2NYE

Crystal structure of the Bateman2 domain of yeast Snf4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of the Bateman2 domain of yeast Snf4: dimeric association and relevance for AMP binding.

Rudolph, M.J.Amodeo, G.A.Iram, S.Hong, S.P.Pirino, G.Carlson, M.Tong, L.

(2007) Structure 15: 65-74

  • DOI: 10.1016/j.str.2006.11.014
  • Primary Citation of Related Structures:  2NYC

  • PubMed Abstract: 
  • AMP-activated protein kinase (AMPK) is a central regulator of energy homeostasis in mammals. AMP is believed to control the activity of AMPK by binding to the gamma subunit of this heterotrimeric enzyme. This subunit contains two Bateman domains, eac ...

    AMP-activated protein kinase (AMPK) is a central regulator of energy homeostasis in mammals. AMP is believed to control the activity of AMPK by binding to the gamma subunit of this heterotrimeric enzyme. This subunit contains two Bateman domains, each of which is composed of a tandem pair of cystathionine beta-synthase (CBS) motifs. No structural information is currently available on this subunit, and the molecular basis for its interactions with AMP is not well understood. We report here the crystal structure at 1.9 Angstrom resolution of the Bateman2 domain of Snf4, the gamma subunit of the yeast ortholog of AMPK. The structure revealed a dimer of the Bateman2 domain, and this dimerization is supported by our light-scattering, mutagenesis, and biochemical studies. There is a prominent pocket at the center of this dimer, and most of the disease-causing mutations are located in or near this pocket.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nuclear protein SNF4
A, B
144Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SNF4 (CAT3, SCI1)
Find proteins for P12904 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P12904
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.238 
  • Space Group: F 4 3 2
Unit Cell:
Length (Å)Angle (°)
a = 235.618α = 90.00
b = 235.618β = 90.00
c = 235.618γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
DENZOdata reduction
REFMACrefinement
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-12-12
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-31
    Type: Experimental preparation