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 

Starting Models: experimental
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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: https://doi.org/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 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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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glucokinase
A, C
458Xenopus laevisMutation(s): 0 
Gene Names: gck
EC: 2.7.1.2
UniProt
Find proteins for Q91753 (Xenopus laevis)
Explore Q91753 
Go to UniProtKB:  Q91753
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ91753
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glucokinase regulatory protein
B, D
619Xenopus laevisMutation(s): 0 
Gene Names: gckr
UniProt
Find proteins for Q91754 (Xenopus laevis)
Explore Q91754 
Go to UniProtKB:  Q91754
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ91754
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
F6R PDBBind:  3W0L Kd: 95 (nM) from 1 assay(s)
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  (Full details and data files)

  • Version 1.0: 2013-07-17
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description