4Z5X

Glycogen phosphorylase in complex with gallic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Natural flavonoids as antidiabetic agents. The binding of gallic and ellagic acids to glycogen phosphorylase b.

Kyriakis, E.Stravodimos, G.A.Kantsadi, A.L.Chatzileontiadou, D.S.Skamnaki, V.T.Leonidas, D.D.

(2015) Febs Lett. 589: 1787-1794

  • DOI: 10.1016/j.febslet.2015.05.013
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We present a study on the binding of gallic acid and its dimer ellagic acid to glycogen phosphorylase (GP). Ellagic acid is a potent inhibitor with Kis of 13.4 and 7.5 μM, in contrast to gallic acid which displays Kis of 1.7 and 3.9 mM for GPb and GP ...

    We present a study on the binding of gallic acid and its dimer ellagic acid to glycogen phosphorylase (GP). Ellagic acid is a potent inhibitor with Kis of 13.4 and 7.5 μM, in contrast to gallic acid which displays Kis of 1.7 and 3.9 mM for GPb and GPa, respectively. Both compounds are competitive inhibitors with respect to the substrate, glucose-1-phoshate, and non-competitive to the allosteric activator, AMP. However, only ellagic acid functions with glucose in a strongly synergistic mode. The crystal structures of the GPb-gallic acid and GPb-ellagic acid complexes were determined at high resolution, revealing that both ligands bind to the inhibitor binding site of the enzyme and highlight the structural basis for the significant difference in their inhibitory potency.


    Organizational Affiliation

    Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Str., 41221 Larissa, Greece.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycogen phosphorylase, muscle form
A
843Oryctolagus 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
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
GDE
Query on GDE

Download SDF File 
Download CCD File 
A
3,4,5-trihydroxybenzoic acid
Gallate
C7 H6 O5
LNTHITQWFMADLM-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GDEKi: 1730000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.159 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 128.486α = 90.00
b = 128.486β = 90.00
c = 116.634γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-13
    Type: Initial release
  • Version 1.1: 2015-06-03
    Type: Database references
  • Version 1.2: 2015-07-15
    Type: Database references
  • Version 1.3: 2018-03-07
    Type: Data collection