2ZF5

Crystal Structure of highly thermostable glycerol kinase from a hyperthermophilic archaeon

Summary for 2ZF5

• Entry DOI: 10.2210/pdb2zf5/pdb
• Descriptor: Glycerol kinase (2 entities in total)
• Functional Keywords: glycerol kinase, hyperthermophilic archaeon, atp-binding, glycerol metabolism, nucleotide-binding, transferase
• Biological source: Thermococcus kodakarensis
• Total number of polymer chains: 2
• Total formula weight: 111938.95

Authors

Koga, Y.,Katsumi, R.,You, D.-J.,Matsumura, H.,Takano, K.,Kanaya, S. (deposition date: 2007-12-20, release date: 2008-05-06, Last modification date: 2023-11-01)

Primary citation

Koga, Y.,Katsumi, R.,You, D.-J.,Matsumura, H.,Takano, K.,Kanaya, S.
Crystal structure of highly thermostable glycerol kinase from a hyperthermophilic archaeon in a dimeric form
Febs J., 275:2632-2643, 2008

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.

PubMed: 18422647
DOI: 10.1111/j.1742-4658.2008.06410.x

Experimental method

X-RAY DIFFRACTION (2.4 Å)