5O0J

ADP-dependent glucokinase from Pyrococcus horikoshii

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Structural basis for ADP-dependent glucokinase inhibition by 8-bromo-substituted adenosine nucleotide.

Grudnik, P., Kaminski, M.M., Rembacz, K.P., Kuska, K., Madej, M., Potempa, J., Dawidowski, M., Dubin, G.

(2018) J. Biol. Chem. 293: 11088-11099

  • DOI: 10.1074/jbc.RA117.001562
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • In higher eukaryotes, several ATP-utilizing enzymes known as hexokinases activate glucose in the glycolysis pathway by phosphorylation to glucose-6-phosphate. In contrast to canonical hexokinases which use ATP, ADP-dependent glucokinase (ADPGK) catal ...

    In higher eukaryotes, several ATP-utilizing enzymes known as hexokinases activate glucose in the glycolysis pathway by phosphorylation to glucose-6-phosphate. In contrast to canonical hexokinases which use ATP, ADP-dependent glucokinase (ADPGK) catalyzes non-canonical phosphorylation of glucose to glucose-6-phosphate using ADP as a phosphate donor. Initially discovered in Archaea, the human homolog of ADPGK was described only recently. ADPGK's involvement in modified bioenergetics of activated T cells has been postulated and elevated ADPGK expression has been reported in various cancer tissues. However, the physiological role of ADPGK is still poorly understood and effective ADPGK inhibitors still await discovery. Here we show that 8-bromo substituted adenosine nucleotide inhibits human ADPGK. By solving the crystal structure of archaeal ADPGK in complex with 8-bromoadenosine phosphate (8-Br-AMP) at 1.81 Å resolution we identified the mechanism of inhibition. We observed that 8-Br-AMP is a competitive inhibitor of ADPGK and that the bromine substitution induces marked structural changes within the protein's active site by engaging crucial catalytic residues. The results obtained using Jurkat model of activated human T-cells suggest its moderate activity in cellular setting. We propose that our structural insights provide a critical basis for rational development of novel ADPGK inhibitors.

    Organizational Affiliation: 

    Jagiellonian University, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADP-dependent glucokinase
A
453Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)Mutation(s): 0 
Gene Names: glkA
EC: 2.7.1.147
Find proteins for O58328 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Go to UniProtKB:  O58328
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLC
Query on GLC
Download SDF File 
Download CCD File 
A
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
8BR
Query on 8BR
Download SDF File 
Download CCD File 
A
8-BROMO-ADENOSINE-5'-MONOPHOSPHATE
C10 H13 Br N5 O7 P
DNPIJKNXFSPNNY-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.161 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 115.838α = 90.00
b = 74.714β = 99.46
c = 62.951γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-05-16 
  • Released Date: 2018-05-30 
  • Deposition Author(s): Grudnik, P., Dubin, G.
Funding OrganizationLocationGrant Number
National Science CenterPolandUMO-2015/19/D/NZ1/02009
National Science CenterPolandUMO-2012/07/E/NZ1/01907

Revision History 

  • Version 1.0: 2018-05-30
    Type: Initial release
  • Version 1.1: 2018-06-27
    Type: Data collection, Database references
  • Version 1.2: 2018-07-25
    Type: Data collection, Database references