TRNA synthetase, aminoacyl, role

There is a family of enzymes that catalyze the attachment of amino acids to then-cognate tRNAs, aminoacyl-tRNA synthetases. There is one or more of these enzymes for each of the 20 amino acids that occur commonly in proteins. Each of these enzymes recognizes (a) a specific amino acid and (b) its cognate tRNA. Imagine a soup of 20 amino acids and 20 tRNAs, one for each amino acid. For example, the aminoacyl-tRNA synthetase for, saline would specifically pick valine out of the soup and catalyze its attachment to the tRNA for valine, tRNA . Simply, we can write the product of the reaction as val-tRNA . This is a lovely example of the role of molecular recognition in a critical life process. 

Aminoacyl-tRNA synthetases (aaRSs) compose a family of essential enzymes that attach amino acids covalently to tRNA molecules during protein synthesis. Some aaRSs possess a hydrolytic amino acid editing function to ensure the fidelity of protein synthesis. In addition, aminoacylation can occur by indirect pathways that rely on mischarged tRNA intermediates and enzymes other than aaRSs. Throughout evolution, structural and functional divergence of aaRSs has yielded diverse secondary roles. 

Aminoacyl-tRNA synthetases (aaRSs) are critical components of the translation machinery for protein synthesis in every living cell (1). Each aaRS enzyme in this family links a single amino acid covalently to one or more tRNA isoacceptors to form charged tRNAs. Identity elements within the tRNAs serve as molecular determinants or antideterminants that aid in selection by cognate aaRSs (2). Some aaRSs also have an amino acid editing mechanism to clear their mistakes (3). The canonical aaRSs and aaRS-like proteins have functionally diverged to perform many other important roles in the cell (4, 5). Their versatility and adaptability have provided unique opportunities to develop biotechnology tools and to advance medical research. 

Fan L, Sanschagrin PC, Kaguni LS, Kuhn LA. The accessory subunit of mtDNA polymerase shares structural homology with aminoacyl-tRNA synthetases implications for a dual role as a primer recognition factor and processivity clamp. Proc. Natl. Acad. Sci. U.S.A. 1999 96 9527-9532. 

Ivakhno SS, Kornelyuk AI. Cytokine-Uke activities of some aminoacyl-tRNA synthetases and auxiliary p43 cofactor of aminoacylation reaction and their role in oncogenesis. Exp. Oncol. 2004 26 250-255. 

The liver also plays an essential role in dietary amino acid metabolism. The liver absorbs the majority of amino acids, leaving some in the blood for peripheral tissues. The priority use of amino acids is for protein synthesis rather than catabolism. By what means are amino acids directed to protein synthesis in preference to use as a fuel The K jyj value for the aminoacyl-tRNA synthetases is lower than that of the enzymes taking part in amino acid catabolism. Thus, amino acids are used to synthesize aminoacyl-tRNAs before they are catabolized. When catabolism does take place, the first step is the removal of nitrogen, which is subsequently processed to urea. The liver secretes from 20 to 30 g of urea a day. The a-ketoacids are then used for gluconeogenesis or fatty acid synthesis. Interestingly, the liver cannot remove nitrogen from the branch-chain amino acids (leucine, isoleucine, and valine). Transamination takes place in the muscle. 

The cycle of peptide-chain elongation continues until one of the three stop codons (UAA, UAG, UGA) is reached. There is no aminoacyl-tRNA complementary to these codons, and instead a termination factor or a release factor (RF) with bound GTP binds to the ribosome and induces hydrolysis of both the aminoacyl-linkage and GTP, thereby releasing the completed polypeptide chain from the ribosome. The 475 amino acid-long sequence of rabbit liver RF has been deduced from its cDNA sequence, and it shows 90% homology with mammalian trypto-phanyl-tRNA synthetase (Lee et al., 1990). It has also been reported that for efficient and accurate termination, an additional fourth nucleotide (most commonly an A or a G) after the stop codon is required (Tate and Brown, 1992). The exact role of the fourth nucleotide in the termination of protein synthesis is not fully understood at present. 

QUESTION 1 9.6 Explain the critically important roles of aminoacyl-tRNA synthetases in protein synthesis. 

Figure 11.14 Amino acylation mechanisms catalyzed by aminoacyl-tRNA synthetases The two classes of aminoacyl-tRNA synthetases (aRS s) differ in the site of aminoacylation. Class I aRS s aminoacylate 2 -OH whereas class 11 aRS s add amino acids to 3 -OH of the terminal ribose of the 3 -terminal CCA of cognate tRNA. Magnesinm ions complexed with ATP to enter the active site of aRS may play a dual role in the activation step by both stabilizing the conformation of the ATP (Mg ion bridges the P- and y-phosphates) and participating in adenylate formation (second Mg is found between a- and P-phosphates in some aRS s). In class I aRS, both Lys of MSK and His of HIGH stabilize the bipyramidal oxyphosphorane transition state while R of motif 2 in class II aRS participates in the stabilization of the putative pentacoordinate transition state. The resulting mixed anhydride aminoacyl adenylate is held by the enzyme for the next reaction, i.e. the attack by the 2 -OH (class I) or 3 -OH (class II) of the terminal adenosine at the carbonyl of the aminoacyl adenylate. The amino acid then becomes esterified to the cognate tRNA.

To illustrate the explicit role of water here we consider three biochemical processes (a) aminoacylation of tRNA in the presence of aminoacyl-tRNA synthetase, (b) translation in the ribosome, and (c) DNA replication. In the case... 

Aminoacyl-tRNA synthetases appear to play a role in repression control of some biosynthetic pathways [207-209]. Possibly the role is an... 

For the isoleucine-valine system, there is evidence for the involvement of valyl-tRNA synthetase (Eidlic and Neidhardt [97]) and isoleucyl-tRNA synthetase (Blatt and Umbarger [98]) in repression. Likewise, leucyl-tRNA synthetase has been implicated in the regulation of the formation of the leucine biosynthetic enzymes (Calvo et al. [99]). In multivalent repression of the branched-chain amino acids [100], all three aminoacyl-tRNA synthetases appear to play a role. Leucyl-tRNA has been proposed as a regulatory element (Hatfield and Burns [101]). 

In addition to their critical role in protein synthesis, it has become clear that AARSs are involved in several other cellular pathways. Some AARSs regulate their own transcription and translation, while others contribute to splicing activities in mitochondria. Nuclear aminoacylation of tRNAs by imported AARSs is thought to be a quality control mechanism to ensure that only mature, fully active tRNAs are released efficiently to the cytoplasm for protein synthesis. Programmed cell death (apoptosis) also appears to have an AARS component—human tyrosyl-tRNA synthetase can be proteolytically cleaved into two polypeptides with distinct cytokine activities, despite the lack of such activity in the full-length TyrRS. It is likely that in time many more nontranslational functions of AARS will be identified. 

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