PDBsum entry 1g7c

Translation

PDB id: 1g7c

Contents

Protein chains

440 a.a. *

90 a.a. *

Ligands

5GP

Waters ×448

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Crystal structures of nucleotide exchange intermediates in the eef1a-Eef1balpha complex.

Authors

G.R.Andersen, L.Valente, L.Pedersen, T.G.Kinzy, J.Nyborg.

Ref.

Nat Struct Biol, 2001, 8, 531-534. [DOI no: 10.1038/88598]

PubMed id

11373622

Abstract

In the elongation cycle of protein biosynthesis, the nucleotide exchange factor eEF1Balpha catalyzes the exchange of GDP bound to the G-protein, eEF1A, for GTP. To obtain more information about the recently solved eEF1A-eEF1Balpha structure, we determined the structures of the eEF1A-eEF1Balpha-GDP-Mg2+, eEF1A-eEF1Balpha-GDP and eEF1A-eEF1Balpha-GDPNP complexes at 3.0, 2.4 and 2.05 A resolution, respectively. Minor changes, specifically around the nucleotide binding site, in eEF1A and eEF1Balpha are consistent with in vivo data. The base, sugar and alpha-phosphate bind as in other known nucleotide G-protein complexes, whereas the beta- and gamma-phosphates are disordered. A mutation of Lys 205 in eEF1Balpha that inserts into the Mg2+ binding site of eEF1A is lethal. This together with the structures emphasizes the essential role of Mg2+ in nucleotide exchange in the eEF1A-eEF1Balpha complex.

Figure 1.
Figure 1. Electron densities around the nucleotides after the final refinement. a, Sigmaa-weighted 2F[o] - F[c] electron density map contoured at 1.2 for the GDP -Mg2+ complex. The 'M' labels a residual electron density that most likely contains a Mg2+ ion. b, Sigmaa-weighted 2F[o] - F[c] electron density map contoured at 1.2 for the GDP complex. c, Sigmaa-weighted 2F[o] - F[c] electron density map contoured at 1.2 for the GDPNP complex. Water atoms are shown as red spheres. The electron densities were plotted with the map_cover option in O25 using a radius of 1.5 Å. Labels on residues in eEF1A and eEF1B are red and blue, respectively. All shown atoms were omitted from map calculations.

Figure 2.
Figure 2. The exchange mechanism. The shown structures are EF-Tu -GDP (PDB accession code 1TUI), eEF1A -eEF1B -GDP -Mg2+ (PDB accession code 1IJF), eEF1A -eEF1B (PDB accession code 1F60), eEF1A -eEF1B -GDPNP (PDB accession code 1G7C) and EF-Tu -GDPNP (PDB accession code 1EFT). Regions around the binding site of EF-Tu -GDPNP are labeled G1 -G5 according to the nomenclature of Sprang28 and colored identically in the other structures. The G2 region, part of the switch 1 region, is only shown for the EF-Tu -GDPNP, because it is distant from the nucleotide in the other structures. Comparison with EF-Tu -GDP, EF-Tu -GDPNP and EF-Tu -EF-Ts indicate that the shown peptide in the P-loop of eEF1A is likely to flip in the exchange reaction. Mg2+ ions are shown as blue spheres.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2001, 8, 531-534) copyright 2001.

Secondary reference #1

Title

Structural basis for nucleotide exchange and competition with tRNA in the yeast elongation factor complex eef1a:eef1balpha.

Authors

G.R.Andersen, L.Pedersen, L.Valente, I.Chatterjee, T.G.Kinzy, M.Kjeldgaard, J.Nyborg.

Ref.

Mol Cell, 2000, 6, 1261-1266. [DOI no: 10.1016/S1097-2765(00)00122-2]

PubMed id

11106763

Note In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above were identified by an automated search of PubMed on title and author names, giving a percentage match of 92%.

Figure 3.
Figure 3. The Interface between eEF1A Domain 2 and eEF1Bα Overlaps with aa-tRNA Binding(A) The CCA-aa end of tRNA (gold) superimposes with two loops of eEF1Bα (gray) when domain 2 (not shown) of the eEF1A:eEF1Bα complex is superimposed with domain 2 (not shown) of EF-Tu in complex with aa-tRNA.(B) The flexibility of the loop demonstrated in the NMR structure may allow aa-tRNA to displace eEF1Bα. The NMR of eEF1Bα is shown yellow, the X-ray structure in gray, and the CCA-aa end of tRNA in gold. A space-filling representation of atoms in eEF1A within 10 Šof Phe-163[b] is shown in gray.

The above figure is reproduced from the cited reference with permission from Cell Press