2YZA

Crystal structure of kinase domain of Human 5'-AMP-activated protein kinase alpha-2 subunit mutant (T172D)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for compound C inhibition of the human AMP-activated protein kinase alpha 2 subunit kinase domain

Handa, N.Takagi, T.Saijo, S.Kishishita, S.Takaya, D.Toyama, M.Terada, T.Shirouzu, M.Suzuki, A.Lee, S.Yamauchi, T.Okada-Iwabu, M.Iwabu, M.Kadowaki, T.Minokoshi, Y.Yokoyama, S.

(2011) Acta Crystallogr.,Sect.D 67: 480-487

  • DOI: 10.1107/S0907444911010201
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • AMP-activated protein kinase (AMPK) is a serine/threonine kinase that functions as a sensor to maintain energy balance at both the cellular and the whole-body levels and is therefore a potential target for drug design against metabolic syndrome, obes ...

    AMP-activated protein kinase (AMPK) is a serine/threonine kinase that functions as a sensor to maintain energy balance at both the cellular and the whole-body levels and is therefore a potential target for drug design against metabolic syndrome, obesity and type 2 diabetes. Here, the crystal structure of the phosphorylated-state mimic T172D mutant kinase domain from the human AMPK α2 subunit is reported in the apo form and in complex with a selective inhibitor, compound C. The AMPK α2 kinase domain exhibits a typical bilobal kinase fold and exists as a monomer in the crystal. Like the wild-type apo form, the T172D mutant apo form adopts the autoinhibited structure of the `DFG-out' conformation, with the Phe residue of the DFG motif anchored within the putative ATP-binding pocket. Compound C binding dramatically alters the conformation of the activation loop, which adopts an intermediate conformation between DFG-out and DFG-in. This induced fit forms a compound-C binding pocket composed of the N-lobe, the C-lobe and the hinge of the kinase domain. The pocket partially overlaps with the putative ATP-binding pocket. These three-dimensional structures will be useful to guide drug discovery.


    Organizational Affiliation

    RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.




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): 1 
Gene Names: PRKAA2 (AMPK, AMPK2)
EC: 2.7.11.1
Find proteins for P54646 (Homo sapiens)
Go to Gene View: PRKAA2
Go to UniProtKB:  P54646
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.227 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 39.187α = 90.00
b = 67.336β = 91.26
c = 50.651γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
REFMACrefinement
BSSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-05-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-04-11
    Type: Database references