PDBsum entry 1efc

RNA binding protein

PDB id: 1efc

Contents

Protein chains

386 a.a. *

Ligands

GDP ×2

Metals

_MG ×2

Waters ×446

* Residue conservation analysis

PDB id:

1efc

Name:

RNA binding protein

Title:

Intact elongation factor from e.Coli

Structure:

Protein (elongation factor). Chain: a, b. Synonym: eftu. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PDB file)

Resolution:

2.05Å R-factor: 0.203 R-free: 0.268

Authors:

H.Song,M.R.Parsons,S.Rowsell,G.Leonard,S.E.V.Phillips

Key ref:

H.Song et al. (1999). Crystal structure of intact elongation factor EF-Tu from Escherichia coli in GDP conformation at 2.05 A resolution. J Mol Biol, 285, 1245-1256. PubMed id: 9918724 DOI: 10.1006/jmbi.1998.2387

Date:

24-Nov-98 Release date: 18-Mar-99

Protein chains

P0CE47  (EFTU1_ECOLI) -  Elongation factor Tu 1 from Escherichia coli (strain K12)

Seq: 394 a.a.

Struc: 386 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1006/jmbi.1998.2387

J Mol Biol 285:1245-1256 (1999)

PubMed id: 9918724

Crystal structure of intact elongation factor EF-Tu from Escherichia coli in GDP conformation at 2.05 A resolution.

H.Song, M.R.Parsons, S.Rowsell, G.Leonard, S.E.Phillips.

ABSTRACT

The crystal structure of intact elongation factor Tu (EF-Tu) from Escherichia coli in GDP-bound conformation has been determined using a combination of multiple isomorphous replacement (MIR) and multiwavelength anomalous diffraction (MAD) methods. The current atomic model has been refined to a crystallographic R factor of 20.3 % and free R-factor of 26.8 % in the resolution range of 10-2.05 A. The protein consists of three domains: domain 1 has an alpha/beta structure; while domain 2 and domain 3 are beta-barrel structures. Although the global fold of the current model is similar to those of published structures, the secondary structural assignment has been improved due to the high quality of the current model. The switch I region (residues 40-62) is well ordered in this structure. Comparison with the structure of EF-Tu in GDP-bound form from Thermus aquaticus shows that although the individual domain structures are similar in these two structures, the orientation of domains changes significantly. Interactions between domains 1 and 3 in our E. coli EF-Tu-GDP complex are quite different from those of EF-Tu with bound GTP from T. aquaticus, due to the domain rearrangement upon GTP binding. The binding sites of the Mg2+ and guanine nucleotide are revealed in detail. Two water molecules that co-ordinate the Mg2+ have been identified to be well conserved in the GDP and GTP-bound forms of EF-Tu structures, as well as in the structure of Ras p21 with bound GDP. Comparisons of the Mg2+ binding site with other guanine nucleotide binding proteins in GDP-bound forms show that the Mg2+ co-ordination patterns are well preserved among these structures.

Selected figure(s)

Figure 1.
Figure 1. Ribbon diagrams of EF-Tu molecules. (a) EC-EF-Tu-GDP; (b) same view of EF-Tu-GTP from T. aquaticus (TA-EF-Tu-GTP). The switch I region is shown in yellow and the switch II region in green. The rest of the polypeptide backbone is shown in purple, royal blue and dark blue for domain 1 (residues 8-204), domain 2 (residues 205-298) and domain 3 (299-393), respectively. GDP or GTP molecules are shown in ball- and-stick models, and Mg 2+ are shown as cyan spheres. The Figure was drawn with MOLSCRIPT (Kraulis, 1991), as are Figures 4 and 5.

Figure 5.
Figure 5. Stereo view of the interface between domain 1 and domain 3. The switch I and II regions are shown in yellow and green, respectively. The rest of the poly- peptide chain in domain 1 is shown in purple, and that of the domain 3 in slate blue. Hydrogen bonds are shown as broken lines, and water molecules as cyan spheres. Residues involved in interactions between domains 1 and 3 are shown as ball-and-stick. (a) EC-EF- Tu-GDP; (b) TA-EF-Tu-GTP.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 285, 1245-1256) copyright 1999.

Figures were selected by the author.