2H6D

Protein Kinase Domain of the Human 5'-AMP-activated protein kinase catalytic subunit alpha-2 (AMPK alpha-2 chain)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A conserved mechanism of autoinhibition for the AMPK kinase domain: ATP-binding site and catalytic loop refolding as a means of regulation.

Littler, D.R.Walker, J.R.Davis, T.Wybenga-Groot, L.E.Finerty, P.J.Newman, E.Mackenzie, F.Dhe-Paganon, S.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 143-151

  • DOI: 10.1107/S1744309109052543
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The AMP-activated protein kinase (AMPK) is a highly conserved trimeric protein complex that is responsible for energy homeostasis in eukaryotic cells. Here, a 1.9 A resolution crystal structure of the isolated kinase domain from the alpha2 subunit of ...

    The AMP-activated protein kinase (AMPK) is a highly conserved trimeric protein complex that is responsible for energy homeostasis in eukaryotic cells. Here, a 1.9 A resolution crystal structure of the isolated kinase domain from the alpha2 subunit of human AMPK, the first from a multicellular organism, is presented. This human form adopts a catalytically inactive state with distorted ATP-binding and substrate-binding sites. The ATP site is affected by changes in the base of the activation loop, which has moved into an inhibited DFG-out conformation. The substrate-binding site is disturbed by changes within the AMPKalpha2 catalytic loop that further distort the enzyme from a catalytically active form. Similar structural rearrangements have been observed in a yeast AMPK homologue in response to the binding of its auto-inhibitory domain; restructuring of the kinase catalytic loop is therefore a conserved feature of the AMPK protein family and is likely to represent an inhibitory mechanism that is utilized during function.


    Organizational Affiliation

    The Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada. dene@phys.unsw.edu.au



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5'-AMP-activated protein kinase catalytic subunit alpha-2
A
276Homo sapiensMutation(s): 0 
Gene Names: PRKAA2AMPKAMPK2
EC: 2.7.11.1 (PDB Primary Data), 2.7.11.27 (UniProt), 2.7.11.31 (UniProt)
Find proteins for P54646 (Homo sapiens)
Go to UniProtKB:  P54646
NIH Common Fund Data Resources
PHAROS  P54646
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.454α = 90
b = 67.41β = 91.3
c = 50.493γ = 90
Software Package:
Software NamePurpose
SBC-Collectdata collection
HKL-2000data reduction
PHASERphasing
RESOLVEmodel building
ARP/wARPmodel building
REFMACrefinement
HKL-2000data scaling
RESOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2006-06-27
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description