4Y0G

beta2 carbohydrate binding module (CBM) of AMP-activated protein kinase (AMPK)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Determinants of oligosaccharide specificity of the carbohydrate-binding modules of AMP-activated protein kinase.

Mobbs, J.I.Koay, A.Di Paolo, A.Bieri, M.Petrie, E.J.Gorman, M.A.Doughty, L.Parker, M.W.Stapleton, D.I.Griffin, M.D.Gooley, P.R.

(2015) Biochem.J. 468: 245-257

  • DOI: 10.1042/BJ20150270
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • AMP-activated protein kinase (AMPK) is an αβγ heterotrimer that is important in regulating energy metabolism in all eukaryotes. The β-subunit exists in two isoforms (β1 and β2) and contains a carbohydrate-binding module (CBM) that interacts with glyc ...

    AMP-activated protein kinase (AMPK) is an αβγ heterotrimer that is important in regulating energy metabolism in all eukaryotes. The β-subunit exists in two isoforms (β1 and β2) and contains a carbohydrate-binding module (CBM) that interacts with glycogen. The two CBM isoforms (β1- and β2-CBM) are near identical in sequence and structure, yet show differences in carbohydrate-binding affinity. β2-CBM binds linear carbohydrates with 4-fold greater affinity than β1-CBM and binds single α1,6-branched carbohydrates up to 30-fold tighter. To understand these affinity differences, especially for branched carbohydrates, we determined the NMR solution structure of β2-CBM in complex with the single α1,6-branched carbohydrate glucosyl-β-cyclodextrin (gBCD) which supported the dynamic nature of the binding site, but resonance broadening prevented defining where the α1,6 branch bound. We therefore solved the X-ray crystal structures of β1- and β2-CBM, in complex with gBCD, to 1.7 and 2.0 Å (1 Å=0.1 nm) respectively. The additional threonine (Thr101) of β2-CBM expands the size of the surrounding loop, creating a pocket that accommodates the α1,6 branch. Hydrogen bonds are formed between the α1,6 branch and the backbone of Trp99 and Lys102 side chain of β2-CBM. In contrast, the α1,6 branch could not be observed in the β1-CBM structure, suggesting that it does not form a specific interaction. The orientation of gBCD bound to β1- and β2-CBM is supported by thermodynamic and kinetic data obtained through isothermal titration calorimetry (ITC) and NMR. These results suggest that AMPK containing the muscle-specific β2-isoform may have greater affinity for partially degraded glycogen.


    Organizational Affiliation

    *Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5'-AMP-activated protein kinase subunit beta-2
A, B
90Rattus norvegicusMutation(s): 0 
Gene Names: Prkab2
Find proteins for Q9QZH4 (Rattus norvegicus)
Go to UniProtKB:  Q9QZH4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.150 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 112.973α = 90.00
b = 27.627β = 133.88
c = 78.882γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
XDSdata reduction
Blu-Icedata collection
Cootmodel building
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-08
    Type: Initial release
  • Version 1.1: 2015-06-03
    Type: Database references