Maria Selmer

Structure of the 70S Ribosome Complexed with Mrna and tRNA.

The crystal structure of the bacterial 70S ribosome refined to 2.8 angstrom resolution reveals atomic details of its interactions with messenger RNA (mRNA) and transfer RNA (tRNA). A metal ion stabilizes a kink in the mRNA that demarcates the boundary between A and P sites, which is potentially important to prevent slippage of mRNA. Metal ions also stabilize the intersubunit interface. The interactions of E-site tRNA with the 50S subunit have both similarities and differences compared to those in the archaeal ribosome. The structure also rationalizes much biochemical and genetic data on translation.

The structure of the ribosome with elongation factor G trapped in the posttranslocational state.

Ribosomes Caught in Translation To synthesize proteins, the ribosome must select cognate transfer RNAs (tRNAs) based on base-pairing with the messenger RNA (mRNA) template (a process known as decoding), form a peptide bond, and then move the mRNA:tRNA assembly relative to the ribosome (a process known as translocation). Decoding and translocation require protein guanosine triphosphatases (GTPases), and, while high-resolution structures of the ribosome have greatly furthered our understanding of ribosome function, the detailed mechanism of these GTPases during the elongation cycle remains unclear. Two Research Articles now give a clearer view of these steps in bacterial protein synthesis (see the Perspective by Liljas). Schmeing et al. (p. 688, published online 15 October) present the crystal structure of the ribosome bound to Elongation factor-Tu (EF-Tu) and amino-acyl tRNA that gives insight into how EF-Tu contributes to accurate decoding. Gao et al. (p. 694, published online 15 October) describe the crystal structure of the ribosome bound to Elongation factor-G (EF-G) trapped in a posttranslocation state by the antibiotic fusidic acid that gives insight into how EF-G functions in translocation. Crystal structures of the ribosome bound to elongation factors provide insights into translocation and decoding. Elongation factor G (EF-G) is a guanosine triphosphatase (GTPase) that plays a crucial role in the translocation of transfer RNAs (tRNAs) and messenger RNA (mRNA) during translation by the ribosome. We report a crystal structure refined to 3.6 angstrom resolution of the ribosome trapped with EF-G in the posttranslocational state using the antibiotic fusidic acid. Fusidic acid traps EF-G in a conformation intermediate between the guanosine triphosphate and guanosine diphosphate forms. The interaction of EF-G with ribosomal elements implicated in stimulating catalysis, such as the L10-L12 stalk and the L11 region, and of domain IV of EF-G with the tRNA at the peptidyl-tRNA binding site (P site) and with mRNA shed light on the role of these elements in EF-G function. The stabilization of the mobile stalks of the ribosome also results in a more complete description of its structure.

Crystal Structures of the Ribosome in Complex with Release Factors RF1 and RF2 Bound to a Cognate Stop Codon

During protein synthesis, translational release factors catalyze the release of the polypeptide chain when a stop codon on the mRNA reaches the A site of the ribosome. The detailed mechanism of this process is currently unknown. We present here the crystal structures of the ribosome from Thermus thermophilus with RF1 and RF2 bound to their cognate stop codons, at resolutions of 5.9 Angstrom and 6.7 Angstrom, respectively. The structures reveal details of interactions of the factors with the ribosome and mRNA, including elements previously implicated in decoding and peptide release. They also shed light on conformational changes both in the factors and in the ribosome during termination. Differences seen in the interaction of RF1 and RF2 with the L11 region of the ribosome allow us to rationalize previous biochemical data. Finally, this work demonstrates the feasibility of crystallizing ribosomes with bound factors at a defined state along the translational pathway.

Post‐termination complex disassembly by ribosome recycling factor, a functional tRNA mimic

Ribosome recycling factor (RRF) together with elongation factor G (EF‐G) disassembles the post‐ termination ribosomal complex. Inhibitors of translocation, thiostrepton, viomycin and aminoglycosides, inhibited the release of tRNA and mRNA from the post‐termination complex. In contrast, fusidic acid and a GTP analog that fix EF‐G to the ribosome, allowing one round of tRNA translocation, inhibited mRNA but not tRNA release from the complex. The release of tRNA is a prerequisite for mRNA release but partially takes place with EF‐G alone. The data are consistent with the notion that RRF binds to the A‐site and is translocated to the P‐site, releasing deacylated tRNA from the P‐ and E‐sites. The final step, the release of mRNA, is accompanied by the release of RRF and EF‐G from the ribosome. With the model post‐termination complex, 70S ribosomes were released from the post‐termination complex by the RRF reaction and were then dissociated into subunits by IF3.

Crystal structure of the ribosome recycling factor bound to the ribosome

In bacteria, disassembly of the ribosome at the end of translation is facilitated by an essential protein factor termed ribosome recycling factor (RRF), which works in concert with elongation factor G. Here we describe the crystal structure of the Thermus thermophilus RRF bound to a 70S ribosomal complex containing a stop codon in the A site, a transfer RNA anticodon stem-loop in the P site and tRNAfMet in the E site. The work demonstrates that structures of translation factors bound to 70S ribosomes can be determined at reasonably high resolution. Contrary to earlier reports, we did not observe any RRF-induced changes in bridges connecting the two subunits. This suggests that such changes are not a direct requirement for or consequence of RRF binding but possibly arise from the subsequent stabilization of a hybrid state of the ribosome.

Structure of the L1 protuberance in the ribosome.

