1YGP

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.179 
  • R-Value Observed: 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

  • DOI: 10.1126/science.273.5281.1539
  • Structures With Same Primary Citation

  • 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
    • Parallel Evolution in Two Homologues of Phosphorylase
      Rath, V.L., Fletterick, R.J.
      (1994) Nat Struct Biol 1: 681
    • Purification and Crystallization of Glycogen Phosphorylase from Saccharomyces Cerevisiae
      Rath, V.L., Hwang, P.K., Fletterick, R.J.
      (1992) J Mol Biol 225: 1027

    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 PHOSPHORYLASEA, B879Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: YEAST GLYCOGEN PHOSPHORYLASE
EC: 2.4.1.1
Find proteins for P06738 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P06738 
Go to UniProtKB:  P06738
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download CCD File 
A, B
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.91α = 90
b = 143.93β = 90
c = 169.26γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
R-AXISdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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