PDBsum entry 1d2e

RNA binding protein

PDB id: 1d2e

Contents

Protein chains

397 a.a. *

Ligands

GDP ×4

Metals

_MG ×4

Waters ×1201

* Residue conservation analysis

References listed in PDB file

Key reference

Title

High resolution crystal structure of bovine mitochondrial ef-Tu in complex with gdp.

Authors

G.R.Andersen, S.Thirup, L.L.Spremulli, J.Nyborg.

Ref.

J Mol Biol, 2000, 297, 421-436. [DOI no: 10.1006/jmbi.2000.3564]

PubMed id

10715211

Abstract

The crystal structure of bovine mitochondrial elongation factor Tu (EF-Tu) in complex with GDP has been determined at a resolution of 1. 94 A. The structure is similar to that of EF-Tu:GDP from Escherichia coli and Thermus aquaticus, but the orientation of the GDP-binding domain 1 is changed relative to domains 2 and 3. Sixteen conserved water molecules common to EF-Tu and other G-proteins in the GDP-binding site are described. These water molecules create a network linking separated parts of the binding pocket. Mitochondrial EF-Tu binds nucleotides less tightly than prokaryotic EF-Tu possibly due to an increased mobility in regions close to the GDP-binding site. The C-terminal extension of mitochondrial EF-Tu has structural similarities with DNA recognising zinc fingers suggesting that the extension may be involved in recognition of RNA.

Figure 1.
Figure 1. (a) Cartoon of EF-Tum with helices (red) and strands (cyan). The protein is organized in three struc- tural domains as known from EF-Tut and EF-Tue. Domain 1 (right) contains the binding site for GDP and Mg 2+ and comprises the N-terminal half of the protein. Helices B, C and D are located to the left of the central b-sheet and helices A, E and F to the right. The C-term- inal half is folded into two structural domains 2 (top left) and 3 (bottom left). In contrast to EF-Tut and EF- Tue, EF-Tum contains a small helix at the C-terminal of domain 3 (bottom left). The definition of the secondary structure is given in Figure 2 and the topology is described in Figure 2 of Song et al. (1999). (b) Density around the GDP binding site in the final sigmaA- weighted 3Fo - 2Fc map contoured at two standard deviations. The guanine ring is inserted between K182 and L221. D184 (right) forms two hydrogen bonds to N1 and N2 of the base. Water molecules (red spheres). Figure 3(c) shows this region in more detail.

Figure 4.
Figure 4. (a) The GDP binding site of EF-Tum (molecule A). The Mg 2+ and its six ligands (thin red lines). Besides the four water molecules coordinating the Mg 2+ , 12 additional water molecules are shown. The waters are roughly organized in two clusters, one around the Mg 2+ and the phosphate groups, and the other around the ribose ring of the GDP. (b) The Mg 2+ binding site with selected distances shorter than 3.1 Å . The six Mg-ligand distances (red), others (blue). Interatomic distances between w1-w4 are not shown, but have an average value of 2.96 Å . The water molecule w8 is displaced slightly away from the typical position due to the presence of Y92-OH. Except for w8, all other water molecules have at least two possible hydrogen bond donors/acceptors. The water molecules bridge the different parts of the binding site, e.g. w7 bridges the NH+3 group of K70 with Omc of P128. (c) Binding site for the ribose and guanine ring of GDP. The guanine ring is inserted between the aliphatic part of K182 and L221. The NH+3 group of K70 forms hydrogen bonds to w9 and w10, and Omc of D67, instead of hydrogen bonding to the endocyclic O of the ribose. As for the Mg 2+ -binding site, the well ordered water molecules connect separated parts of the binding site. The water molecules w9, w10, w11 and w13 connect D155, K182, the ribose ring of GDP and T72. (d) The environment of the NKXD sequence with helix D (right) and the loop connecting helices E -F (top). Compared to EF-Tue (yellow), EF-Tum (gray) contains two extra residues, while EF-Tut contains eight extra residues. The loop connecting helices D-E in EF-Tue and EF-Tut contains an arginine residue, forming a saltbridge to helix D, R172e-E150e, which is absent in EF-Tum.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 297, 421-436) copyright 2000.

Secondary reference #1

Title

Crystal structure of intact elongation factor ef-Tu from escherichia coli in gdp conformation at 2.05 a resolution.

Authors

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

Ref.

J Mol Biol, 1999, 285, 1245-1256. [DOI no: 10.1006/jmbi.1998.2387]

PubMed id

9918724

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 reproduced from the cited reference with permission from Elsevier

Secondary reference #2

Title

Helix unwinding in the effector region of elongation factor ef-Tu-Gdp.

Authors

G.Polekhina, S.Thirup, M.Kjeldgaard, P.Nissen, C.Lippmann, J.Nyborg.

Ref.

Structure, 1996, 4, 1141-1151. [DOI no: 10.1016/S0969-2126(96)00122-0]

PubMed id

8939739

Figure 6.
Figure 6. Comparison of the Mg2+-binding sites in T. aquaticus EF-Tu-GDP and EF-Tu-GDPNP. (a) EF-Tu-GDP and (b) EF-Tu-GDPNP; GDP and GDPNP are shown in ball-and-stick representation. The atoms are coloured as in Figure 4. (Figure produced with MOLSCRIPT [37].)

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