PDBsum entry 2pmd

Translation

PDB id: 2pmd

Contents

Protein chains

414 a.a. *

Ligands

GDP ×2

GNP

PPV ×6

Waters ×160

* Residue conservation analysis

PDB id:

2pmd

Name:

Translation

Title:

The structures of aif2gamma subunit from the archaeon sulfolobus solfataricus in the gdp-bound form.

Structure:

Translation initiation factor 2 gamma subunit. Chain: a, b. Synonym: eif-2-gamma, aif2- gamma. Engineered: yes

Source:

Sulfolobus solfataricus. Organism_taxid: 2287. Gene: eif2g. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.65Å R-factor: 0.220 R-free: 0.275

Authors:

O.S.Nikonov,E.A.Stolboushkina,A.D.Nikulin,D.Hasenohrl,U.Blaesi, D.J.Manstein,R.V.Fedorov,M.B.Garber,S.V.Nikonov

Key ref:

O.Nikonov et al. (2007). New Insights into the Interactions of the Translation Initiation Factor 2 from Archaea with Guanine Nucleotides and Initiator tRNA. J Mol Biol, 373, 328-336. PubMed id: 17825838 DOI: 10.1016/j.jmb.2007.07.048

Date:

21-Apr-07 Release date: 06-Nov-07

Protein chains

Q980A5  (IF2G_SULSO) -  Translation initiation factor 2 subunit gamma from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

Seq: 415 a.a.

Struc: 414 a.a.

Enzyme reactions

• Enzyme class: E.C.3.6.5.3 - protein-synthesizing GTPase.
• Reaction: GTP + H2O = GDP + phosphate + H⁺

GTP + H2O = GDP (Bound ligand (Het Group name = GDP) corresponds exactly) + phosphate + H(+) (Bound ligand (Het Group name = PPV) matches with 55.56% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.jmb.2007.07.048

J Mol Biol 373:328-336 (2007)

PubMed id: 17825838

New Insights into the Interactions of the Translation Initiation Factor 2 from Archaea with Guanine Nucleotides and Initiator tRNA.

O.Nikonov, E.Stolboushkina, A.Nikulin, D.Hasenöhrl, U.Bläsi, D.J.Manstein, R.Fedorov, M.Garber, S.Nikonov.

ABSTRACT

Heterotrimeric a/eIF2alphabetagamma (archaeal homologue of the eukaryotic translation initiation factor 2 with alpha, beta and gamma subunits) delivers charged initiator tRNA (tRNAi) to the small ribosomal subunit. In this work, we determined the structures of aIF2gamma from the archaeon Sulfolobus solfataricus in the nucleotide-free and GDP-bound forms. Comparison of the free, GDP and Gpp(NH)p-Mg(2+) forms of aIF2gamma revealed a sequence of conformational changes upon GDP and GTP binding. Our results show that the affinity of GDP to the G domain of the gamma subunit is higher than that of Gpp(NH)p. In analyzing a pyrophosphate molecule binding to domain II of the gamma subunit, we found a cleft that is very suitable for the acceptor stem of tRNA accommodation. It allows the suggestion of an alternative position for Met-tRNA(i)(Met) on the alphagamma intersubunit dimer, at variance with a recently published one. In the model reported here, the acceptor stem of the tRNAi is approximately perpendicular to that of tRNA in the ternary complex elongation factor Tu-Gpp(NH)p-tRNA. According to our analysis, the elbow and T stem of Met-tRNA(i)(Met) in this position should make extensive contact with the alpha subunit of aIF2. Thus, this model is in good agreement with experimental data showing that the alpha subunit of aIF2 is necessary for the stable interaction of aIF2gamma with Met-tRNA(i)(Met).

Selected figure(s)

Figure 1.
Fig. 1. (a) Amino acid sequence of aIF2γ from Sso. Residues, conformations of which are changed in free and GDP forms of aIF2γ, are boxed. The two conserved regions, which surround the nucleotide base, are shown in magenta. The P-loop is shown in green. Switch 1 and switch 2 are shown in brown and blue, respectively. (b) Stereo representation of one of the two aIF2γ–GDP molecules. Numbered C^α atoms are shown as gold spheres. Pyrophosphates are shown in magenta, Gpp(NH)p is shown in green and GDP is shown in red.

Figure 2.
Fig. 2. (a) Conformational changes upon GDP and GTP binding. Conformations of the P-loop in nucleotide-free, GDP-bound and Gpp(NH)p-bound^7 forms. The nucleotide-free form is shown in red, the GDP form is shown in dark blue and the Gpp(NH)p form is shown in light blue. (b) Conformations of switch 2 in nucleotide-free, GDP-bound and Gpp(NH)p-bound^7 forms. The color scheme is the same as that described in (a).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 373, 328-336) copyright 2007.

Figures were selected by an automated process.