ADP-dependent glucokinase from Pyrococcus horikoshii

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report

This is version 2.2 of the entry. See complete history


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: https://doi.org/10.1074/jbc.RA117.001562
  • Primary Citation of Related Structures:  
    5O0I, 5O0J

  • 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) catalyzes noncanonical 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 the Jurkat model of activated human T cells suggest its moderate activity in a cellular setting. We propose that our structural insights provide a critical basis for rational development of novel ADPGK inhibitors.

  • Organizational Affiliation

    the Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, and marcin.kaminski@stjude.org.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ADP-dependent glucokinase454Pyrococcus horikoshii OT3Mutation(s): 0 
Gene Names: glkAPH0589
Find proteins for O58328 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Explore O58328 
Go to UniProtKB:  O58328
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO58328
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
O4 S
Query on EDO

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A]
C2 H6 O2
Query on ACT

Download Ideal Coordinates CCD File 
C2 H3 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.171 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.135α = 90
b = 77.135β = 90
c = 133.889γ = 120
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science CenterPolandUMO-2015/19/D/NZ1/02009
National Science CenterPolandUMO-2012/07/E/NZ1/01907

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-30
    Type: Initial release
  • Version 2.0: 2018-06-27
    Changes: Atomic model, Data collection, Database references
  • Version 2.1: 2018-07-25
    Changes: Data collection, Database references
  • Version 2.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description