Elongation factor G (EF‐G) catalyzes the translocation step of protein synthesis in bacteria, and like the other bacterial elongation factor, EF‐Tu‐‐whose structure is already known‐‐it is a member of the GTPase superfamily. We have determined the crystal structure of EF‐G‐‐GDP from Thermus thermophilus. It is an elongated molecule whose large, N‐terminal domain resembles the G domain of EF‐Tu, except for a 90 residue insert, which covers a surface that is involved in nucleotide exchange in EF‐Tu and other G proteins. The tertiary structures of the second domains of EF‐G and EF‐Tu are nearly identical, but the relative placement of the first two domains in EF‐G‐‐GDP resembles that seen in EF‐Tu‐‐GTP, not EF‐Tu‐‐GDP. The remaining three domains of EF‐G look like RNA binding domains, and have no counterparts in EF‐Tu.

The elongation phase of protein synthesis is promoted by two G proteins, elongation factor Tu (EF-Tu), which delivers aminoacyl tRNAs to the ribosome, and elongation factor G (EF-G), which catalyzes translocation. Crystallographic investigations have revealed that EF-G.GDP resembles the EF-Tu.GTP.(aminoacyl tRNA) complex, and it has been proposed that the translocase function of EF-G is derived from this similarity [Nissen, P., et al. (1995) Science 270, 1464]. However, its significance is uncertain because the affinity of EF-G.GDP for the ribosome is much lower than that of the ternary complex it resembles and because EF-Tu.GDP, the form of EF-Tu that has low ribosome affinity, has a conformation radically different from that of EF-Tu.GTP or EF-Tu in the ternary complex. The small-angle X-ray scattering study described here was undertaken to ascertain if the form of EF-G that has high ribosome affinity, EF-G.GTP, the structure of which is unknown, could be a mimic of EF-Tu.GDP. The data show that nucleotide-free EF-G, EF-G.GDP, EF-G. GTP, and EF-G.GMPPCP cannot be distinguished by solution scattering and that it is likely they all resemble crystalline EF-G.GDP. Since an EF-Tu-like change would easily have been detected, it follows that it does not occur in EF-G. These observations have significant implications for the mechanism of translocation.

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Short RNAs (25-36 nucleotides in length) with sequences of the translational initiation region of bacteriophage R17 protein A mRNA were produced by chemical and in vitro transcription techniques and labeled at their 5' or 3' ends with fluorescent probes. The interaction of these labeled RNAs with the 30S subunit of Escherichia coli was studied by using fluorescence spectroscopic techniques. All the RNAs bound tightly to 30S subunits (Kd less than or equal to 200 nM). Resonance energy transfer experiments demonstrated the proximity of the ends of the RNAs to each other and to two fluorescently labeled sites on the 30S subunit: the 3' end of 16S rRNA and the cysteine residue of ribosomal protein S21. By using the distances calculated from energy transfer between the 3' end of 16S rRNA and the ends of RNAs of varying lengths, a topological map of this region of mRNA on the 30S subunit was constructed.

Fluorescence resonance energy transfer (FRET) was used to monitor pH-dependent structural changes in the cholera toxin B subunit (CTB) and the membranes with which CTB associates. The distance separating the single tryptophan (Trp88) of each CTB monomer and a pyrene probe linked to the membrane-imbedded tail of ganglioside GM1 is not influenced by pH in a range from 3.5 to 7.5, consistent with the position of Trp88 in the GM1 binding site of CTB. In contrast, the distance between the pyrene probe on GM1 and coumarin, stilbene, or fluorescein probes covalently linked to specific sites on CTB appears to increase significantly as the pH is lowered to 5.0 or less. This conformational change is not accompanied by detectable changes in the distance between Trp88 and these extrinsic probe positions in the presence of nonfluorescent GM1. However, when the distance from Trp88 to the extrinsic probes is monitored as a function of pH in the absence of GM1, a conformational change is seen which indicates that receptor binding influences the character of pH-dependent conformational changes that occur within CTB. Interestingly, the observed change in CTB conformation is accompanied by a change in the relative position of GM1 within the membrane as judged by FRET from the pyrene probe on GM1 to a 7-nitrobenz-2-oxa-1,3-diazol-4-yl (NBD) probe linked to the polar head group of phosphatidylethanolamine and positioned at the membrane surface. Taken together, the data imply that low endosomal pH is capable of inducing structural changes in CTB, which, in turn, exert effects on the structure of the membrane to which CTB is bound. These phenomena may have a role in (1) processing of cholera toxin within the endosomal compartments of some target cell types, (2) determining the lag time between cholera toxin binding and the target cell response to cholera intoxication, or (3) the efficiency of CTB and cholera toxin as mucosal adjuvants.