4DCH

Insights into Glucokinase Activation Mechanism: Observation of Multiple Distinct Protein Conformations


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Insights into Mechanism of Glucokinase Activation: OBSERVATION OF MULTIPLE DISTINCT PROTEIN CONFORMATIONS.

Liu, S.Ammirati, M.J.Song, X.Knafels, J.D.Zhang, J.Greasley, S.E.Pfefferkorn, J.A.Qiu, X.

(2012) J.Biol.Chem. 287: 13598-13610

  • DOI: 10.1074/jbc.M111.274126
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human glucokinase (GK) is a principal regulating sensor of plasma glucose levels. Mutations that inactivate GK are linked to diabetes, and mutations that activate it are associated with hypoglycemia. Unique kinetic properties equip GK for its regulat ...

    Human glucokinase (GK) is a principal regulating sensor of plasma glucose levels. Mutations that inactivate GK are linked to diabetes, and mutations that activate it are associated with hypoglycemia. Unique kinetic properties equip GK for its regulatory role: although it has weak basal affinity for glucose, positive cooperativity in its binding of glucose causes a rapid increase in catalytic activity when plasma glucose concentrations rise above euglycemic levels. In clinical trials, small molecule GK activators (GKAs) have been efficacious in lowering plasma glucose and enhancing glucose-stimulated insulin secretion, but they carry a risk of overly activating GK and causing hypoglycemia. The theoretical models proposed to date attribute the positive cooperativity of GK to the existence of distinct protein conformations that interconvert slowly and exhibit different affinities for glucose. Here we report the respective crystal structures of the catalytic complex of GK and of a GK-glucose complex in a wide open conformation. To assess conformations of GK in solution, we also carried out small angle x-ray scattering experiments. The results showed that glucose dose-dependently converts GK from an apo conformation to an active open conformation. Compared with wild type GK, activating mutants required notably lower concentrations of glucose to be converted to the active open conformation. GKAs decreased the level of glucose required for GK activation, and different compounds demonstrated distinct activation profiles. These results lead us to propose a modified mnemonic model to explain cooperativity in GK. Our findings may offer new approaches for designing GKAs with reduced hypoglycemic risk.


    Organizational Affiliation

    Structural Biology and Biophysics, Pfizer Groton Laboratories, Groton, Connecticut 06340, USA. shenping.liu@pfizer.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glucokinase
A
473Homo sapiensMutation(s): 0 
Gene Names: GCK
EC: 2.7.1.2
Find proteins for P35557 (Homo sapiens)
Go to Gene View: GCK
Go to UniProtKB:  P35557
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4DC
Query on 4DC

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Download CCD File 
A
(2R)-3-cyclopentyl-2-[4-(methylsulfonyl)phenyl]-N-(1,3-thiazol-2-yl)propanamide
C18 H22 N2 O3 S2
NEQSWPCDHDQINX-MRXNPFEDSA-N
 Ligand Interaction
IOD
Query on IOD

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Download CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
GLC
Query on GLC

Download SDF File 
Download CCD File 
A
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4DCKd: 500 nM (100) BINDINGDB
4DCEC50: 500 - 26700 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 49.917α = 90.00
b = 85.794β = 104.40
c = 72.939γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
PDB_EXTRACTdata extraction
Web-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-08
    Type: Initial release
  • Version 1.1: 2012-04-11
    Type: Database references
  • Version 1.2: 2012-05-09
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description