Synthetases reactions catalyzed

Figure 4.16 A schematic view of the active site of tyrosyl-tRNA synthetase. Tyrosyl adenylate, the product of the first reaction catalyzed by the enzyme, is bound to two loop regions residues 38-47, which form the loop after p strand 2, and residues 190-193, which form the loop after P strand 5. The tyrosine and adenylate moieties are bound on opposite sides of the P sheet outside the catboxy ends of P strands 2 and 5.

Figure 28-12. Selenocysteine (top) and the reaction catalyzed by selenophosphate synthetase (bottom).

The key reaction that links primary and secondary metabolism is provided by the enzyme phenylalanine ammonia lyase (PAL) which catalyzes the deamination of l-phenylalanine to form iran.v-cinnamic acid with the release of NH3 (see Fig. 3.3). Tyrosine is similarly deaminated by tyrosine ammonia lyase (TAL) to produce 4-hydroxycinnamic acid and NH3. The released NH3 is probably fixed by the glutamine synthetase reaction. These deaminations initiate the main phenylpropanoid pathway. 

The reaction catalyzed by KDO 8-phosphate synthetase (reaction 2, Scheme 35) was first observed by Levin and Racker9 in extracts from Pseudomonas aeruginosa (see Scheme 1), and later by Ghalambor and Heath29 in extracts from Escherichia coli 0111 B4 and J-5. In the initial experiments of Levin and Racker,135 the fate of D-ribose 5-phosphate in crude bacterial extracts was studied, and the KDO 8-phosphate discovered by the authors is really derived from D-ribose 5-phosphate by three, sequential, enzyme-catalyzed reactions (see Scheme 36). 

These circumstances became apparent to the authors when they attempted to study the formation of KDO 8-phosphate as catalyzed by purified bacterial extracts. These extracts did not catalyze the formation of KDO 8-phosphate from D-ribose 5-phosphate, but required D-arabinose 5-phosphate as the substrate Heath and Ghalambor29 showed that the KDO 8-phosphate synthetase reaction, observed in Pseudomonas extracts by Levin and Racker, is also catalyzed by extracts from Escherichia coli strains 0 111 B4 and J-5. Rick and Osborn136 showed that the KDO 8-phosphate synthetase from a Salmonella typhimurium mutant conditionally defective in cell-wall synthesis had a KM of 6 mM as compared to a KM of 170 pM for the enzyme from wild-type cells. 

In contrast to humans, bacteria have the biochemical ability to synthesize folic acid from simpler molecules. Here we have a clear biochemical difference between human beings and infectious organisms that we can exploit to our benefit. The reaction catalyzed by an enzyme known as dihydropteroate synthetase, in which a complex heterocycle is linked to p-aminobenzoic acid, is key. Now recognize the structural similarity between sulfanilamide, or other sulfonamides, and p-aminobenzoic acid ... 

The ligation reactions catalyzed by ligases ( synthetases, class 6) are energy-dependent and are therefore always coupled to the hydrolysis of nucleoside triphosphates. 

Carbamoyl-phosphate synthetase (ammonia) [EC 6.3.4.16], also known as carbamoyl-phosphate synthetase I, catalyzes the reaction of two molecules of ATP with carbon dioxide, ammonia, and water to produce two molecules of ADP, orthophosphate, and carbamoyl phosphate. Carbamoyl-phosphate synthetase (glutamine-hydrolyzing) [EC 6.3.5.5], also known as carbamoyl-phosphate synthetase II, catalyzes the reaction of two molecules of ATP with carbon dioxide, glutamine, and water to produce two molecules of ADP, orthophosphate, glutamate, and carbamoyl phosphate. 

Several drugs that interfere with production ofdTMP by blocking the reaction catalyzed by thymidy-late synthetase are Inhibitors ofDNA synthesis and cell proliferation. 

The translation of the mRNA into proteins is the final step in the biological flow of information (see Fig. 6.1). Similar to other macromolecular polymerizations, protein synthesis can be divided into initiation, chain elongation, and termination. Critical players in this process are the aminoacyl transfer RNAs (tRNAs). These molecules form the interface between the mRNA and the growing polypeptide. Activation of tRNA involves the addition of an amino acid to its acceptor stem, a reaction catalyzed by an aminoacyl-tRNA synthetase. Each aminoacyl-tRNA synthetase is highly specific for one amino acid and its corresponding tRNA molecule. The anticodon loop of each aminoacyl-tRNA interacts... 

The pyruvate dehydrogenase complex from Escherichia coli is considerably more complex than tryptophan synthetase. It has a molecular weight of approximately 4.6 millon and contains three enzymes pyruvate dehydrogenase (Et), dihydrolipoyl transacetylase (E2), and dihydrolipoyl dehydrogenase (E3).82 The overall reaction catalyzed by the complex is... 

RGURE 13-8 ATP hydrolysis in two steps (a) The contribution of ATP to a reaction is often shown as a single step, but is almost always a two-step process, (b) Shown here is the reaction catalyzed by ATP-dependent glutamine synthetase. (T)A phosphoryl group istransferred from ATP to glutamate, then (5) the phosphoryl group is displaced by NH3 and released as P,. 

The formation of ATP (or GTP) at the expense of the energy released by the oxidative decarboxylation of a-ketoglutarate is a substrate-level phosphorylation, like the synthesis of ATP in the glycolytic reactions catalyzed by glyceraldehyde 3-phosphate dehydrogenase and pyruvate kinase (see Fig. 14-2). The GTP formed by succinyl-CoA synthetase can donate its terminal phosphoryl group to ADP to form ATP, in a reversible reaction catalyzed by nucleoside diphosphate kinase (p. 505) ... 

Energy Yield from the Citric Acid Cycle The reaction catalyzed by succinyl-CoA synthetase produces the high-energy compound GTP. How is the free energy contained in GTP incorporated into the cellular ATP pool ... 

Fatty acids are converted to their coenzyme A esters in a reversible reaction catalyzed by acyl-CoA synthetase ... 

MECHANISM FIGURE 18-11 Nitrogen-acquiring reactions in the synthesis of urea. The urea nitrogens are acquired in two reactions, each requiring ATP. (a) in the reaction catalyzed by carbamoyl phosphate synthetase 1, the first nitrogen enters from ammonia. The terminal phosphate groups of two molecules of ATP are used to form one molecule of carbamoyl phosphate. In other words, this reaction has two activa-... 

TPP-mediated formation of a-hydroxyketones may or may not involve a decarboxylation step. An example for the former type is the reaction catalyzed by acetolactate synthetase (equation 20). This is a biosynthetically important reaction as acetolactate is the precursor... 

Since the reaction catalyzed by glutamine synthetase has three substrates (L-glutamate, NH3, and metal-ATP) and three products (L-glutamine, P , and metal-ADP), the kinetic mechanism as deduced by steady-state kinetics... 

Fig. 22. Proposed catalytic sequence of reactions catalyzed by glutamine synthetase.

Many years ago Meister s group (96-101) synthesized of a number of inhibitors or substrate analogs that would mimic the intermediates in the proposed pathway of the reactions catalyzed by glutamine synthetase. Two of these are listed below, along with the structures for substrates and two alleged intermediates. 

As discussed earlier, the enzymic reaction catalyzed by glutamine synthetase requires the presence of divalent metal ions. Extensive work has been conducted on the binding of Mn2+ to the enzyme isolated from E. coli (82, 109-112). Three types of sites, each with different affinities for Mn2+, exist per dodecamer n, (12 sites, 1 per subunit) of high affinity, responsible for inducing a change from a relaxed metal ion free protein to a conformationally tightened catalytically active protein n2 (12 sites) of moderate affinity, involved in active site activation via a metal-ATP complex and n3 (48 sites) of low affinity unnecessary for catalysis, but perhaps involved in overall enzyme stability. The state of adenylylation and pH value alter the metal ion specificity and affinities. 

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