Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 31.56 kDa 
• Atom Count: 2232 
• Residue Count: 256 
• Unique protein chains: 1

2H6D

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

• DOI: 10.2210/pdb2H6D/pdb

• Classification: SIGNALING PROTEIN,TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2006-05-31 Released: 2006-06-27 
• Deposition Author(s): Littler, D.R., Walker, J.R., Wybenga-Groot, L., Newman, E.M., Butler-Cole, C., Mackenzie, F., Finerty, P.J., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

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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 

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

• PubMed: 20124709 
• 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 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.

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Organizational Affiliation: 

The Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
5'-AMP-activated protein kinase catalytic subunit alpha-2	A	276	Homo sapiens	Mutation(s): 0  Gene Names: PRKAA2, AMPK, AMPK2 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 GTEx  ENSG00000162409

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 = 39.454	α = 90
b = 67.41	β = 91.3
c = 50.493	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-2000	data reduction
PHASER	phasing
RESOLVE	model building
ARP/wARP	model building
REFMAC	refinement
HKL-2000	data scaling
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-05-31 
• Released Date: 2006-06-27 
Deposition Author(s): Littler, D.R., Walker, J.R., Wybenga-Groot, L., Newman, E.M., Butler-Cole, C., Mackenzie, F., Finerty, P.J., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

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