Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 68.16 kDa 
• Atom Count: 4045 
• Modelled Residue Count: 478 
• Deposited Residue Count: 590 
• Unique protein chains: 3

2Y8L

Structure of the regulatory fragment of mammalian aMPK in complex with two ADP

• DOI: 10.2210/pdb2Y8L/pdb

• Classification: TRANSFERASE
• Organism(s): Rattus norvegicus, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-02-07 Released: 2011-03-16 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.253 
• R-Value Work: 0.228 
• R-Value Observed: 0.229 

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

• PubMed: 21399626 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-AMP-ACTIVATED PROTEIN KINASE CATALYTIC SUBUNIT ALPHA-1	A	173	Rattus norvegicus	Mutation(s): 0  Gene Names: Prkaa1, Ampk1 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT BETA-2	B	87	Homo sapiens	Mutation(s): 0  Gene Names: PRKAB2
Find proteins for O43741 (Homo sapiens) Explore O43741  Go to UniProtKB:  O43741
NIH Common Fund Data Resources
PHAROS:  O43741 GTEx:  ENSG00000131791

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT GAMMA-1	E	330	Rattus norvegicus	Mutation(s): 0  Gene Names: Prkag1
Find proteins for P80385 (Rattus norvegicus) Explore P80385  Go to UniProtKB:  P80385

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	E	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
AMP	E	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ADP	Kd :  1500   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.253 
• R-Value Work: 0.228 
• R-Value Observed: 0.229 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.567	α = 90
b = 121.464	β = 90
c = 125.922	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-02-07 
• Released Date: 2011-03-16 
Deposition Author(s): 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.

Revision History  

• Version 1.0: 2011-03-16
  Type: Initial release
  
• Version 1.1: 2014-01-22
  Changes: Version format compliance