Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 70.67 kDa 
• Atom Count: 4623 
• Modelled Residue Count: 554 
• Deposited Residue Count: 615 
• Unique protein chains: 3

3TE5

structure of the regulatory fragment of sacchromyces cerevisiae ampk in complex with NADH

• PDB DOI: 10.2210/pdb3TE5/pdb

• Classification: TRANSFERASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-08-12 Released: 2011-11-09 
• Deposition Author(s): Mayer, F.V., Heath, R., Underwood, E., Sanders, M.J., Carmena, D., McCartney, 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.281 
• R-Value Work: 0.241 
• R-Value Observed: 0.243 

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

• PubMed: 22019086 
• DOI: 10.1016/j.cmet.2011.09.009
• Primary Citation of Related Structures:  
  3T4N, 3TDH, 3TE5


• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbon catabolite-derepressing protein kinase	A	179	Saccharomyces cerevisiae S288C	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SNF1 protein kinase subunit beta-2	B	113	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: SIP2, SPM2, YGL208W, G1155
UniProt
Find proteins for P34164 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P34164  Go to UniProtKB:  P34164

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear protein SNF4	C	323	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: SNF4, CAT3, YGL115W, SCI1
UniProt
Find proteins for P12904 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P12904  Go to UniProtKB:  P12904

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAI	D [auth C]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C21 H29 N7 O14 P2 BOPGDPNILDQYTO-NNYOXOHSSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
NAI	PDBBind:  3TE5	Kd: 1.23e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.281 
• R-Value Work: 0.241 
• R-Value Observed: 0.243 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.732	α = 90
b = 240.236	β = 90
c = 79.183	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
PHASER	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-08-12 
• Released Date: 2011-11-09 
Deposition Author(s): Mayer, F.V., Heath, R., Underwood, E., Sanders, M.J., Carmena, D., McCartney, 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.

Revision History  

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