The L1 protuberance of the 50S ribosomal subunit is implicated in the release/disposal of deacylated tRNA from the E site. The apparent mobility of this ribosomal region has thus far prevented an accurate determination of its three-dimensional structure within either the 50S subunit or the 70S ribosome. Here we report the crystal structure at 2.65 Å resolution of ribosomal protein L1 from Sulfolobus acidocaldarius in complex with a specific 55-nucleotide fragment of 23S rRNA from Thermus thermophilus. This structure fills a major gap in current models of the 50S ribosomal subunit. The conformations of L1 and of the rRNA fragment differ dramatically from those within the crystallographic model of the T. thermophilus 70S ribosome. Incorporation of the L1–rRNA complex into the structural models of the T. thermophilus 70S ribosome and the Deinococcus radiodurans 50S subunit gives a reliable representation of most of the L1 protuberance within the ribosome.

Crystal structure of an mRNA-binding fragment of Moorella thermoacetica elongation factor SelB.

SelB is an elongation factor needed for the co‐translational incorporation of selenocysteine. Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin. In bacteria, the C‐terminal part of SelB recognizes this hairpin, while the N‐terminal part binds GTP and tRNA in analogy with elongation factor Tu (EF‐Tu). We present the crystal structure of a C‐terminal fragment of SelB (SelB‐C) from Moorella thermoacetica at 2.12 Å resolution, solved by a combination of selenium and yttrium multiwavelength anomalous dispersion. This 264 amino acid fragment contains the entire C‐terminal extension beginning after the EF‐Tu‐homologous domains. SelB‐C consists of four similar winged‐helix domains arranged into the shape of an L. This is the first example of winged‐helix domains involved in RNA binding. The location of conserved basic amino acids, together with data from the literature, define the position of the mRNA‐binding site. Steric requirements indicate that a conformational change may occur upon ribosome interaction. Struc tural observations and data in the literature suggest that this change happens upon mRNA binding.

Structure of ribosomal protein TL5 complexed with RNA provides new insights into the CTC family of stress proteins

The crystal structure of Thermus thermophilus ribosomal protein TL5 in complex with a fragment of Escherichia coli 5S rRNA has been determined at 2.3 A resolution. The protein consists of two domains. The structure of the N-terminal domain is close to the structure of E. coli ribosomal protein L25, but the C-terminal domain represents a new fold composed of seven beta-strands connected by long loops. TL5 binds to the RNA through its N-terminal domain, whereas the C-terminal domain is not included in this interaction. Cd(2+) ions, the presence of which improved the crystal quality significantly, bind only to the protein component of the complex and stabilize the protein molecule itself and the interactions between the two molecules in the asymmetric unit of the crystal. The TL5 sequence reveals homology to the so-called general stress protein CTC. The hydrophobic cores which stabilize both TL5 domains are highly conserved in CTC proteins. Thus, all CTC proteins may fold with a topology close to that of TL5.

Staphylococcus aureus elongation factor G – structure and analysis of a target for fusidic acid

Fusidic acid (FA) is a bacteriostatic antibiotic that locks elongation factor G (EF‐G) on the ribosome in a post‐translocational state. It is used clinically against Gram‐positive bacteria such as pathogenic strains of Staphylococcus aureus, but no structural information has been available for EF‐G from these species. We have solved the apo crystal structure of EF‐G from S. aureus to 1.9 Å resolution. This structure shows a dramatically different overall conformation from previous structures of EF‐G, although the individual domains are highly similar. Between the different structures of free or ribosome‐bound EF‐G, domains III–V move relative to domains I–II, resulting in a displacement of the tip of domain IV relative to domain G. In S. aureus EF‐G, this displacement is about 25 Å relative to structures of Thermus thermophilus EF‐G in a direction perpendicular to that in previous observations. Part of the switch I region (residues 46–56) is ordered in a helix, and has a distinct conformation as compared with structures of EF‐Tu in the GDP and GTP states. Also, the switch II region shows a new conformation, which, as in other structures of free EF‐G, is incompatible with FA binding. We have analysed and discussed all known fusA‐based fusidic acid resistance mutations in the light of the new structure of EF‐G from S. aureus, and a recent structure of T. thermophilus EF‐G in complex with the 70S ribosome with fusidic acid [Gao YG et al. (2009) Science326, 694–699]. The mutations can be classified as affecting FA binding, EF‐G–ribosome interactions, EF‐G conformation, and EF‐G stability.

The plastic energy landscape of protein folding: A triangular folding mechanism with an equilibrium intermediate for a small protein domain

Protein domains usually fold without or with only transiently populated intermediates, possibly to avoid misfolding, which could result in amyloidogenic disease. Whether observed intermediates are productive and obligatory species on the folding reaction pathway or dispensable by-products is a matter of debate. Here, we solved the crystal structure of a small protein domain, SAP97 PDZ2 I342W C378A, and determined its folding pathway. The presence of a folding intermediate was demonstrated both by single and double-mixing kinetic experiments using urea-induced (un)folding as well as ligand-induced folding. This protein domain was found to fold via a triangular scheme, where the folding intermediate could be either on- or off-pathway, depending on the experimental conditions. Furthermore, we found that the intermediate was present at equilibrium, which is rarely seen in folding reactions of small protein domains. The folding mechanism observed here illustrates the roughness and plasticity of the protein folding energy landscape, where several routes may be employed to reach the native state. The results also reconcile the folding mechanisms of topological variants within the PDZ domain family.