1PYG

STRUCTURAL BASIS FOR THE ACTIVATION OF GLYCOGEN PHOSPHORYLASE B BY ADENOSINE MONOPHOSPHATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Work: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for the activation of glycogen phosphorylase b by adenosine monophosphate.

Sprang, S.R.Withers, S.G.Goldsmith, E.J.Fletterick, R.J.Madsen, N.B.

(1991) Science 254: 1367-1371

  • DOI: 10.1126/science.1962195
  • Primary Citation of Related Structures:  
    1PYG

  • PubMed Abstract: 
  • The three-dimensional structure of the activated state of glycogen phosphorylase (GP) as induced by adenosine monophosphate (AMP) has been determined from crystals of pyridoxalpyrophosphoryl-GP. The same quaternary changes relative to the inactive co ...

    The three-dimensional structure of the activated state of glycogen phosphorylase (GP) as induced by adenosine monophosphate (AMP) has been determined from crystals of pyridoxalpyrophosphoryl-GP. The same quaternary changes relative to the inactive conformation as those induced by phosphorylation are induced by AMP, although the two regulatory signals function through different local structural mechanisms. Moreover, previous descriptions of the phosphorylase active state have been extended by demonstrating that, on activation, the amino- and carboxyl-terminal domains of GP rotate apart by 5 degrees, thereby increasing access of substrates to the catalytic site. The structure also reveals previously unobserved interactions with the nucleotide that accounts for the specificity of the nucleotide binding site for AMP in preference to inosine monophosphate.


    Related Citations: 
    • Multiple Phosphate Positions in the Catalytic Site of Glycogen Phosphorylase: Structure of the Pyridoxal-5'-Pyrophosphate Coenzyme-Substrate Analog
      Sprang, S.R., Madsen, N.B., Withers, S.G.
      (1992) Protein Sci 1: 1100
    • Domain Separation in the Activation of Glycogen Phosphorylase A
      Goldsmith, E.J., Sprang, S.R., Hamlin, R., Xuong, N.-H., Fletterick, R.J.
      (1989) Science 245: 528
    • 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
    • Structure of the Nucleotide Activation Switch in Glycogen Phosphorylase A
      Sprang, S., Goldsmith, E., Fletterick, R.
      (1987) Science 237: 1012
    • Catalytic Site of Glycogen Phosphorylase: Structural Changes During Activation and Mechanistic Implications
      Withers, S.G., Madsen, N.B., Sprang, S.R., Fletterick, R.J.
      (1982) Biochemistry 21: 5372
    • Evidence for Direct Phosphate-Phosphate Interaction between Pyridoxal Phosphate and Substrate in the Glycogen Phosphorylase Catalytic Mechanism
      Withers, S.G., Madsen, N.B., Sykes, B.D., Takagi, M., Shimomura, S., Fukui, T.
      (1981) J Biol Chem 256: 10759
    • The Structure of Glycogen Phosphorylase a at 2.5 Angstroms Resolution
      Sprang, S., Fletterick, R.J.
      (1979) J Mol Biol 131: 523

    Organizational Affiliation

    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas 75235-9050.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLYCOGEN PHOSPHORYLASE BABCD842Oryctolagus cuniculusMutation(s): 0 
Gene Names: PYGM
EC: 2.4.1.1
Find proteins for P00489 (Oryctolagus cuniculus)
Explore P00489 
Go to UniProtKB:  P00489
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download CCD File 
A, B, C, D
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
PDP
Query on PDP

Download CCD File 
A, B, C, D
PYRIDOXAL-5'-DIPHOSPHATE
C8 H11 N O9 P2
BLPOUZDLIYAHLN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AMPKd :  3000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Work: 0.185 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.9α = 90
b = 209.9β = 90
c = 123.4γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 1992-07-07 
  • Released Date: 1994-01-31 
  • Deposition Author(s): Sprang, S.

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance