Polymorphism in crystallin elongation factor Tu-GDP from Escherichia coli

An alpha to beta conformational switch in EF-Tu

BACKGROUND

The bacterial elongation factor EF-Tu recognizes and transports aminoacyl-tRNAs to mRNA-programmed ribosomes. EF-Tu shares many structural and functional properties with other GTPases whose conformations are regulated by guanine nucleotides.

RESULTS

An intact form of Escherichia coli EF-Tu complexed with GDP has been crystallized in the presence of the EF-Tu-specific antibiotic GE2270 A. The three-dimensional structure has been solved by X-ray diffraction analysis and refined to a final crystallographic R factor of 17.2% at a resolution of 2.5 A. The location of the GE2270 A antibiotic-binding site could not be identified.

CONCLUSIONS

The structure of EF-Tu-GDP is nearly identical to that of a trypsin-modified form of EF-Tu-GDP, demonstrating conclusively that the protease treatment had not altered any essential structural features. The present structure represents the first view of an ordered Switch I region in EF-Tu-GDP and reveals similarities with two other GTPases complexed with GDP: Ran and ADP-ribosylation factor-1. A comparison of the Switch I regions of the GTP and GDP forms of EF-Tu also reveals that a segment, six amino acids in length, completely converts from an alpha helix in the GTP complex to beta secondary structure in the GDP form. The alpha to beta switch in EF-Tu may represent a prototypical activation mechanism for other protein families.

The crystal structure of elongation factor EF-Tu from Thermus aquaticus in the GTP conformation

BACKGROUND

Elongation factor Tu (EF-Tu) is a GTP-binding protein that is crucial for protein biosynthesis. In the GTP form of the molecule, EF-Tu binds tightly to aminoacyl-tRNA, forming a ternary complex that interacts with the ribosomal acceptor site. During this interaction, GTP is hydrolyzed, and EF-Tu.GDP is ejected.

RESULTS

The crystal structure of EF-Tu from Thermus aquaticus, complexed to the GTP analogue GDPNP, has been determined at 2.5 A resolution and compared to the structure of Escherichia coli EF-Tu.GDP. During the transition from the GDP (inactive) to the GTP (active) form, domain 1, containing the GTP-binding site, undergoes internal conformational changes similar to those observed in ras-p21. In addition, a dramatic rearrangement of domains is observed, corresponding to a rotation of 90.8 degrees of domain 1 relative to domains 2 and 3. Residues that are affected in the binding of aminoacyl-tRNA are found in or near the cleft formed by the domain interface.

CONCLUSION

GTP binding by EF-Tu leads to dramatic conformational changes which expose the tRNA binding site. It appears that tRNA binding to EF-Tu induces a further conformational change, which may affect the GTPase activity.

Pre-nucleation crystallization studies on aminoacyl-tRNA synthetases by dynamic light-scattering

Dynamic light-scattering (DLS) studies on solutions of proteins approaching their precipitation point were made with asparaginyl- (NRSEC), leucyl- (LRSEC) and valyl- (VRSEC) tRNA synthetases from Escherichia coli. The three aminoacyl-tRNA synthetases have not been crystallized previously. As a control system, we used E. coli polypeptide elongation factor Tu (EF-Tu). Apart from the different proteins used here, the methods we employed differed from previous studies in that (1) instead of making a series of measurements on individual samples at various concentrations, the protein solutions were titrated with the precipitants, and (2) the results of the light-scattering measurements were analysed by a new maximum entropy procedure that calculates a particle size distribution in a highly reproducible way. The particle size distributions of protein solutions titrated with precipitants showed two major peaks in most cases. For both peaks, relative areas and mean diffusion coefficients were determined. The diffusion constants were corrected for the viscosity of the solutions. From comparing the results on the proteins known to crystallize (EF-Tu) with the amorphously precipitating systems (LRSEC, NRSEC) we find two necessary, but not sufficient, conditions for the formation of crystals: the diffusion coefficient of the monomer peak stays constant until very close to the precipitation point; the percentage of large aggregates stays small (less than 10% of the scattered light intensity) during the titration. For VRSEC, both ammonium sulphate and sodium citrate showed a low percentage of large aggregates and a constant diffusion coefficient of the main (protein monomer) peak below the precipitation point. This indicates that both would be possible precipitants for the crystallization of this enzyme. Crystallization trials using both these salts were carried out, and although no condition could as yet be found for obtaining crystals with ammonium sulphate solutions, crystals of the enzyme have been obtained with sodium citrate.

Refined structure of elongation factor EF-Tu from Escherichia coli

The crystal structure of trypsin-modified elongation factor Tu from Escherichia coli, in complex with the cofactor guanosine diphosphate has been refined to a crystallographic R-factor of 19.3%, at 2.6 A resolution. In the model described, the root-mean-square deviation from ideality is 0.019 A for bond distances and 3.9 degrees for angles. The protein consists of three domains: an alpha/beta domain (residues 1 to 200), containing the binding site of the GDP cofactor, and consisting of a six-stranded beta-pleated sheet, six alpha-helices, and two all-beta domains (residues 209 to 299 and 300 to 393), belonging to the tertiary structural class of antiparallel beta-barrels. The GDP-binding domain has a folding that is found in other GDP-binding proteins. Elongation factor Tu interacts with proteins, nucleic acids and nucleotides, making this molecule well suited as a model system for the study of these interactions.

