2QRE

Crystal structure of the adenylate sensor from AMP-activated protein kinase in complex with 5-aminoimidazole-4-carboxamide 1-beta-D-ribofuranotide (ZMP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.235 

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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMZ
Query on AMZ

Download SDF File 
Download CCD File 
E, G
AMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE
AICAR
C9 H15 N4 O8 P
NOTGFIUVDGNKRI-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.235 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 168.470α = 90.00
b = 78.146β = 124.04
c = 108.512γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
HKL-2000data reduction
ADSCdata collection
CNSphasing

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