2QRC

Crystal structure of the adenylate sensor from AMP-activated protein kinase in complex with ADP and AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Insight into AMPK Regulation: ADP Comes into Play.

Jin, X.Townley, R.Shapiro, L.

(2007) Structure 15: 1285-1295

  • DOI: 10.1016/j.str.2007.07.017
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The AMP-activated protein kinase (AMPK), a sensor of cellular energy status found in all eukaryotes, responds to changes in intracellular adenosine nucleotide levels resulting from metabolic stresses. Here we describe crystal structures of a heterotr ...

    The AMP-activated protein kinase (AMPK), a sensor of cellular energy status found in all eukaryotes, responds to changes in intracellular adenosine nucleotide levels resulting from metabolic stresses. Here we describe crystal structures of a heterotrimeric regulatory core fragment from Schizosaccharomyces pombe AMPK in complex with ADP, ADP/AMP, ADP/ATP, and 5-aminoimidazole-4-carboxamide 1-beta-D-ribofuranotide (AICAR phosphate, or ZMP), a well-characterized AMPK activator. Prior crystallographic studies had revealed a single site in the gamma subunit that binds either ATP or AMP within Bateman domain B. Here we show that ZMP binds at this site, mimicking the binding of AMP. An analogous site in Bateman domain A selectively accommodates ADP, which binds in a distinct manner that also involves direct ligation to elements from the beta subunit. These observations suggest a possible role for ADP in regulating AMPK response to changes in cellular energy status.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SNF1-like protein kinase ssp2
A, C
137Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: ssp2
EC: 2.7.11.1
Find proteins for O74536 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O74536
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SPCC1919.03c protein
B, D
97Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: amk2
Find proteins for P78789 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  P78789
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Protein C1556.08c
G, E
334Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: cbs2
Find proteins for Q10343 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q10343
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
E, G
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
AMP
Query on AMP

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.206 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 168.293α = 90.00
b = 78.087β = 124.13
c = 108.553γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance