Special Feature of the 50S Subunit The Tunnel

A tunnel transverses the 50S subunit, running from the peptidyl-transferase (PTF) center at the foot of the central protuberance up to the base at the cytoplasmic side of the large subunit with a length of about 100 A and a width of 10-20 A (Fig. 2-1D 11, 10 ). The first hint that this tunnel existed was provided by electron microscopy (EM) of two-dimensional (2D) crystals of 80S isolated from chicken embryos 12 and 50S subunits from Bacillus stearothermophilus 13 . By that time it had already...

From Microsomes to Ribosomes

As we have seen, it was not until the beginning of the 1950s, and in a context quite different from their original characterization, that the 'small particles' or 'microsomes', operationally defined in terms of fractional sedimentation, optical inspection, Figure 1-8 A scheme for the interaction of microsomal RNA and soluble RNA-amino acid (Ref. 27 , Figure 5). Figure 1-8 A scheme for the interaction of microsomal RNA and soluble RNA-amino acid (Ref. 27 , Figure 5). and chemical composition,...

The Domain Structure of the Ribosomal Subunits

The shear complexity of protein synthesis forces any participating component to maintain their structure and function through evolution. This principle justifies the assumption that not only all tRNAs, but also all 16S (and 16S-like) and 23S (and 23S-like) rRNAs have the same general secondary and tertiary structures 55 . Therefore, the secondary structures of 16S, 23S, and 5S rRNA could be derived by analyzing the pattern of variation within aligned rRNA sequences from different species (see...

The E coli RNA degradosome

Two temperature-sensitive mutations, now known as rne3071 and rnel, were identified because of their effect on the maturation of 5S ribosomal RNA 55 and the degradation of mRNA 56 . Subsequent studies showed that both mutations are in the structural gene for RNase E 57-59 . It is now generally accepted that RNase E has a role in both the maturation of ribosomal RNA and the degradation of mRNA. Recent work has shown that RNase E is also essential for tRNA maturation and evidence from these...

The Hybridsite Model for Elongation

This model is based on the observation that bases of rRNA were protected against chemical modification when tRNAs were bound specifically to the ribosomal A-, P- and E-sites. Each tRNA position on the ribosome was correlated with a specific protection pattern, e.g., binding of AcPhe-tRNA (a simple mimic of a peptidyl-tRNA) to the P-site defined the P-site pattern, whereas binding of a ternary complex Phe-tRNA-EF-Tu-GTP to the A-site (after pre-filling the P-site with a deacylated-tRNA) produced...

Future Prospects

There is now a firm fundamental understanding of the mechanism of translation initiation in eukaryotes. Much of this knowledge has been traditionally obtained through the use of genetic analysis in yeast and biochemical assays in mammalian systems. More recently, a great deal of progress has been made by solving the 3D structures of individual translation factors, collecting vast new information on the interactions among initiation factors, and the analysis of functional multi-subunit...

Specialized initiation events translational coupling 70S initiation and leaderless mRNAs

In the bacteria, most mRNAs are transcribed from transcriptional units that usually contain several, often functionally related, genes. The product is a polycistronic mRNA, where each cistron carries the information of a single protein. In E. coli, polycistronic mRNAs usually contain four cistrons. Such mRNAs contain multiple translation initiation sites, one for each cistron, with a Shine-Dalgarno (SD) sequence and an AUG initiation codon. Recognition of the translation start sites within the...

I2i45i2i47

Gingras, N. Sonenberg et al., Cell, I997, 89, 95I-96I. 209 H. Matsuo, H. Li, A. M. McGuire et al., Nat. Struct. Biol. I997, 4, 7I7-724. 210 J. Marcotrigiano, A.-C. Gingras, N. Sonenberg et al., Nucleic Acids Symp. Ser. ed. 1997, 8-11. 211 G. C. Scheper, B. van Kollenburg, J. Hu et al., J. Biol. Chem. 212 J. Zuberek, A. Wyslouch-Cieszynska, A. Niedzwiecka et al., RNA, 2003, 213 K. Tomoo, X. Shen, K. Okabe et al., Biochem. J. 2002,362, 539-544. 214 A. Niedzwiecka, J....

Decoding of an aatRNA Cognate versus Nearcognate aatRNAs

A model for the discrimination between cognate and near-cognate aa-tRNAs was proposed by Potapov about 20 years ago 68 . According to this model, the decoding center of the ribosome recognizes the anticodon-codon duplex, in particular sensing the stereochemical correctness of the partial Watson-Crick base-pairing and the positioning of the phosphate-sugar backbone within this structure. A test of this hypothesis was performed with an mRNA that carried a DNA codon (deoxycodon) at one of the...

EIF2 Interactions with MettRNA mRNA eIF5 and eIF3

EIF2 can be divided into three structural domains (Fig. 7.2-4C). The C-terminal half is closely related in sequence to the archaeal ortholog (aIF2 ), and most probably has a two-domain structure similar to that solved by NMR for Methanococcus Jannaschii aIF2 58 (Fig. 7.2-5B). The first domain in the latter consists of a four-stranded -sheet with two helices packed against one face of the -sheet. It is connected by an a-helical linker to the second domain, comprised of a three-stranded sheet...

EIF2Plays a Central Role in Binding Guanine Nucleotides and Initiator tRNA

The eIF2y belongs to the superfamily of GTP-binding proteins and is closely related to the bacterial and eukaryotic elongation factors, EF-Tu and eEFla, respectively, which deliver charged elongator tRNAs in ternary complexes with GTP to the ribo-some during the elongation phase of protein synthesis. The molecular masses and sequences of eIF2y proteins are well conserved among animals, plants, and fungi Table 7.2-1 , and orthologs also exist in archaea Fig. 7.2-2 . The sequence similarities...

The Trigger for RFmediated Release of the Nascent Chain and the Outcome

If the arrival of the stop codon in the A site is the discriminating factor for decoding RFs, it is logical to presume that the cognate stop codon is the initial signal for the RF to accommodate into the A site by undergoing a conformational transformation. An analogous situation might be the selection process of cognate tRNAs see Chap. 8.2 here codon-anticodon interaction at the A site presumably transfers a signal to the GTPase center inducing EF-Tu-dependent GTP hydrolysis, which in turn...