9GPB

THE ALLOSTERIC TRANSITION OF GLYCOGEN PHOSPHORYLASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The allosteric transition of glycogen phosphorylase.

Barford, D.Johnson, L.N.

(1989) Nature 340: 609-616

  • DOI: 10.1038/340609a0

  • PubMed Abstract: 
  • The crystal structure of R-state glycogen phosphorylase b has been determined at 2.9 A resolution. A comparison of T-state and R-state structures of the enzyme explains its cooperative behaviour on ligand binding and the allosteric regulation of its ...

    The crystal structure of R-state glycogen phosphorylase b has been determined at 2.9 A resolution. A comparison of T-state and R-state structures of the enzyme explains its cooperative behaviour on ligand binding and the allosteric regulation of its activity. Communication between catalytic sites of the dimer is provided by a change in packing geometry of two helices linking each site with the subunit interface. Activation by AMP or by phosphorylation results in a quaternary conformational change that switches these two helices into the R-state conformation.


    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 --: --
    • 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
    • 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
    • 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, University of Oxford, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLYCOGEN PHOSPHORYLASE B
A, B, C, D
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
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
A, B, C, D
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: 2.9 Å
  • R-Value Work: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 119.000α = 90.00
b = 190.000β = 109.35
c = 88.200γ = 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: Non-polymer description, Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other