Preliminary crystallographic analysis of a complex between tetracycline and the trypsin-modified form of Escherichia coli elongation factor Tu

Crystals of a complex between the antibiotic tetracycline and the trypsin-modified form of the Escherichia coli protein elongation factor Tu have been grown in a form suitable for high-resolution X-ray diffraction analysis. The crystals belong to space group P2(1), with cell dimensions a = 69.7 A, b = 156.4 A, c = 135.4 A and beta = 95.3 degrees, and contain six molecules of the complex per asymmetric unit. The crystals are well ordered and diffract to a resolution of 2.3 A.

Crystallization and preliminary X-ray diffraction studies of intact EF-Tu from Thermus aquaticus YT-1

Many attempts have been made to elucidate the three-dimensional structure from elongation factor Tu, but so far the only crystals suitable for X-ray crystallography contained a partially degraded protein. Here, we report the crystallization of a fully active, intact EF-Tu from thermus aquaticus. The crystals belong to hexagonal space group P6(3)(22) and diffract up to 2.6 A. The cell dimensions are a = b = 178 A, c = 238 A and 6 molecules are contained per asymmetric unit.

Three-dimensional image reconstruction of helical aggregates of trypsin modified elongation factor EF-Tu from Escherichia coli: comparison with the reconstructed image of intact EF-Tu

The three-dimensional structure of trypsin-modified EF-Tu polymers was analyzed to a resolution of 30 A with electron image reconstruction techniques after negative staining. In a 70% saturated ammonium sulfate solution the modified protein forms cylindrical aggregates with a diameter of about 340 A. The repeat distance of the structure along the cylindrical axis is 448 A. The large number of subunits in one repeat hampers the assessment of the helical symmetry. The Fourier analysis and three-dimensional synthesis were therefore carried out with three different selection rules. The three reconstructed density distributions show marked differences. In all of them twofold axes perpendicular to the cylindrical axis are present. The half unit cell content of one of the reconstructions shows a striking similarity with the shape of intact EF-Tu.GDP previously proposed in a similar study. We suggest that in the assemblies investigated here dimers of trypsin-modified EF-Tu.GDP are arranged along a one-start basic helix with 15.4 subunits per turn and a pitch of 64 A. The shape of the monomeric proteolyzed EF-Tu.GDP in this helical arrangement is very similar to that of the intact molecule in cylindrical assemblies studied at this resolution.

Bulk preparation and crystallization of the Escherichia coli elongation factor Tu-Ts complex

A simple procedure for the preparation of 10-500 mg of the Escherichia coli elongation Tu-Ts complex is described. The protocol is based on the separate purification and quantitation of EF-Tu-GDP and EF-Ts, followed by mixing of equimolar amounts of each protein and removal of the displaced GDP by dialysis. Single crystals grown from the final product have been analyzed by X-ray diffraction techniques. The procedure is also applicable to the bulk preparation and crystallization of the trypsin-modified Tu-Ts complex. Quantitation of the elongation factors by three methods is presented.

Induction of elongation factor Tu-GDP crystal polymorphism by polyethylene glycol contaminants

Trypsin-modified elongation factor (EF-)Tu-GDP from Escherichia coli is known to crystallize in several different unit cells under apparently identical conditions. The crystal polymorphism was investigated and found to be correlated with the source of polyethylene glycol used in the crystallization procedure. The use of highly purified polyethylene glycol promoted the growth of a new crystal form belonging to space group P2(1)2(1)2(1) with cell dimensions of a = 71.9 A, b = 74.7 A, c = 170.9 A and two molecules per asymmetric unit. In extensive crystallization trials, substances that typically contaminate commercial preparations of polyethylene glycol were screened. The final results show that the presence of the divalent anions, HPO4(2-) or SO4(2-), at different concentrations induce the growth of two known crystal forms belonging to space groups C222(1) and P4(3)2(1)2. The relevancy of the findings is discussed.

Paracrystalline arrays of protein-synthesis elongation factor Tu. Comparison with polymerized actin

Homogeneous protein synthesis elongation factor Tu from Escherichia coli forms aggregates at high concentrations of ammonium sulfate which have a filamentous appearance in the light microscope. Electron microscopy of negatively stained preparations shows that these aggregates are paracrystalline, including three different forms. On the basis of analyses by optical diffraction, this polymorphism can be explained in terms of three different tubular foldings of the same basic two-dimensional surface lattice. This can be compared with that underlying the structure of actin filaments, thus providing a crucial test of the putative relationship between the elongation factor and actin [Rosenbusch, J. P. et al. (1976) J. Supramol. Struct. 5, 391-396]. The differences between the surface lattices, in conjunction with the negative results of sensitive immunochemical tests for possible cross-reactivities between the two proteins, suggest that any such relationship is very remote.

A small angle X-ray study of the elongation factor complex Tu . GDP from Escherichia coli

The protein elongation factor complex Tu. GDP from Escherichia coli was investigated in the presence of 0.01 mM GDP using the small-angle X-ray method. The overall shape and the molecular parameters of the Tu . GDP complex were determined using a least-squares method where the experimental data were used directly without desmearing. The best fit to the experimental data was obtained assuming the molecule to be an ellipsoid of revolution with the semiaxes A = B = 4.08 nm, and C = 1.18nm. Determination of the molecular weight gave the result Mr = 46 000, which corresponds to a water content equal to 26% (by weight).