Amino acid synthesis adenylation

Aminoacyl adenylates (296), which are formed from protein amino acids and ATP, act as acylating agents towards t-RNAs, acylating their terminal 3 -hydroxy groups. These charged tRNAs are then used in protein synthesis. Little is known about the reactivity of aminoacyl adenylates (296), and studies are now reported of a model compound, alanyl ethyl phosphate (297). As expected, hydrolysis in both acid and base involves attack at the C=0 group of (297) with departure of ethyl phosphate. Metal ions (Cu +, Zn +) were found to act as catalysts of the hydrolysis. 

The aminoacyl-tRNA synthetases join amino acids to their appropriate tRNA molecules for protein synthesis. They have the very important task of selecting both a specific amino acid and a specific tRNA and joining them. The enzymes differ in size and other properties. However, they all appear to function by a common basic chemistry that makes use of cleavage of ATP at Pa (Eq. 12-48) via an intermediate aminoacyl adenylate and that is outlined also in Eq. 17-36. These enzymes are discussed in Chapter 29. ... 

Another way in which the phosphorylation state of the adenylate system can regulate the cycle depends upon the need for GDP in step/of the cycle (Fig. 17-4). Within mitochondria, GTP is used largely to reconvert AMP to ADP. Consequently, formation of GDP is promoted by AMP, a compound that arises in mitochondria from the utilization of ATP for activation of fatty acids (Eq. 13-44) and activation of amino acids for protein synthesis (Eq. 17-36). 

The soluble enzyme system responsible for its synthesis contains a large 280-kDa protein that not only activates the amino acids as aminoacyl adenylates and transfers them to thiol groups of 4 -phosphopantetheine groups covalently attached to the enzyme but also serves as a template for joining the amino acids in proper sequence.211-214 Four amino acids—proline, valine, ornithine (Om), and leucine—are all bound. 

Synthesis of peptides from amino acids in the solid state or in aqueous solution has been reported with the aid of ATP, Mg2 and free imidazole 34 36). a 4.5 % yield of glycine peptides has been reported in the solid state, 0.6 % yield in aqueous solution 36). Gly-N-pA is formed in a yield of 72.5 % from glycine and chemically synthesized ImpA in aqueous solution, pH 8.0, at room temperature 37). At initial of pH 6.0 glycyl 5 -adenylate (gly-O-pA) and 2 (3 )-0-glycyl adenosine 5 -phosphate (pA-g W are formed 37). 

The intermediate for peptide synthesis is probably aminoacyl 5 -adenylate, formed from amino acids and proteinoid nucleotide complex. In the proteinoid nucleotide complex, the phosphate of adenylate may be attached to the imidazole of histidine in... 

The attachment of an amino acid to a tRNA is catalyzed by an enzyme called aminoacyl-tRNA synthetase. A separate aminoacyl-tRNA synthetase exists for every amino acid, making 20 synthetases in total. The synthesis reaction occurs in two steps. The first step is the reaction of an amino acid and ATP to form an aminoacyl-adenylate (also known as aminoacyl-AMP). 

Aminoacylation is a two-step process, catalyzed by a set of enzymes known as aminoacyl-tRNA synthetases. Twenty aminoacyl-tRNA synthetases reside in each cell, one per amino acid in the genetic code. In the first step of aminoacyl-tRNA synthesis, ATP and the appropriate amino acid form an aminoacyl adenylate intermediate. Inorganic pyrophosphate is released and subsequently broken down to free phosphate by the enzyme inorganic pyrophosphatase. The aminoacyl adenylate is a high-energy intermediate, and in the second step, the transfer of amino acids to the acceptor end of tRNA occurs without any further input of ATP, as shown in Figure 11-2. 

Several systems based on the potentialities of amino acid-phosphoric acid mixed anhydrides have been devised to check the idea that the genetic code developed from an early pathway of RNA-dependent peptide synthesis in an RNA world [168]. RNA sequences have thus been selected that are capable of self-aminoacylation using amino acid adenylates, catalyzing a reaction chemically similar to the aminoacylation of fRNA by the protein aminoacyl fRNA synthetases [169]. 

