2YA3

STRUCTURE OF THE REGULATORY FRAGMENT OF MAMMALIAN AMPK IN COMPLEX WITH COUMARIN ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of Mammalian Ampk and its Regulation by Adp

Xiao, B.Sanders, M.J.Underwood, E.Heath, R.Mayer, F.Carmena, D.Jing, C.Walker, P.A.Eccleston, J.F.Haire, L.F.Saiu, P.Howell, S.A.Aasland, R.Martin, S.R.Carling, D.Gamblin, S.J.

(2011) Nature 472: 230

  • DOI: 10.1038/nature09932
  • Primary Citation of Related Structures:  
    2YA3, 2Y8Q, 4CFH, 2Y8L

  • PubMed Abstract: 
  • The heterotrimeric AMP-activated protein kinase (AMPK) has a key role in regulating cellular energy metabolism; in response to a fall in intracellular ATP levels it activates energy-producing pathways and inhibits energy-consuming processes. AMPK has been implicated in a number of diseases related to energy metabolism including type 2 diabetes, obesity and, most recently, cancer ...

    The heterotrimeric AMP-activated protein kinase (AMPK) has a key role in regulating cellular energy metabolism; in response to a fall in intracellular ATP levels it activates energy-producing pathways and inhibits energy-consuming processes. AMPK has been implicated in a number of diseases related to energy metabolism including type 2 diabetes, obesity and, most recently, cancer. AMPK is converted from an inactive form to a catalytically competent form by phosphorylation of the activation loop within the kinase domain: AMP binding to the γ-regulatory domain promotes phosphorylation by the upstream kinase, protects the enzyme against dephosphorylation, as well as causing allosteric activation. Here we show that ADP binding to just one of the two exchangeable AXP (AMP/ADP/ATP) binding sites on the regulatory domain protects the enzyme from dephosphorylation, although it does not lead to allosteric activation. Our studies show that active mammalian AMPK displays significantly tighter binding to ADP than to Mg-ATP, explaining how the enzyme is regulated under physiological conditions where the concentration of Mg-ATP is higher than that of ADP and much higher than that of AMP. We have determined the crystal structure of an active AMPK complex. The structure shows how the activation loop of the kinase domain is stabilized by the regulatory domain and how the kinase linker region interacts with the regulatory nucleotide-binding site that mediates protection against dephosphorylation. From our biochemical and structural data we develop a model for how the energy status of a cell regulates AMPK activity.


    Organizational Affiliation

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
5'-AMP-ACTIVATED PROTEIN KINASE CATALYTIC SUBUNIT ALPHA-1 A173Rattus norvegicusMutation(s): 0 
Gene Names: Prkaa1Ampk1
EC: 2.7.11.1 (PDB Primary Data), 2.7.11.27 (UniProt), 2.7.11.31 (UniProt), 2.7.11.26 (UniProt)
Find proteins for P54645 (Rattus norvegicus)
Explore P54645 
Go to UniProtKB:  P54645
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT BETA-2 B87Homo sapiensMutation(s): 0 
Gene Names: PRKAB2
Find proteins for O43741 (Homo sapiens)
Explore O43741 
Go to UniProtKB:  O43741
NIH Common Fund Data Resources
PHAROS:  O43741
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT GAMMA-1 E330Rattus norvegicusMutation(s): 0 
Gene Names: Prkag1
Find proteins for P80385 (Rattus norvegicus)
Explore P80385 
Go to UniProtKB:  P80385
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
J7V
Query on J7V

Download Ideal Coordinates CCD File 
E
3'-(7-diethylaminocoumarin-3-carbonylamino)-3'-deoxy-ADP
C24 H29 N7 O12 P2
XAOIOCVKONGQFV-ZLFGVDQTSA-N
 Ligand Interaction
AMP
Query on AMP

Download Ideal Coordinates CCD File 
E
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.943α = 90
b = 124.06β = 90
c = 125.315γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-16
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance