3HYH | pdb_00003hyh

Crystal structure of the protein kinase domain of yeast AMP-activated protein kinase Snf1

• PDB DOI: https://doi.org/10.2210/pdb3HYH/pdb
• Entry: 3HYH supersedes: 3FAM

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


• Deposited: 2009-06-22 Released: 2009-06-30 
• Deposition Author(s): Rudolph, M.J., Amodeo, G.A., Bai, Y., Tong, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.280 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.237 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Literature

Crystal structure of the protein kinase domain of yeast AMP-activated protein kinase Snf1

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

(2005) Biochem Biophys Res Commun 337: 1224-1228

• PubMed: 16236260 
• DOI: https://doi.org/10.1016/j.bbrc.2005.09.181
• Primary Citation Related Structures: 
  3HYH


• PubMed Abstract: 
  

  AMP-activated protein kinase (AMPK) is a master metabolic regulator, and is an important target for drug development against diabetes, obesity, and other diseases. AMPK is a hetero-trimeric enzyme, with a catalytic (alpha) subunit, and two regulatory (beta and gamma) subunits. Here we report the crystal structure at 2.2A resolution of the protein kinase domain (KD) of the catalytic subunit of yeast AMPK (commonly known as SNF1). The Snf1-KD structure shares strong similarity to other protein kinases, with a small N-terminal lobe and a large C-terminal lobe. Two negative surface patches in the structure may be important for the recognition of the substrates of this kinase.

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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: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 62.69 kDa 
• Atom Count: 3,958 
• Modeled Residue Count: 471 
• Deposited Residue Count: 550 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbon catabolite-derepressing protein kinase	A, B	275	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: CAT1, CCR1, D8035.20, GLC2, PAS14, SNF1, YDR477W 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: 2.20 Å
• R-Value Free:  0.280 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.237 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.028	α = 90
b = 75.137	β = 90
c = 113.699	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-30 
Deposition Author(s): Rudolph, M.J., Amodeo, G.A., Bai, Y., Tong, L.
• This entry supersedes: 3FAM

Revision History  

• Version 1.0: 2009-06-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references