4B8S

Crystal Structure of Thermococcus litoralis ADP-dependent Glucokinase (GK)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal Structure, Saxs and Kinetic Mechanism of Hyperthermophilic Adp-Dependent Glucokinase from Thermococcus Litoralis Reveal a Conserved Mechanism for Catalysis.

Rivas-Pardo, J.A.Herrera-Morande, A.Castro-Fernandez, V.Fernandez, F.J.Vega, M.C.Guixe, V.

(2013) Plos One 8: 66687

  • DOI: 10.1371/journal.pone.0066687
  • Primary Citation of Related Structures:  
  • Also Cited By: 5O5Z, 5O5Y, 5O5X

  • PubMed Abstract: 
  • ADP-dependent glucokinases represent a unique family of kinases that belong to the ribokinase superfamily, being present mainly in hyperthermophilic archaea. For these enzymes there is no agreement about the magnitude of the structural transitions as ...

    ADP-dependent glucokinases represent a unique family of kinases that belong to the ribokinase superfamily, being present mainly in hyperthermophilic archaea. For these enzymes there is no agreement about the magnitude of the structural transitions associated with ligand binding and whether they are meaningful to the function of the enzyme. We used the ADP-dependent glucokinase from Thermococcus litoralis as a model to investigate the conformational changes observed in X-ray crystallographic structures upon substrate binding and to compare them with those determined in solution in order to understand their interplay with the glucokinase function. Initial velocity studies indicate that catalysis follows a sequential ordered mechanism that correlates with the structural transitions experienced by the enzyme in solution and in the crystal state. The combined data allowed us to resolve the open-closed conformational transition that accounts for the complete reaction cycle and to identify the corresponding clusters of aminoacids residues responsible for it. These results provide molecular bases for a general mechanism conserved across the ADP-dependent kinase family.


    Organizational Affiliation

    Departamento de BiologĂ­a, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADP-DEPENDENT GLUCOKINASE
A
467Thermococcus litoralis (strain ATCC 51850 / DSM 5473 / JCM 8560 / NS-C)Mutation(s): 0 
Gene Names: glkA
EC: 2.7.1.147
Find proteins for Q7M537 (Thermococcus litoralis (strain ATCC 51850 / DSM 5473 / JCM 8560 / NS-C))
Go to UniProtKB:  Q7M537
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
GLC
Query on GLC

Download SDF File 
Download CCD File 
A
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
AMP
Query on AMP

Download SDF File 
Download CCD File 
A
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.169 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 106.468α = 90.00
b = 106.468β = 90.00
c = 130.093γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-10
    Type: Initial release