1YGP

PHOSPHORYLATED FORM OF YEAST GLYCOGEN PHOSPHORYLASE WITH PHOSPHATE BOUND IN THE ACTIVE SITE.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A protein phosphorylation switch at the conserved allosteric site in GP.

Lin, K.Rath, V.L.Dai, S.C.Fletterick, R.J.Hwang, P.K.

(1996) Science 273: 1539-1542


  • PubMed Abstract: 
  • A phosphorylation-initiated mechanism of local protein refolding activates yeast glycogen phosphorylase (GP). Refolding of the phosphorylated amino-terminus was shown to create a hydrophobic cluster that wedges into the subunit interface of the enzym ...

    A phosphorylation-initiated mechanism of local protein refolding activates yeast glycogen phosphorylase (GP). Refolding of the phosphorylated amino-terminus was shown to create a hydrophobic cluster that wedges into the subunit interface of the enzyme to trigger activation. The phosphorylated threonine is buried in the allosteric site. The mechanism implicates glucose 6-phosphate, the allosteric inhibitor, in facilitating dephosphorylation by dislodging the buried covalent phosphate through binding competition. Thus, protein phosphorylation-dephosphorylation may also be controlled through regulation of the accessibility of the phosphorylation site to kinases and phosphatases. In mammalian glycogen phosphorylase, phosphorylation occurs at a distinct locus. The corresponding allosteric site binds a ligand activator, adenosine monophosphate, which triggers activation by a mechanism analogous to that of phosphorylation in the yeast enzyme.


    Related Citations: 
    • Mechanism of Regulation in Yeast Glycogen Phosphorylase
      Lin, K.,Hwang, P.K.,Fletterick, R.J.
      (1995) J.Biol.Chem. 270: 26833
    • Purification and Crystallization of Glycogen Phosphorylase from Saccharomyces Cerevisiae
      Rath, V.L.,Hwang, P.K.,Fletterick, R.J.
      (1992) J.Mol.Biol. 225: 1027
    • Parallel Evolution in Two Homologues of Phosphorylase
      Rath, V.L.,Fletterick, R.J.
      (1994) Nat.Struct.Mol.Biol. 1: 681


    Organizational Affiliation

    Department of Biochemistry and Biophysics, University of California at San Francisco, 513 Parnassus, San Francisco, CA 94143, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
YEAST GLYCOGEN PHOSPHORYLASE
A, B
879Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: GPH1
EC: 2.4.1.1
Find proteins for P06738 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P06738
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
A, B
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: 2.8 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 103.910α = 90.00
b = 143.930β = 90.00
c = 169.260γ = 90.00
Software Package:
Software NamePurpose
R-AXISdata reduction
X-PLORphasing
X-PLORrefinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-12-23
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance