2V8Q

Crystal structure of the regulatory fragment of mammalian AMPK in complexes with AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Basis for AMP Binding to Mammalian AMP-Activated Protein Kinase

Xiao, B.Heath, R.Saiu, P.Leiper, F.C.Leone, P.Jing, C.Walker, P.A.Haire, L.Eccleston, J.F.Davis, C.T.Martin, S.R.Carling, D.Gamblin, S.J.

(2007) Nature 449: 496

  • DOI: 10.1038/nature06161
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • AMP-activated protein kinase (AMPK) regulates cellular metabolism in response to the availability of energy and is therefore a target for type II diabetes treatment. It senses changes in the ratio of AMP/ATP by binding both species in a competitive m ...

    AMP-activated protein kinase (AMPK) regulates cellular metabolism in response to the availability of energy and is therefore a target for type II diabetes treatment. It senses changes in the ratio of AMP/ATP by binding both species in a competitive manner. Thus, increases in the concentration of AMP activate AMPK resulting in the phosphorylation and differential regulation of a series of downstream targets that control anabolic and catabolic pathways. We report here the crystal structure of the regulatory fragment of mammalian AMPK in complexes with AMP and ATP. The phosphate groups of AMP/ATP lie in a groove on the surface of the gamma domain, which is lined with basic residues, many of which are associated with disease-causing mutations. Structural and solution studies reveal that two sites on the gamma domain bind either AMP or Mg.ATP, whereas a third site contains a tightly bound AMP that does not exchange. Our binding studies indicate that under physiological conditions AMPK mainly exists in its inactive form in complex with Mg.ATP, which is much more abundant than AMP. Our modelling studies suggest how changes in the concentration of AMP ([AMP]) enhance AMPK activity levels. The structure also suggests a mechanism for propagating AMP/ATP signalling whereby a phosphorylated residue from the alpha and/or beta subunits binds to the gamma subunit in the presence of AMP but not when ATP is bound.


    Organizational Affiliation

    MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5'-AMP-ACTIVATED PROTEIN KINASE CATALYTIC SUBUNIT ALPHA-1
A
157Rattus norvegicusMutation(s): 0 
Gene Names: Prkaa1 (Ampk1)
EC: 2.7.11.1
Find proteins for P54645 (Rattus norvegicus)
Go to UniProtKB:  P54645
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT BETA-2
B
87Homo sapiensMutation(s): 0 
Gene Names: PRKAB2
Find proteins for O43741 (Homo sapiens)
Go to Gene View: PRKAB2
Go to UniProtKB:  O43741
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT GAMMA-1
E
330Rattus norvegicusMutation(s): 0 
Gene Names: Prkag1
Find proteins for P80385 (Rattus norvegicus)
Go to UniProtKB:  P80385
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download SDF File 
Download CCD File 
E
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AMPKd: 24500 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.522α = 90.00
b = 119.390β = 90.00
c = 129.310γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-09-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance