Amino-acyl tRNA

The regions of the tRNA molecule teferred to in Chapter 35 (and illustrated in Figure 35-11) now become important. The thymidine-pseudouridine-cyti-dine (T PC) arm is involved in binding of the amino-acyl-tRNA to the ribosomal surface at the site of protein synthesis. The D arm is one of the sites important for the proper recognition of a given tRNA species by its proper aminoacyl-tRNA synthetase. The acceptor arm, located at the 3 -hydroxyl adenosyl terminal, is the site of attachment of the specific amino acid. 

ISOLEUCYL-tRNA SYNTHETASE, AMINO-ACYL tRNA SYNTHETASES Isolobal,... 

METHIONYL-tRNA SYNTHETASE METHIONYL-tRNA FORMYLTRANSFERASE METHIONYL-tRNA SYNTHETASE AMINO-ACYL tRNA SYNTHETASES Method of continuous variation,... 

Pharmacology Tigecycline, a glycylcycline, inhibits protein translation in bacteria by binding to the 308 ribosomal subunit and blocking entry of amino-acyl tRNA molecules into the A site of the ribosome. This prevents incorporation of amino acid residues into elongating peptide chains. 

Remarkably, incorporation of fluorinated amino acids into proteins can also be accomplished in vivo. This supposes that the fluorinated amino acid analogs are recognized by the appropriate amino acyl-tRNA synthetase enzyme with efficiency similar to that of the natural amino acid. The proliferase response elicited by a fluorinated analog (a trifluoroisoleucine derivative) of murine interleukin-2 produced in an appropriate Escherichia coli strain was nearly as high as that of the authentic cytokine, indicating folding into an authentic, native structure [84],... 

Abbreviations aa-tRNA Amino-acyl tRNA eLF Eukaryotic translation initiation factor IF Prokaryotic translation initiation factor eEF Eukaryotic translation elongation factor EF Prokaryotic translation elongation factor eRF Eukaryotic translation termination factor (release factor) RF Prokaryotic translation release factor RRF Ribosome recycling factor Rps Protein of the prokaryotic small ribosomal subunit Rpl Protein of the eukaryotic large ribosomal subunit S Protein of the prokaryotic small ribosomal subunit L Protein of the prokaryotic large ribosomal subunit PTC Peptidyl transferase center RNC Ribosome-nascent chain-mRNA complex ram Ribosomal ambiguity mutation RAC Ribosome-associated complex NMD Nonsense-mediated mRNA decay... 

Similar to macrolides, lincosamides also target the SOS ribosome subunit. More specifically, they inhibit the enzyme peptidyl transferase, which in turn inhibits the activity of ribosomes, preventing the binding of amino acyl-tRNA to the A site on the SOS subunit. That activity blocks the synthesis of proteins. 

By observing changes in nucleotides that alter substrate specificity, researchers have identified nucleotide positions that are involved in discrimination by the amino-acyl-tRNA synthetases. These nucleotide positions seem to be concentrated in the amino acid arm and the anticodon arm, including the nucleotides of the anticodon itself, but are also located in other parts of the tRNA molecule. Determination of the crystal structures of aminoacyl-tRNA synthetases complexed with their cognate tRNAs and ATP has added a great deal to our understanding of these interactions (Fig. 27-17). 

Most of the chemical activity of ribosomes occurs in the interface between the 30S and 50S subunits. Entrance and exit tunnels for both mRNA and the amino-acylated tRNAs are formed between these subunits. The mRNA apparently moves across the platform as the tRNAs move from A to P to E sites experiencing codon selection (decoding) and peptidyltransferase activity. Many loop ends from 16S RNA interact with those of 23S RNA.41 88... 

The amino acids in the cytoplasm will not form polypeptides unless activated by ester formation with appropriate tRNA molecules. The ester linkages are through the 3 -OH of the terminal adenosine nucleotide (Equation 25-9) and are formed only under the influence of a synthetase enzyme that is specific for the particular amino acid. The energy for ester formation comes from ATP hydrolysis (Sections 15-5F and 20-10). The product is called an amino-acyl-tRNA. 

Synthases differ with respect to their site of attachment to tRNA. Some synthases form the 2 ester, some form the 3 ester, and still others produce a mixture of the two. The specificity of the synthases was determined by analyzing their ability to act on tRNA derivatives lacking one or the other terminal hydroxyl group. Once esterified to the terminal ribose, the aminoacyl group can migrate between the vicinal 2 and 3 hydroxyl groups. Thus, in cells, amino-acyl-tRNAs are mixtures of 2 and 3 esters. Only the 3 derivative is a substrate for the subsequent transpeptidation reaction catalyzed by the ribosome. 

XY Yu, JM Hill, G Yu, W Wang, AF Kluge, P Wendler, P Gallant. Synthesis and structure-activity relationships of a series of novel thiazoles as inhibitors of amino-acyl-tRNA synthetases. Boorg Med Chem Lett 9 375-380, 1999. 

Entry of these agents into susceptible organisms is mediated by transport proteins unique to the bacterial inner cytoplasmic membrane. Binding of the drug to the 30S subunit of the bacterial ribosome is believed to block access of the amino acyl-tRNA to the mRNA-ribosome complex at the acceptor site, thus inhibiting bacterial protein synthesis.2... 

The configuration of AMPS, lsO was shown to be (Rp), corresponding to inversion of configuration, by stereospecific phosphorylation, using the adenylate kinase-pyruvate kinase system, and analysis for bridging and nonbridging l80. Similar approaches have been applied to amino acyl-tRNA synthetases, which also catalyze inversion of P of ATP [79]. 

Protein synthesis (PS) Paul Zamecnic, Mahlon Hoagland (ribosomes, amino acyl-tRNA) Gobind Khorana, Robert Holley Marshall Nirenberg (genetic code protein synthesis, Nobel Prize, 1968, medicine) 9.2... 

Inhibition of protein synthesis by aminoglycoside antibiotics, especially by streptomycin, is bactericidal (rev.46)). The antibiotic binds to the smaller ribosomal subunit and leads to the formation of abortive initiation complexes of ribosomes, streptomycin and amino acyl tRNA which progressively trap ribosomes in the form of such biologically irreversible complexes. When protein synthesis is prematurely terminated by puromycin and ribosomes are thus made available for reinitiation of de novo protein biosynthesis, the bactericidal action of streptomycin is accelerated47). Destruction of ribosomes under the influence of primaquine operationally also results in non-occurrence of protein synthesis and in a marked bactericidal effect48, 49 ... 

The N-terminal a-NH2 group appears to be involved in more modification than does the C-terminus. Acetylation, formylation and methylation are three quite common N-terminal derivatives, and just like in the case of the C-terminal end, amino acids can be added to the N-terminus of the finished polypeptide chain in the absence of ribosomes, but in this case the donor is amino acyl-tRNA. 

N-(a-AMIN0ACYL)-5 -0-SULFAM0YLADEN0SINES NATURAL PRODUCT BASED INHIBITORS OF AMINO ACYL tRNA SYNTHETASES... 

Suitable N-substituted sulfamoyladenosines (1) inhibit amino acyl tRNA synthetases (aaTRS s) by mimicking the enzyme bound reaction intermediate 2 (Scheme 1)/ Thus the Structure Activity Relationship (SAR) obtained by varying the R group in structure 1 should probe the key interactions for amino acid selectivity in the aaTRS under investigation. 

A -(a-Aminoacyl)-5 -0-Sulfamoyladenosines Natural Product Based Inhibitors of Amino Acyl tRNA Synthetases 288... 

A given amino acid can match more than one kind of codon. However, a given codon can normally match only one amino acid. There are thus 61 codons to match only 20 amino acids. There are also 3 terminal codons that specify a stop signal to protein synthesis. Amino acyl-tRNA synthetase is an enzyme that attaches amino acids to their corresponding transfer RNA. 

Methionine is linked to these two kinds of tRNAs by the same amino-acyl-tRNA synthetase. A specific enzyme then formylates the amino group of methionine that is attached to tRNAf (Figure 29.21). The activated formyl donor in this... 

Puromycin Causes premature chain termination. The molecule resembles the 3 end of the amino-acylated tRNA and will enter the A site. It transfers to the growing chain causing premature termination. 

Fig. 2). Macrolide antibiotic probably takes up its position adjacent to the amino group of the amino acyl tRNA, compared with the position of the N3 atom of A2486 (A2451). 

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