1GC5

CRYSTAL STRUCTURE OF A NOVEL ADP-DEPENDENT GLUCOKINASE FROM THERMOCOCCUS LITORALIS

• PDB DOI: https://doi.org/10.2210/pdb1GC5/pdb

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


• Deposited: 2000-07-20 Released: 2001-07-25 
• Deposition Author(s): Ito, S., Fushinobu, S., Yoshioka, I., Koga, S., Matsuzawa, H., Wakagi, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.252 
• R-Value Work: 0.204 

Literature

Structural Basis for the ADP-Specificity of a Novel Glucokinase from a Hyperthermophilic Archaeon

Ito, S., Fushinobu, S., Yoshioka, I., Koga, S., Matsuzawa, H., Wakagi, T.

(2001) Structure 9: 205-214

• PubMed: 11286887 
• DOI: https://doi.org/10.1016/s0969-2126(01)00577-9
• Primary Citation of Related Structures:  
  1GC5


• PubMed Abstract: 
  

  ATP is the most common phosphoryl group donor for kinases. However, certain hyperthermophilic archaea such as Thermococcus litoralis and Pyrococcus furiosus utilize unusual ADP-dependent glucokinases and phosphofructokinases in their glycolytic pathways. These ADP-dependent kinases are homologous to each other but show no sequence similarity to any of the hitherto known ATP-dependent enzymes.

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Organizational Affiliation: 

Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo 113-8657, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 54.05 kDa 
• Atom Count: 3,884 
• Modelled 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
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.252 
• R-Value Work: 0.204 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.8	α = 90
b = 109.8	β = 90
c = 129.8	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-07-25 
Deposition Author(s): Ito, S., Fushinobu, S., Yoshioka, I., Koga, S., Matsuzawa, H., Wakagi, T.

Revision History  

• Version 1.0: 2001-07-25
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations