RRNA three-dimensional structure

Self-splicing KNA. The precursor to the 26S rRNA of Tetrahymena contains a 413-nucleotide intron, which was shown by Cedi and coworkers to be selfsplicing, i.e., not to require a protein catalyst for maturation.581 582 This pre-rRNA is a ribozyme with true catalytic properties (Chapter 12). It folds into a complex three-dimensional structure which provides a binding site for free guanosine whose 3-OH attacks the phosphorus at the 5 end of the intron as shown in Fig. 28-18A, step a. The reaction is a simple displacement on phosphorus, a transesterification similar to that in the first step of pancreatic ribonuclease action (Eq. 12-25). The resulting free 3-OH then attacks the phosphorus atom at the other end of the intron (step b) to accomplish the splicing and to release the intron as a linear polynucleotide. The excised intron undergoes... 

Ribosomal RNA (rRNA) is involved in the protein synthesis. It is found in the ribosomes which occur in the cytoplasm. Ribosomes contain about 35% protein and 65% rRNA. Experimental evidence suggests that rRNA molecules have structures that consist of a single strand of nucleotides whose sequence varies considerably from species to species. The strand is folded and twisted to form a series of single stranded loops separated by sections of double helix, which is believed to be formed by hydrogen bonding between complementary base pairs. The general pattern of loops and helixes is very similar between species even though the sequences of nucleotides are different. However, little is known about the three dimensional structures of rRNA molecules and their interactions with the proteins found in the ribosome. 

Ribosomal RNA (rRNA) is the most abundant form of RNA in living cells. (In most cells, rRNA constitutes approximately 80% of the total RNA.) The secondary structure of rRNA is extraordinarily complex (Figure 17.23). Although there are species differences in the primary nucleotide sequences of rRNA, the overall three-dimensional structure of this class of molecules is conserved. As its name suggests, rRNA is a component of ribosomes. 

Although their sequences differ, the three-dimensional structure of these 16-S-like rRNAs from (a) E. coli and (b) Saccha-romyces cervisiae (yeast) appear remarkably similar. 

As discussed in detail later, tRNA molecules adopt a well-defined three-dimensional architecture in solution that Is crucial in protein synthesis. Larger rRNA molecules also have locally well-defined three-dimensional structures, with more flexible links In between. Secondary and tertiary structures also have been recognized in mRNA, particularly near the ends of molecules. Clearly, then, RNA molecules are like proteins in that they have structured domains connected by less structured, flexible stretches. 

The sequences of the small and large rRNAs from several thousand organisms are now known. Although the primary nucleotide sequences of these rRNAs vary considerably, the same parts of each type of rRNA theoretically can form base-paired stem-loops, which would generate a similar three-dimensional structure for each rRNA in all organisms. The actual three-dimensional structures of bacterial rRNAs from Thermus thermopolis recently have been determined by x-ray crystallography of the 70S ribosome. The multiple, much smaller ribosomal proteins for the most part are associated... 

Analogous rRNAs from many different species fold into quite similar three-dimensional structures containing numerous stem-loops and binding sites for proteins, mRNA, and tRNAs. Much smaller rlbosomal proteins are associated with the periphery of the rRNAs. 

Nucleic acids can play roles farbeyond merely harbouring the coding information for proteins. Single-stranded nucleic acids can fold into intricate structures capable of molecular recognition and even catalysis. Three-dimensional structures are specified by the primary structure, namely the deoxynucleotide (or nucleotide, for RNA) sequence (5 - 3, by analogy to the situation in which the amino-acid residue sequence determines the three-dimensional structures of polypeptides. In nature, transfer RNAs (tRNAs) use their three-dimensional shape for molecular recognition, while some ribosomal RNAs (rRNAs) are able to catalyse crucial steps even within the protein synthetic pathways themselves. 

The sequence-dictated three-dimensional conformation of an RNA molecule is essential in the functionality of several RNA types The ribosomic RNAs fold into structures that scaffold the ribosomes, and the tRNAs fold into defined structures that allow their recognition by both amino-acyl tRNA synthetase and ribosomes. In both cases, some nucleotide sequences that remain single stranded are involved in the enzymatic processes performed by the molecules. Thus, the sequence of an RNA dictates its structure and allows it to perform its function. Both are strictly connected. One single mutation in a rRNA or a tRNA may completely change the favored three-dimensional structure of the molecule and totally impair the RNA s function (s). 

Honig How well did the model builders do in predicting the three dimensional structure of rRNA ... 

Despite the unity in secondary structural patterns, little is known about the three-dimensional, or tertiary, structure of rRNAs. Even less is known about the quaternary interactions that occur when ribosomal proteins combine with rRNAs and when the ensuing ribonucleoprotein complexes, the small and large subunits, come together to form the complete ribosome. Furthermore, assignments of functional roles to rRNA molecules are still tentative and approximate. (We return to these topics in Chapter 33.)... 

In contrast to DNA, RNAs do not form extended double helices. In RNAs, the base pairs (see p.84) usually only extend over a few residues. For this reason, substructures often arise that have a finger shape or clover-leaf shape in two-dimensional representations. In these, the paired stem regions are linked by loops. Large RNAs such as ribosomal 16S-rRNA (center) contain numerous stem and loop regions of this type. These sections are again folded three-dimensionally—i.e., like proteins, RNAs have a tertiary structure (see p.86). However, tertiary structures are only known of small RNAs, mainly tRNAs. The diagrams in Fig. B and on p.86 show that the clover-leaf structure is not recognizable in a three-dimensional representation. 

E. coli has a specific three-dimensional conformation featuring extensive intrachain base pairing. The predicted secondary structure of the rRNAs (Fig. 27-10) has largely been confirmed in the high-resolution models, but fails to convey the extensive network of tertiary interactions evident in the complete structure. 

Figure 29-2 (A) Secondary structure model for the 1542-residue E. coli 16S rRNA based on comparative sequence analysis.733 Dots indicate G U or A G pairs dashes indicate G C or A U pairs. Strongly implied tertiary interactions are shown by solid green lines. Helix numbering according to Brimacombe. Courtesy of Robin Gutell. (B) Simplified schematic drawing of type often used. (C) Positions of the A, P, and E sites on the 30S ribosomal subunit from Carter et al7° (D) Stereoscopic view of the three-dimensional fold of the 16S RNA from Thermus thermophilus as revealed by X-ray structural analysis at 0.3 nm resolution. Features labeled are the head (H), beak (Be), neck (N), platform (P), shoulder (Sh), spur (Sp), and body (Bo). (E-H) Selected parts of the 16S RNA. In (E) and (F) the helices are numbered as in (A). (F) and (H) are stereoscopic views. The decoding site...

Recently, information concerning protein locations within the 30S subunit has been combined with a secondary structure model of 16S rRNA and the location of protein binding sites in rRNA to generate a partial three-dimensional picture of where the rRNA and proteins are situated in this ribosomal subunit (fig. 28.7). 

Ribosomal RNA (rRNA) is a component of the ribosomes, the protein synthesis factories in the cell. rRNA molecules are extremely abundant, making up at least 80 percent of the RNA molecules found in a typical eukaryotic cell. Virtually all ribosomal proteins are in contact with rRNA. Most of the contacts between ribosomal subunits are made between the 16S and 23 S rRNAs such that the interactions involving rRNA are a key part of ribosome function. The environment of the tRNA-binding sites is largely determined by rRNA. The rRNA molecules have several roles in protein synthesis. 16S rRNA plays an active role in the functions of the 308 subunit. It interacts directly with mRNA, with the 508 subunit, and with the anticodons of tRNAs in the P- and A-sites. Peptidyl transferase activity resides exclusively in the 238 rRNA. Finally, the rRNA molecules have a structural role. They fold into three-dimensional shapes that form the scaffold on which the ribosomal proteins assemble. 

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