2QLV

Crystal structure of the heterotrimer core of the S. cerevisiae AMPK homolog SNF1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.239 

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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the heterotrimer core of Saccharomyces cerevisiae AMPK homologue SNF1.

Amodeo, G.A.Rudolph, M.J.Tong, L.

(2007) Nature 449: 492-495

  • DOI: 10.1038/nature06127
  • Primary Citation of Related Structures:  
    2QLV

  • PubMed Abstract: 
  • AMP-activated protein kinase (AMPK) is a central regulator of energy homeostasis in mammals and is an attractive target for drug discovery against diabetes, obesity and other diseases. The AMPK homologue in Saccharomyces cerevisiae, known as SNF1, is ...

    AMP-activated protein kinase (AMPK) is a central regulator of energy homeostasis in mammals and is an attractive target for drug discovery against diabetes, obesity and other diseases. The AMPK homologue in Saccharomyces cerevisiae, known as SNF1, is essential for responses to glucose starvation as well as for other cellular processes, although SNF1 seems to be activated by a ligand other than AMP. Here we report the crystal structure at 2.6 A resolution of the heterotrimer core of SNF1. The ligand-binding site in the gamma-subunit (Snf4) has clear structural differences from that of the Schizosaccharomyces pombe enzyme, although our crystallographic data indicate that AMP can also bind to Snf4. The glycogen-binding domain in the beta-subunit (Sip2) interacts with Snf4 in the heterotrimer but should still be able to bind carbohydrates. Our structure is supported by a large body of biochemical and genetic data on this complex. Most significantly, the structure reveals that part of the regulatory sequence in the alpha-subunit (Snf1) is sequestered by Snf4, demonstrating a direct interaction between the alpha- and gamma-subunits and indicating that our structure may represent the heterotrimer core of SNF1 in its activated state.


    Organizational Affiliation

    Department of Biological Sciences, Columbia University, New York, New York 10027, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Carbon catabolite derepressing protein kinaseAD171Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SNF1CAT1CCR1GLC2PAS14
EC: 2.7.11.1
Find proteins for P06782 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P06782
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein SIP2BE252Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SIP2SPM2
Find proteins for P34164 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P34164 
Go to UniProtKB:  P34164
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear protein SNF4CF315Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SNF4CAT3
Find proteins for P12904 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P12904 
Go to UniProtKB:  P12904
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.239 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.33α = 90
b = 81.84β = 102.22
c = 174.74γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-09-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-18
    Changes: Refinement description