3VEV

Glucokinase in complex with an activator and glucose

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 1.4 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:  
    3VF6, 3VEV, 3VEY, 4DCH, 4DHY

  • 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 regulatory ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glucokinase A470Homo sapiensMutation(s): 0 
Gene Names: GCK
EC: 2.7.1.2 (PDB Primary Data), 2.7.1.1 (UniProt)
Find proteins for P35557 (Homo sapiens)
Explore P35557 
Go to UniProtKB:  P35557
NIH Common Fund Data Resources
PHAROS:  P35557
GTEx:  ENSG00000106633
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0H4
Query on 0H4
Download Ideal Coordinates CCD File 
A
(2S)-3-cyclopentyl-N-(5-methylpyridin-2-yl)-2-[2-oxo-4-(trifluoromethyl)pyridin-1(2H)-yl]propanamide
C20 H22 F3 N3 O2
QRULBTPYHROTAY-INIZCTEOSA-N		 Ligand Interaction
GLC
Query on GLC
Download Ideal Coordinates CCD File 
A
alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.17α = 90
b = 82.11β = 90
c = 86.22γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2012-01-09 
  • Released Date: 2012-02-08 
    • Deposition Author(s): Liu, S.

Revision History 

  • Version 1.0: 2012-02-08
    Type: Initial release
  • Version 1.1: 2012-02-15
    Changes: Other
  • Version 1.2: 2012-04-11
    Changes: Database references
  • Version 1.3: 2012-05-09
    Changes: Database references
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary