4B8R | pdb_00004b8r

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

• PDB DOI: https://doi.org/10.2210/pdb4B8R/pdb

• Classification: TRANSFERASE
• Organism(s): Thermococcus litoralis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-08-30 Released: 2013-07-10 
• Deposition Author(s): Herrera-Morande, A., Rivas-Pardo, J.A., Fernandez, F.J., Guixe, V., Vega, M.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

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

• PubMed: 23818958 
• DOI: https://doi.org/10.1371/journal.pone.0066687
• Primary Citation Related Structures: 
  4B8R, 4B8S


• 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 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.

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Organizational Affiliation: 
• Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 57.18 kDa 
• Atom Count: 4,364 
• Modeled Residue Count: 467 
• Deposited Residue Count: 467 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-DEPENDENT GLUCOKINASE	A	467	Thermococcus litoralis	Mutation(s): 0  EC: 2.7.1.147 (PDB Primary Data), 2.7.1 (UniProt)
UniProt
Find proteins for Q7M537 (Thermococcus litoralis (strain ATCC 51850 / DSM 5473 / JCM 8560 / NS-C)) Explore Q7M537  Go to UniProtKB:  Q7M537

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DTT	S [auth A], T [auth A]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C4 H10 O2 S2 VHJLVAABSRFDPM-IMJSIDKUSA-N
PGE	AA [auth A], BA [auth A], Z [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
TRS	Q [auth A], R [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG	U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	CA [auth A], DA [auth A], EA [auth A], FA [auth A], GA [auth A], HA [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.104	α = 90
b = 109.104	β = 90
c = 129.559	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-10 
Deposition Author(s): Herrera-Morande, A., Rivas-Pardo, J.A., Fernandez, F.J., Guixe, V., Vega, M.C.

Revision History  

• Version 1.0: 2013-07-10
  Type: Initial release
  
• Version 1.1: 2013-07-17
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description