3W0L

The crystal structure of Xenopus Glucokinase and Glucokinase Regulatory Protein complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 

wwPDB Validation 3D Report Full Report



Literature

Molecular basis for the role of glucokinase regulatory protein as the allosteric switch for glucokinase

Choi, J.M., Seo, M.H., Kyeong, H.H., Kim, E., Kim, H.S.

(2013) Proc Natl Acad Sci U S A 110: 10171-10176

  • DOI: 10.1073/pnas.1300457110
  • Primary Citation of Related Structures:  
    3W0L

  • PubMed Abstract: 

    • Glucokinase (GK) is a monomeric allosteric enzyme and plays a pivotal role in blood glucose homeostasis. GK is regulated by GK regulatory protein (GKRP), and indirectly by allosteric effectors of GKRP. Despite the critical roles of GK and GKRP, the m ...

    Glucokinase (GK) is a monomeric allosteric enzyme and plays a pivotal role in blood glucose homeostasis. GK is regulated by GK regulatory protein (GKRP), and indirectly by allosteric effectors of GKRP. Despite the critical roles of GK and GKRP, the molecular basis for the allosteric regulation mechanism of GK by GKRP remains unclear. We determined the crystal structure of Xenopus GK and GKRP complex in the presence of fructose-6-phosphate at 2.9 Å. GKRP binds to a super-open conformation of GK mainly through hydrophobic interaction, inhibiting the GK activity by locking a small domain of GK. We demonstrate the molecular mechanism for the modulation of GK activity by allosteric effectors of GKRP. Importantly, GKRP releases GK in a sigmoidal manner in response to glucose concentration by restricting a structural rearrangement of the GK small domain via a single ion pair. We find that GKRP acts as an allosteric switch for GK in blood glucose control by the liver.

    Organizational Affiliation: 

    Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Glucokinase regulatory proteinB, D619Xenopus laevisMutation(s): 0 
Gene Names: gckr
Find proteins for Q91754 (Xenopus laevis)
Explore Q91754 
Go to UniProtKB:  Q91754
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GlucokinaseA, C458Xenopus laevisMutation(s): 0 
Gene Names: gck, gck.L, gck-A
EC: 2.7.1.2 (PDB Primary Data), 2.7.1 (UniProt)
Find proteins for Q91753 (Xenopus laevis)
Explore Q91753 
Go to UniProtKB:  Q91753
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F6R
Query on F6R
Download CCD File 
B, D
FRUCTOSE -6-PHOSPHATE
C6 H13 O9 P
GSXOAOHZAIYLCY-HSUXUTPPSA-N		 Ligand Interaction
SO4
Query on SO4
Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
NA
Query on NA
Download CCD File 
A, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
F6RKd :  95   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.318α = 90
b = 130.03β = 90
c = 175.117γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-17
    Type: Initial release