We can also get some information by comparing the modern biosynthetic pathways to the capabilities of prebiotic chemistry. Amino acids are usually activated in living organisms by reaction with ATP both through the ribosomal and non-ribosomal peptide synthesis pathways. Amino acyl fRNA synthetases bind ATP and free amino acids to cause the highly unfavorable adenylate anhydride formation to be close to equilibrium in the active site. 

Cell-free systems capable of synthesising polypeptides have been prepared from protoscoleces of E. granulosus (7), larval T. crassiceps (588) and H. diminuta (633). In general, these studies have demonstrated that protein synthesis in cestodes, although showing some specificity, is similar to that in mammals in that it requires polysomes, amino acid adenylates, aminoacyl-tRNAs, pH 5 fraction, ATP, GTP, magnesium and either sodium or potassium ions. 

Jhe synthesis of proteins, as characterized by the in vitro incorporation of amino acids into the protein component of cytoplasmic ribonu-cleoprotein, is known to require the nonparticulate portion of the cytoplasm, ATP (adenosine triphosphate) and GTP (guanosine triphosphate) (15, 23). The initial reactions involve the carboxyl activation of amino acids in the presence of amino acid-activating enzymes (aminoacyl sRNA synthetases) and ATP, to form enzyme-bound aminoacyl adenylates and the enzymatic transfer of the aminoacyl moiety from aminoacyl adenylates to soluble ribonucleic acid (sRNA) which results in the formation of specific RNA-amino acid complexes—see, for example, reviews by Hoagland (12) and Berg (1). The subsequent steps in pro-... 

According to this proposal, the incorporation of proline into collagen follows the acyl adenylate and acyl RNA stages now generally believed to occur in protein synthesis. A bound hydroxyproline intermediate is postulated, from which hydroxyproline is transferred to soluble RNA. We prefer to suggest that different RNA acceptor molecules exist for hydroxyproline and proline this would be consistent with recent work which indicates that the soluble RNA molecule contains the information for incorporation of a particular amino acid into protein (3). Although it is conceivable that there is hydroxylation of prolyl-sRNA to yield hydroxyprolyl-sRNA, an additional mechanism would be needed... 

The formation of IAA conjugates is widely believed to be a means for removal of excess IAA produced during certain times of plant development and also in mutant plants where indolic precursors and IAA metabolites accumulate.32 In all higher and many lower plants, applied IAA is rapidly conjugated to form IAA—aspartate.33 The ability of plant tissues to make aspartate conjugates of a variety of active auxins is induced by pretreatment with auxin,34 and this induction was shown to be blocked by inhibitors of RNA and protein synthesis. After almost 50 years of study, an in vitro system from plants was described that accounts for the formation of IAA amide conjugates35 via a mechanism where the acidic auxin is adenylated followed by acyl transfer to the amino acid. The gene for this reaction had been discovered almost 20 years before, when GH3 from soybean was shown... 

Another motif recurs in this activation reaction. The enzyme-hound acyl-adenylate intermediate is not unique to the synthesis of acyl CoA. Acyl adenylates are frequently formed when carboxyl groups are activated in biochemical reactions. Amino acids are activated for protein synthesis hy a similar mechanism (Section 29.2.1). although the enzymes that catalyze this process are not homologous to acyl CoA synthetase. Thus, activation by adenylation recurs in part because of convergent evolution. 

Glucagon stimulates the adenylate cyclase system in the liver and thereby the formation of cAMP, which gives rise to important metabolic changes, (s. tab. 3.10) Furthermore, there is a consequent decline in cholesterol synthesis, improvement in alanine membrane transport, activation of the enzymes of the urea cycle and stimulation of amino acid degradation. 

In general, mechanisms for the biosynthesis of polyamides can be divided into three different pathways, which mainly differ in the mode of activation of the monomers (adenylation or phosphorylation), the dependency on a template, and the enzyme apparatus. In comparison to the activation by phosphorylation, adenylation involves synthesis of a phosphodiester bond between the hydroxyl group of the carboxylic group of the amino acid and the a-phosphate group of adenosine triphosphate (ATP). Activation by phosphorylation has been proposed that is, for synthesis of the tripeptide glutathione (Gly-Glu-Cys) or transpeptidase, the... 

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