Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 52.72 kDa 
• Atom Count: 4238 
• Residue Count: 453 
• Unique protein chains: 1

5O0J

ADP-dependent glucokinase from Pyrococcus horikoshii

• DOI: 10.2210/pdb5O0J/pdb

• Classification: TRANSFERASE
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-05-16 Released: 2018-05-30 
• Deposition Author(s): Grudnik, P., Dubin, G.
• Funding Organization(s): National Science Center

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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 

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

• PubMed: 29784881 
• DOI: 10.1074/jbc.RA117.001562
• Structures With Same Primary Citation


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
ADP-dependent glucokinase	A	453	Pyrococcus horikoshii OT3	Mutation(s): 0  Gene Names: glkA, PH0589 EC: 2.7.1.147 (PDB Primary Data), 2.7.1 (UniProt)
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
ID	Chains	Name / Formula / InChI Key	2D Diagram
8BR	A	8-BROMO-ADENOSINE-5'-MONOPHOSPHATE C10 H13 Br N5 O7 P DNPIJKNXFSPNNY-UUOKFMHZSA-N
GLC	A	ALPHA-D-GLUCOSE C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
8BR	Ki:  160000   nM  Binding MOAD

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 = 115.838	α = 90
b = 74.714	β = 99.46
c = 62.951	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-05-16 
• Released Date: 2018-05-30 
Deposition Author(s): Grudnik, P., Dubin, G.

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Funding Organization	Location	Grant Number
National Science Center	Poland	UMO-2015/19/D/NZ1/02009
National Science Center	Poland	UMO-2012/07/E/NZ1/01907

Revision History 

• 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