Ribosome three-dimensional structure

Finally, to produce the structural and functional devices of the cell, polypeptides are synthesized by ribosomal translation of the mRNA. The supramolecular complex of the E. coli ribosome consists of 52 protein and three RNA molecules. The power of programmed molecular recognition is impressively demonstrated by the fact that aU of the individual 55 ribosomal building blocks spontaneously assemble to form the functional supramolecular complex by means of noncovalent interactions. The ribosome contains two subunits, the 308 subunit, with a molecular weight of about 930 kDa, and the 1590-kDa 50S subunit, forming particles of about 25-nm diameter. The resolution of the well-defined three-dimensional structure of the ribosome and the exact topographical constitution of its components are still under active investigation. Nevertheless, the localization of the multiple enzymatic domains, e.g., the peptidyl transferase, are well known, and thus the fundamental functions of the entire supramolecular machine is understood [24]. 

The only other E. coli ribosomal protein whose crystallization has so far been reported is L29 (Appelt et al., 1981). On the other hand, attempts to crystallize ribosomal proteins from the thermophilic Bacillus stearothermophilus have been more successful. Protein BL17, which according to its amino acid sequence (Kimura et al., 1980) corresponds to protein L9 from the E. coli ribosome (Kimura et al., 1982), was the first intact ribosomal protein to give crystals useful for X-ray structural analysis (Appelt et al., 1979). Several other B. stearothermophUus ribosomal proteins, namely BL6 and BL30 (Appelt eteU., 1981,1983) from the large and BS5 (Appelt et al., 1983) from the small subunit have been crystallized, and the determination of their three-dimensional structure at a resolution of better than 3 A is now in progress. Furthermore, crystals of aB. stearothermophilus ribosomal protein complex, which corresponds to the complex (L7/L12)4 LIO from E. coli ribosome, have been obtained (Liljas and Newcomer, 1981). 

An understanding of protein synthesis, the most complex biosynthetic process, has been one of the greatest challenges in biochemistry. Eukaryotic protein synthesis involves more than 70 different ribosomal proteins 20 or more enzymes to activate the amino acid precursors a dozen or more auxiliary enzymes and other protein factors for the initiation, elongation, and termination of polypeptides perhaps 100 additional enzymes for the final processing of different proteins and 40 or more kinds of transfer and ribosomal RNAs. Overall, almost 300 different macromolecules cooperate to synthesize polypeptides. Many of these macromolecules are organized into the complex three-dimensional structure of the ribosome. 

Less than 50 years later (1999) their complete three-dimensional structure was known at nearly atomic resolution, and the function of ribosomes in protein synthesis was quite well understood. However, the structure could not have been obtained without the development of a whole range of new methods. 

Figure 29-4 Structure of 23S-28S ribosomal RNAs. (A) The three-dimensional structure of RNA from the 50S subunit of ribosomes of Halocirculci marismortui. Both the 5S RNA and the six structural domains of the 23S RNA are labeled. Also shown is the backbone structure of protein LI. From Ban et al.17 Courtesy of Thomas A. Steitz. (B) The corresponding structure of the 23S RNA from Thermus thermophilus. Courtesy of Yusupov et al.33a (C) Simplified drawing of the secondary structure of E. coli 23S RNA showing the six domains. The peptidyltransferase loop (see also Fig. 29-14) is labeled. This diagram is customarily presented in two halves, which are here connected by dashed lines. Stem-loop 1, which contains both residues 1 and 2000, is often shown in both halves but here only once. From Merryman et al.78 Similar diagrams for Haloarcula marismortui17 and for the mouse79 reveal a largely conserved structure with nearly identical active sites. (D) Cryo-electron microscopic (Cryo-EM) reconstruction of a 50S subunit of a modified E. coli ribosome. The RNA has been modified genetically to have an...

Most ribosomal proteins are rich in lysine and arginine and, therefore, carry a substantial net positive charge. Proteins S20, L7/12, and L10 have over 20% alanine, while L29 is almost as rich in leucine. Proteins S10, S13, L7/L12, L27, L29, and L30 are surprisingly low (<2 mol %) in aromatic amino acids. Proteins S5, S18, and L7 have acetylated N termini while Lll, L3, L7/12, Lll, L16, and L33 contain methylated amino acids. Lll contains nine methyl groups.22 Protein S6 is the major phosphoprotein of eukaryotic ribosomes.103104 Most ribosomal proteins have no known enzymatic activity. Although often difficult to crystallize, high-resolution three-dimensional structures are known for many free ribosomal proteins.24 Most of them have shapes resembling those previously found... 

Figure 29-6 Some protein-RNA interactions within the ribosome. (A) A space-filling model of the 23S and 5S RNA with associated proteins from the ribosome of Haloarcula marismortui. The CCA ends of bound tRNA molecules in the A, P, and E sites are also included. The view is looking into the active site cleft. The proteins with e after the number are related to eukaryotic ribosomal proteins more closely than to those of E. coli.17 Courtesy of T. A. Steitz. (B) Three-dimensional structure of a 70S ribosome from Thermus thermophilus. The 30S subunit is to the right of the 50S subunit. Courtesy of Yusupov et al.33a (C) Stereoscopic view of the helix 21 to helix 23b region of the 16S RNA with associated proteins S6 (upper left), S18 (upper center, front), and S15 (lower back) from T. thermophilus. Courtesy of Agalarov et at.31 (D) Simplified in vitro assembly map of the central domain of the 30S bacterial ribosome. Courtesy of Gloria Culver. (E) Contacts of proteins with the central (platform) domain of the 16S RNA component. The sequence shown is that of Thermus thermophilus. Courtesy of Agalarov et al. (F) Three drawings showing alternative location of the four copies of protein L7/L12. The N-terminal and C-terminal...

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. 

A great deal of work is currently underway in many laboratories on the structure and function of the archaeal ribosome. These data, coupled with equivalent data forthcoming from the bacterial and eucaryal ribosomes, should answer many of the questions raised in this chapter. Of special interest will be the information obtained on the three-dimensional structure of the ribosome in the three domains. 

Information on the three-dimensional structure of RNA can be obtained by tethering cleavage agents to known positions and then by studying the fragments produced by the cleavage reactions. This has been used to study Escherichia coli ribosomal... 

Amino acids are joined together in a specific order determined by tRNAs, ribosomes, and associated enzymes that translate the mRNA. Each amino acid is joined to its neighbor by a peptide bond. The specific amino acid sequence of a protein specifies its three-dimensional structure. Some proteins require the help of chaperonins to fold into a functional configuration. When synthesis of a polypeptide chain is completed on a ribosome, it is released from the ribosome and may join with one or more similar or different polypeptides to constitute a functional protein. 

Transfer RNA (tRNA) molecules transport amino acids to ribosomes for assembly into proteins. Comprising about 15% of cellular RNA the average length of a tRNA molecule is 75 nucleotides. Because each tRNA molecule becomes bound to a specific amino acid, cells possess at least one type of tRNA for each of the 20 amino acids commonly found in protein. The three-dimensional structure of tRNA molecules, which resembles a warped cloverleaf (Figure 17.22), results primarily from extensive intrachain base pairing. tRNA molecules contain a variety of modified bases. Examples include pseudouridine, 4-thiouridine, 1-methylguanosine, and dihydrouridine ... 

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. 

The three-dimensional structures of ribosomal RNA and ribo-somal protein are remarkably similar among species. Suggest reasons for these similarities. 

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