1PYG | pdb_00001pyg

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 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.4 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: https://doi.org/10.1126/science.1962195
  • Primary Citation 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 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.


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

Macromolecule Content 

  • Total Structure Weight: 391.86 kDa 
  • Atom Count: 26,214 
  • Modeled Residue Count: 3,194 
  • Deposited Residue Count: 3,368 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GLYCOGEN PHOSPHORYLASE B
A, B, C, D
842Oryctolagus cuniculusMutation(s): 0 
EC: 2.4.1.1
UniProt
Find proteins for P00489 (Oryctolagus cuniculus)
Explore P00489 
Go to UniProtKB:  P00489
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00489
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

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

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

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-06-05
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 1.4: 2024-10-30
    Changes: Structure summary