Water clusters in the nucleotide-binding pocket of the protein aIF2γ from the archaeon Sulfolobus solfataricus: Proton transmission

Biochimie. 2016 Feb:121:197-203. doi: 10.1016/j.biochi.2015.11.029. Epub 2015 Dec 15.


In Archaea and Eukaryotes, the binding of Met-tRNAi(Met) to the P-site of the ribosome is mediated by translation initiation factor 2 (a/eIF2) which consists of three subunits: α, β and γ. Here, we present the high-resolution structure of intact aIF2γ from Sulfolobus solfataricus (SsoIF2γ) in complex with GTP analog, GDPCP. The comparison of the nucleotide-binding pockets in this structure and in the structure of the ribosome-bound form of EF-Tu reveals their close conformation similarity. The nucleotide-binding pocket conformation observed in this structure could be consider as corresponding to intermediate conformation of EF-Tu nucleotide-binding pocket in its transition from the GTP-bound form to the GDP-bound one. Three clusters of well defined water molecules are associated with amino acid residues of the SsoIF2γ nucleotide-binding pocket and stabilize its conformation. We suppose that two water bridges between the oxygen atoms of the GTP γ-phosphate and negatively charged residues of the pocket can serve as ways to transmit protons arising from the catalytic reaction.

Keywords: Crystal structure; G-protein; GTP hydrolysis; Proton transition; Water clusters; a/eIF2.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Catalysis
  • Guanosine Diphosphate / metabolism
  • Guanosine Triphosphate / metabolism
  • Peptide Elongation Factor Tu / chemistry
  • Peptide Elongation Factor Tu / metabolism
  • Prokaryotic Initiation Factor-2 / chemistry
  • Prokaryotic Initiation Factor-2 / metabolism*
  • Protein Binding
  • Ribosomes / metabolism
  • Solvents / chemistry
  • Sulfolobus solfataricus / metabolism*
  • Water / metabolism
  • X-Ray Diffraction


  • Prokaryotic Initiation Factor-2
  • Solvents
  • Water
  • Guanosine Diphosphate
  • Guanosine Triphosphate
  • Peptide Elongation Factor Tu