of additional electron density for residues 10-19 at the N-terminus which had not previously been localized in the native structure. The conformation of this stretch of residues is different from that observed in glycogen phosphorylase a.


    Related Citations: 
    • Glycogen Phosphorylase B: Description of the Protein Structure 1 1991
      Acharya, K.R.,Stuart, D.I.,Varvill, K.M.,Johnson, L.N.
      () Glycogen Phosphorylase B: Description of the Protein Structure --: --
    • Structural Mechanism for Glycogen Phosphorylase Control by Phosphorylation and AMP
      Barford, D.,Hu, S.-H.,Johnson, L.N.
      (1991) J.Mol.Biol. 218: 233
    • Refined Crystal Structure of the Phosphorylase-Heptulose 2-Phosphate-Oligosaccharide-AMP Complex
      Johnson, L.N.,Acharya, K.R.,Jordan, M.D.,Mclaughlin, P.J.
      (1990) J.Mol.Biol. 211: 645
    • The Allosteric Transition of Glycogen Phosphorylase
      Barford, D.,Johnson, L.N.
      (1989) Nature 340: 609
    • Structural Changes in Glycogen Phosphorylase Induced by Phosphorylation
      Sprang, S.R.,Acharya, K.R.,Goldsmith, E.J.,Stuart, D.I.,Varvill, K.,Fletterick, R.J.,Madsen, N.B.,Johnson, L.N.
      (1988) Nature 336: 215


    Organizational Affiliation

    Laboratory of Molecular Biophysics, Oxford, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLYCOGEN PHOSPHORYLASE B
A
842Oryctolagus cuniculusMutation(s): 0 
Gene Names: PYGM
EC: 2.4.1.1
Find proteins for P00489 (Oryctolagus cuniculus)
Go to Gene View: PYGM
Go to UniProtKB:  P00489
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GFP
Query on GFP

Download SDF File 
Download CCD File 
A
2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE-1-PHOSPHATE
C6 H12 F O8 P
LXEHNDWFCMGWAY-QZABAPFNSA-N
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
A
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Work: 0.180 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 128.500α = 90.00
b = 128.500β = 90.00
c = 116.300γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1992-10-15
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other