1Z0N

the glycogen-binding domain of the AMP-activated protein kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Basis for Glycogen Recognition by AMP-Activated Protein Kinase.

Polekhina, G.Gupta, A.van Denderen, B.J.Feil, S.C.Kemp, B.E.Stapleton, D.Parker, M.W.

(2005) Structure 13: 1453-1462

  • DOI: 10.1016/j.str.2005.07.008
  • Primary Citation of Related Structures:  1Z0M

  • PubMed Abstract: 
  • AMP-activated protein kinase (AMPK) coordinates cellular metabolism in response to energy demand as well as to a variety of stimuli. The AMPK beta subunit acts as a scaffold for the alpha catalytic and gamma regulatory subunits and targets the AMPK h ...

    AMP-activated protein kinase (AMPK) coordinates cellular metabolism in response to energy demand as well as to a variety of stimuli. The AMPK beta subunit acts as a scaffold for the alpha catalytic and gamma regulatory subunits and targets the AMPK heterotrimer to glycogen. We have determined the structure of the AMPK beta glycogen binding domain in complex with beta-cyclodextrin. The structure reveals a carbohydrate binding pocket that consolidates all known aspects of carbohydrate binding observed in starch binding domains into one site, with extensive contact between several residues and five glucose units. beta-cyclodextrin is held in a pincer-like grasp with two tryptophan residues cradling two beta-cyclodextrin glucose units and a leucine residue piercing the beta-cyclodextrin ring. Mutation of key beta-cyclodextrin binding residues either partially or completely prevents the glycogen binding domain from binding glycogen. Modeling suggests that this binding pocket enables AMPK to interact with glycogen anywhere across the carbohydrate's helical surface.


    Related Citations: 
    • Crystallization of the glycogen-binding domain of the AMP-activated protein kinase beta subunit and preliminary X-ray analysis
      Polekhina, G.,Feil, S.C.,Gupta, A.,O'Donnell, P.,Stapleton, D.,Parker, M.W.
      (2005) Acta Crystallogr.,Sect.F 61: 39


    Organizational Affiliation

    St. Vincent's Institute of Medical Research, 41 Victoria Parade, Fitzroy, Victoria 3065, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5'-AMP-activated protein kinase, beta-1 subunit
A, B, C
96Rattus norvegicusGene Names: Prkab1
Find proteins for P80386 (Rattus norvegicus)
Go to UniProtKB:  P80386
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BCD
Query on BCD

Download SDF File 
Download CCD File 
A, B, C
BETA-CYCLODEXTRIN
CYCLO-HEPTA-AMYLOSE
C42 H70 O35
WHGYBXFWUBPSRW-FOUAGVGXSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.184 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 43.750α = 71.90
b = 45.250β = 69.70
c = 50.600γ = 65.40
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
DMphasing
CNSrefinement
REFMACrefinement
DENZOdata reduction
MLPHAREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-10-25
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description