Glyceraldehyde-3-phosphate, amino acid

A basic group removes a proton from the P-carbon of the iminium and forms the enamine. This enamine then reacts as a nucleophile towards the aldehyde group of glyceraldehyde 3-phosphate in a simple addition reaction, and the proton necessary for neutralizing the charge is obtained from an appropriately placed amino acid residue. Finally, the iminium ion loses a proton and hydrolysis releases the product from the enzyme. 

MECHANISM FIGURE 22-18 Tryptophan synthase reaction. This enzyme catalyzes a multistep reaction with several types of chemical rearrangements. An aldol cleavage produces indole and glyceraldehyde 3-phosphate this reaction does not require PLP. Dehydration of serine forms a PLP-aminoacrylate intermediate. In steps and this condenses with indole, and the product is hydrolyzed to release tryptophan. These PLP-facilitated transformations occur at the /3 carbon (C-3) of the amino acid, as opposed to the a-carbon reactions described in Figure 18-6. The /3 carbon of serine is attached to the indole ring system. Tryptophan Synthase Mechanism... 

Figure 1.2 Main pathways leading to secondary metabolites. Abbreviations IPP, isopentenyl diphosphate DMAPP, dimethyl allyl diphosphate CAP, glyceraldehyde-3-phosphate NPAAs, non-protein amino acids AcCoA, acetyl coenzyme A. (See Plate 1 in colour plate section.)...

Several different amino acid side chains can act as nucleophiles in enzyme catalysis. The most powerful nucleophile is the thiol side chain of cysteine, which can be deproto-nated to form the even more nucleophilic thiolate anion. One example in which cysteine is used as a nucleophile is the enzyme glyceraldehyde 3-phosphate dehydrogenase, which uses the redox coenzyme NAD+. As shown in Fig. 10, the aldehyde substrate is attacked by an active site cysteine, Cys-149, to form a hemi-thioketal intermediate, which transfers hydride to NAD+ to form an oxidized thioester intermediate (7). Attack of phosphate anion generates an energy-rich intermediate 3-phosphoglycerate. 

B. In the synthesis of these three amino acids from glucose, serine is produced from the glycolytic intermediate phosphoglyceric acid. Arginine is produced from the TCA cycle intermediate cc-ketoglutarate, and aspartate by transamination of oxaloacetate. Therefore, glyceraldehyde 3-phosphate is the only common intermediate. 

Inactivation of alcohol dehydrogenase from yeast with 14C-labeled [3-(3-bromoacetylpyridinio)-propyl]-adenosine pyrophosphate followed by oxidation showed the presence of 1-carboxymethyl histidine66. After inactivation of the enzyme with labeled [3-(4-bromoacetylpyridinio)-propyl]-adenosine pyrophosphate followed by oxidation, S-carboxymethyl cysteine was identified in the protein. In the case of glyceraldehyde-3-phosphate dehydrogenase, treatment with either coenzyme analogue leads to the modification of the cysteine residue. Treatment with [14C]nicotinamide-5-bromo-4-methylimidazole dinucleotide did not reveal any modified amino-acid-residues. The labeled nicotinamide residue split off during the recovery of the inactivated enzyme. Attempts to synthesize an inactivator labeled with a 14C-acetyl residue did not give satisfactory yields. If the enzyme-coenzyme derivative was treated with tritiated sodium boron hydride, tritium could be introduced (Fig. 22). Studies with... 

The main reaction products of prebiotic chemistry were H2, H20, CH4, CO, C02, NH3, and N2. These compounds formed many intermediates including ions and radicals. The more important molecules that formed were formaldehyde HCHO, hydrogen cyanide HCN, phosphate ions, and cyan amide NH2CN. The final spectrum of products encompassed glycerol, glyceraldehyde - the parent compounds of sugars - carboxylic acids, amino acids, urea, guanidine, purines, and pyrimidines. As an example for the many possible interactions the formation of the nucleobase, uracil is shown in Fig. 2.1. 

Because glyceraldehyde-3-phosphate and dihydroxyacetone phosphate are readily interconverted, these two molecules (referred to the triose phosphates) are both considered to be Calvin cycle products. The synthesis of triose phosphate is sometimes referred to as the C3 pathway. Plants that produce triose phosphates during photosynthesis are called C3 plants. Triose phosphate molecules are used by plant cells in such biosynthetic processes as the formation of polysaccharides, fatty acids, and amino acids. Initially, most triose phosphate is used in the synthesis of starch and sucrose (Figure 13A). The metabolism of each of these molecules is briefly discussed below. 

Terpenoids do not necessarily contain exact multiples of five carbons and allowance has to be made for the loss or addition of one or more fragments and possible molecular rearrangements during biosynthesis. In reality the terpenoids are biosynthesized from acetate units derived from the primary metabolism of fatty acids, carbohydrates and some amino acids (see Fig. 2.10). Acetate has been shown to be the sole primary precursor of the terpenoid cholesterol. The major route for terpenoid biosynthesis, the mevalonate pathway, is summarized in Fig. 2.16. Acetyl-CoA is involved in the generation of the C6 mevalonate unit, a process that involves reduction by NADPH. Subsequent decarboxylation during phosphorylation (i.e. addition of phosphate) in the presence of ATP yields the fundamental isoprenoid unit, isopentenyl pyrophosphate (IPP), from which the terpenoids are synthesized by enzymatic condensation reactions. Recently, an alternative pathway has been discovered for the formation of IPP in various eubacteria and plants, which involves the condensation of glyceraldehyde 3-phosphate and pyruvate to form the intermediate 1-deoxy-D-xylulose 5-phosphate (Fig. 2.16 e.g. Eisenreich et al. 1998). We consider some of the more common examples of the main classes of terpenoids below. 

Triose Phosphate Isomerase Diffusional Encounters with D-Glyceraldehyde-3-Phosphate In this section we use a real system, triose phosphate isomerase (TIM) and its substrate D-glyceraldehyde—3-phosphate (GAP) to demonstrate the capabilities of Brownian dynamics simulations with electrostatics. TIM is a glycolytic enzyme that catalyzes the interconversion of GAP and dihydroxy-acetone phosphate (DHAP). It has been described as an almost perfea catalyst because of its remarkable efficiency. Structurally, TIM is a dimeric enzyme consisting of two identical polypeptide chains of 247 amino acid residues. Each subunit consists of eight loop-p/loop-a units and contains one aaive site. Located near each aaive site is a peptide loop, which is mobile in the native enzyme and folds down to cover the active site when the substrate is bound. Kinetically, the reaction appears to be diffusion controlled and proceeds with a measured rate constant of 4.8 x 10 M s L TIM has consequently been the focus of many kinetic and struaural studies. ... 

The subunit-subunit interaction must be important in the assembly process. It is worth noting that in the case of glyceraldehyde-3-phosphate dehydrogenase the amino acids in the subunit interface are far more conserved than other amino acids elsewhere in that enzyme 189). If this... 

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