3MN3 | pdb_00003mn3

An inhibited conformation for the protein kinase domain of the Saccharomyces cerevisiae AMPK homolog Snf1

• PDB DOI: https://doi.org/10.2210/pdb3MN3/pdb

• Classification: TRANSFERASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-04-20 Released: 2010-09-15 
• Deposition Author(s): Rudolph, M.J., Amodeo, G.A., Tong, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 
  0.246 (Depositor) 
• R-Value Work: 
  0.230 (Depositor) 
• R-Value Observed: 
  0.231 (Depositor) 

Literature

An inhibited conformation for the protein kinase domain of the Saccharomyces cerevisiae AMPK homolog Snf1.

Rudolph, M.J., Amodeo, G.A., Tong, L.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 999-1002

• PubMed: 20823513 
• DOI: https://doi.org/10.1107/S1744309110028265
• Primary Citation Related Structures: 
  3MN3


• PubMed Abstract: 
  

  AMP-activated protein kinase (AMPK) is a master metabolic regulator for controlling cellular energy homeostasis. Its homolog in yeast, SNF1, is activated in response to glucose depletion and other stresses. The catalytic (alpha) subunit of AMPK/SNF1 in yeast (Snf1) contains a protein Ser/Thr kinase domain (KD), an auto-inhibitory domain (AID) and a region that mediates interactions with the two regulatory (beta and gamma) subunits. Here, the crystal structure of residues 41-440 of Snf1, which include the KD and AID, is reported at 2.4 A resolution. The AID is completely disordered in the crystal. A new inhibited conformation of the KD is observed in a DFG-out conformation and with the glycine-rich loop adopting a structure that blocks ATP binding to the active site.

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Organizational Affiliation: 
• Department of Biological Sciences, Columbia University, New York, NY 10027, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 31.03 kDa 
• Atom Count: 2,094 
• Modeled Residue Count: 252 
• Deposited Residue Count: 271 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbon catabolite-derepressing protein kinase	A	271	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: SNF1, CAT1, CCR1, GLC2, PAS14, YDR477W, D8035.20 EC: 2.7.11.1
UniProt
Find proteins for P06782 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P06782  Go to UniProtKB:  P06782

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free:  0.246 (Depositor) 
• R-Value Work:  0.230 (Depositor) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.981	α = 90
b = 76.981	β = 90
c = 286.215	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
DENZO	data reduction
SCALEPACK	data scaling
COMO	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-15 
Deposition Author(s): Rudolph, M.J., Amodeo, G.A., Tong, L.

Revision History  

• Version 1.0: 2010-09-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references