RRNA structural domains

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. 

These findings are interpreted to indicate that erythromycin resistance mutation in domain II caused an increase in the peptide and disrupted an indirectly functional interaction between domains II and V, because such a mutation could affect alteration of the stability of a secondary rRNA structure (hairpin sequence structure) in domain II. In addition, the Shine-Dalgamo (SD) sequence of the rRNA-encoded E-peptide ORE is sequestered in the hairpin structure. Thereby, SD and E-peptide codon are not accessible to ribosomes of wild-type E. coli. The conformational change of the hairpin structure by erythromycin resistance mutation can be recognized by ribosomes for the initiation of translation of E-peptide. Thus, the increase of the peptide is expected to show resistance to macrolide antibiotics such as erythromycin, oleandomycin, and spiramycin but not clindamycin and chloramphenicol without preventing their binding to the target. 

Zinc finger a DNA binding motif first recognized in Xenopus transcription factor IIIA (which binds to the internal control sequence of the 5S rRNA gene). This protein contains nine 30-residue sequences, all rather similar and arranged in tandem. Each contains two invariant Cys residues and two invariant His residues, as well as several conserved hydrophobic residues. Each of these structural domains folds about a single Zn ion, and X-ray analysis indicates that the zinc ion is tetrahedrally liganded by the invariant... 

FIGURE 12.39 The proposed secondary structure for E. coli 16S rRNA, based on comparative sequence analysis in which the folding pattern is assumed to be conserved across different species. The molecule can be subdivided into four domains—I, II, III, and IV—on the basis of contiguous stretches of the chain that are closed by long-range base-pairing interactions. I, the 5 -domain, includes nucleotides 27 through 556. II, the central domain, runs from nucleotide 564 to 912. Two domains comprise the 3 -end of the molecule. Ill, the major one, comprises nucleotides 923 to 1391. IV, the 3 -terminal domain, covers residues 1392 to 1541. 

R. H., Draper, D. E. The RNA-binding domain of ribosomal protein Lll recognizes an rRNA tertiary structure stabilized by both fhiostrepton and magnesium ion. Nucleic Adds Res 2000, 28, 1778—... 

Pharmacology Telithromycin belongs to the ketolide class of antibacterials and is structurally related to the macrolide family of antibiotics. Telithromycin blocks protein synthesis by binding to domains II and V of 23S rRNA of the 508 ribosomal subunit. Pharmacokinetics ... 

Morgan, J.A.T. and Blair, D. (1998) Trematode and monogenean rRNA ITS2 secondary structures support a four-domain model. Journal of Molecular Evolution 47, 406-41 9. 

Agalarov SC, Prasad GS, Funke PM, Stout CD, Williamson Jr JR (2000) Structure of the S15,S18-rRNA complex assembly of the 30S ribosome central domain, Science, 288 107—112... 

Fig. 5. (A) Structure of four plant rRNA segments determined by DMS modification and primer extension. The structures of the 3 minor domain for the four plant species and rabbit 18 S rRNA are shown. Filled circles indicate sites of strong modification and open circles sites of weak or variable modification. The free energy of each structure is indicated in Kcal/mol. The structure and modification data presented for rabbit were published previously." Structures presented for the plant RNAs are based on DMS data. Numbering indicated for soybean RNA is as in Fig. 3. (B) Optimal energy structure for maize 18 S rRNA 3 minor domain. A computer-generated structure of maize 18 S rRNA within the region studied used the parameters of Zuker and co-workers.35 36 DMS-modified residues within double-stranded regions in the structure are indicated.

Fig. 4.3 Seconda structure of large riboso-mal subunit. The seconda structure of rRNA has been divided into six domains (Dorn I to Dom VI) [14]. Various functional sights have...

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