Crystal Structure of highly thermostable glycerol kinase from a hyperthermophilic archaeon

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.178 

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Crystal structure of highly thermostable glycerol kinase from a hyperthermophilic archaeon in a dimeric form

Koga, Y.Katsumi, R.You, D.-J.Matsumura, H.Takano, K.Kanaya, S.

(2008) FEBS J 275: 2632-2643

  • DOI: https://doi.org/10.1111/j.1742-4658.2008.06410.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The crystal structure of glycerol kinase from the hyperthermophilic archaeon Thermococcus kodakaraensis (Tk-GK) in a dimeric form was determined at a resolution of 2.4 A. This is the first crystal structure of a hyperthermophilic glycerol kinase. The overall structure of the Tk-GK dimer is very similar to that of the Escherichia coli glycerol kinase (Ec-GK) dimer. However, two dimers of Ec-GK can associate into a tetramer with a twofold axis, whereas those of Tk-GK cannot. This may be the reason why Tk-GK is not inhibited by fructose 1,6-bisphosphate, because the fructose 1,6-bisphosphate binding site is produced only when a tetrameric structure is formed. Differential scanning calorimetry analyses indicate that Tk-GK is a highly thermostable protein with a melting temperature (T(m)) of 105.4 degrees C for the major transition. This value is higher than that of Ec-GK by 34.1 degrees C. Comparison of the crystal structures of Tk-GK and Ec-GK indicate that there is a marked difference in the number of ion pairs in the alpha16 helix. Four ion pairs, termed IP1-IP4, are formed in this helix in the Tk-GK structure. To examine whether these ion pairs contribute to the stabilization of Tk-GK, four Tk-GK and four Ec-GK derivatives with reciprocal mutations at the IP1-IP4 sites were constructed. The determination of their stabilities indicates that the removal of each ion pair does not affect the stability of Tk-GK significantly, whereas the mutations designed to introduce one of these ion pairs stabilize or destabilize Ec-GK considerably. These results suggest that the ion pairs in the alpha16 helix contribute to the stabilization of Tk-GK in a cooperative manner.

  • Organizational Affiliation

    Department of Material and Life Science, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycerol kinaseA [auth O],
B [auth Y]
497Thermococcus kodakarensis KOD1Mutation(s): 0 
Find proteins for O93623 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore O93623 
Go to UniProtKB:  O93623
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO93623
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.178 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 217.477α = 90
b = 217.477β = 90
c = 66.479γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-05-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Refinement description