title: Water clusters in the nucleotide-binding pocket of the protein aIF2γ from the archaeon Sulfolobus solfataricus: Proton transmission.
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.
authors.affiliation: Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290, Pushchino, Moscow Region, Russian Federation. Electronic address: alik@vega.protres.ru.
authors.forename: Oleg
authors.initials: O
authors.lastname: Nikonov
authors.affiliation: Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290, Pushchino, Moscow Region, Russian Federation.
authors.forename: Olesya
authors.initials: O
authors.lastname: Kravchenko
authors.affiliation: Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290, Pushchino, Moscow Region, Russian Federation.
authors.forename: Valentina
authors.initials: V
authors.lastname: Arkhipova
authors.affiliation: Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290, Pushchino, Moscow Region, Russian Federation.
authors.forename: Elena
authors.initials: E
authors.lastname: Stolboushkina
authors.affiliation: Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290, Pushchino, Moscow Region, Russian Federation.
authors.forename: Stanislav
authors.initials: S
authors.lastname: Nikonov
authors.affiliation: Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290, Pushchino, Moscow Region, Russian Federation.
authors.forename: Maria
authors.initials: M
authors.lastname: Garber
mesh_terms: D002384:Catalysis; D006153:Guanosine Diphosphate / Q000378:metabolism; D006160:Guanosine Triphosphate / Q000378:metabolism; D010444:Peptide Elongation Factor Tu / Q000737:chemistry / Q000378:metabolism; D039881:Prokaryotic Initiation Factor-2 / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding; D012270:Ribosomes / Q000378:metabolism; D012997:Solvents / Q000737:chemistry; D048229:Sulfolobus solfataricus / Q000378:metabolism*; D014867:Water / Q000378:metabolism; D014961:X-Ray Diffraction
chemical_list: D039881:Prokaryotic Initiation Factor-2; D012997:Solvents; D014867:Water; D006153:Guanosine Diphosphate; D006160:Guanosine Triphosphate; D010444:Peptide Elongation Factor Tu
keywords: Crystal structure; G-protein; GTP hydrolysis; Proton transition; Water clusters; a/eIF2