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 
  • R-Value Observed: 0.163 

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This is version 1.3 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:  
    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 ...

    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: 

    Malopolska Center of Biotechnology Jagiellonian University in Krakow, Gronostajowa 7 Street, 30-387 Krakow, Poland.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ADP-dependent glucokinaseA453Pyrococcus horikoshii OT3Mutation(s): 0 
Gene Names: glkA, PH0589
EC: 2.7.1.147 (PDB Primary Data), 2.7.1 (UniProt)
UniProt
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8BR
Query on 8BR
Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]		8-BROMO-ADENOSINE-5'-MONOPHOSPHATE
C10 H13 Br N5 O7 P
DNPIJKNXFSPNNY-UUOKFMHZSA-N		 Ligand Interaction
GLC
Query on GLC
Download Ideal Coordinates CCD File 
D [auth A]alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
8BR Binding MOAD:  5O0J Kd: 1.69e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.838α = 90
b = 74.714β = 99.46
c = 62.951γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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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  (Full details and data files)

  • Version 1.0: 2018-05-30
    Type: Initial release
  • Version 1.1: 2018-06-27
    Changes: Data collection, Database references
  • Version 1.2: 2018-07-25
    Changes: Data collection, Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary