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

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

Author information

1
Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290, Pushchino, Moscow Region, Russian Federation. Electronic address: alik@vega.protres.ru.
2
Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290, Pushchino, Moscow Region, Russian Federation.

Abstract

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

PMID:
26700147
DOI:
10.1016/j.biochi.2015.11.029
[Indexed for MEDLINE]

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