3TDH

Structure of the regulatory fragment of sccharomyces cerevisiae AMPK in complex with AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.248 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

ADP Regulates SNF1, the Saccharomyces cerevisiae Homolog of AMP-Activated Protein Kinase.

Mayer, F.V.Heath, R.Underwood, E.Sanders, M.J.Carmena, D.McCartney, R.R.Leiper, F.C.Xiao, B.Jing, C.Walker, P.A.Haire, L.F.Ogrodowicz, R.Martin, S.R.Schmidt, M.C.Gamblin, S.J.Carling, D.

(2011) Cell Metab 14: 707-714

  • DOI: 10.1016/j.cmet.2011.09.009
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The SNF1 protein kinase complex plays an essential role in regulating gene expression in response to the level of extracellular glucose in budding yeast. SNF1 shares structural and functional similarities with mammalian AMP-activated protein kinase. ...

    The SNF1 protein kinase complex plays an essential role in regulating gene expression in response to the level of extracellular glucose in budding yeast. SNF1 shares structural and functional similarities with mammalian AMP-activated protein kinase. Both kinases are activated by phosphorylation on a threonine residue within the activation loop segment of the catalytic subunit. Here we show that ADP is the long-sought metabolite that activates SNF1 in response to glucose limitation by protecting the enzyme against dephosphorylation by Glc7, its physiologically relevant protein phosphatase. We also show that the regulatory subunit of SNF1 has two ADP binding sites. The tighter site binds AMP, ADP, and ATP competitively with NADH, whereas the weaker site does not bind NADH, but is responsible for mediating the protective effect of ADP on dephosphorylation. Mutagenesis experiments suggest that the general mechanism by which ADP protects against dephosphorylation is strongly conserved between SNF1 and AMPK.


    Organizational Affiliation

    MRC Clinical Sciences Centre, Cellular Stress Group, Hammersmith Hospital Campus, Imperial College, DuCane Road, London, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbon catabolite-derepressing protein kinase
A
179Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SNF1 (CAT1, CCR1, GLC2, PAS14)
EC: 2.7.11.1
Find proteins for P06782 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P06782
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SNF1 protein kinase subunit beta-2
B
113Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SIP2 (SPM2)
Find proteins for P34164 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P34164
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Nuclear protein SNF4
C
323Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SNF4 (CAT3, SCI1)
Find proteins for P12904 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P12904
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download SDF File 
Download CCD File 
C
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AMPKd: 55000 nM BINDINGMOAD
AMPKd: 55000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.248 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 94.970α = 90.00
b = 242.378β = 90.00
c = 79.352γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
GDAdata collection
DENZOdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-09
    Type: Initial release
  • Version 1.1: 2011-11-23
    Type: Database references