Biosynthetic pathways committed step

Triterpenoid saponins are synthesized via the isoprenoid pathway.4 The first committed step in triterpenoid saponin biosynthesis involves the cyclization of 2,3-oxidosqualene to one of a number of different potential products (Fig. 5.1).4,8 Most plant triterpenoid saponins are derived from oleanane or dammarane skeletons although lupanes are also common 4 This cyclization event forms a branchpoint with the sterol biosynthetic pathway in which 2,3-oxidosqualene is cyclized to cycloartenol in plants, or to lanosterol in animals and fungi. 

Metabolic control can be understood to some extent by focusing attention on those enzymes that catalyze rate-limiting steps in a reaction sequence. Such pacemaker enzymes1-4 are often involved in reactions that determine the overall respiration rate of a cell, reactions that initiate major metabolic sequences, or reactions that initiate branch pathways in metabolism. Often the first step in a unique biosynthetic pathway for a compound acts as the pacemaker reaction. Such a reaction may be described as the committed step of the pathway. It usually proceeds with a large decrease in Gibbs energy and tends to be tightly controlled. Both the rate of synthesis of the enzyme protein and the activity of the enzyme, once it is formed, may be inhibited by feedback inhibition which occurs when an end product of a biosynthetic pathway accumulates... 

The first committed step in the biosyntheses of these compounds is the hydrolytic opening of the imidazole ring of GTP, which affords a diaminopyrimidine-type intermediate. In the biosynthetic pathways of folate, tetrahydrobiopterin, and methanopterin (34), the respective diaminopyrimidine intermediate undergoes ring closure by means of an intramolecular condensation that involves parts of the ribose side chain of GTP, which affords a 2-amino -pteridinone compound (29). 

In a biosynthetic pathway, the first irreversible reaction, called the committed step, is usually an important regulatory site. The final product of the pathway (Z) often inhibits the enzyme that catalyzes the committed step (A—>B). 

Figure 24.21. Structure of 3-Phosphoglycerate Dehydrogenase. This enzyme, which catalyzes the committed step in the serine biosynthetic pathway, includes a serine-binding regulatory domain. Serine binding to this domain reduces the activity of the enzyme.

Even prior to the elucidation of the first committed step of the riboflavin pathway, it had been shown that the benzenoid ring of riboflavin is assembled from two identical 4-carbon precursors. More specifically, the final step in the biosynthesis of the vitamin involves a dismutation of 6,7-dimethyl-8-ribityllumazine (6), where one of the substrate molecules serves as donor and the other as acceptor of a 4-carbon segment.19,20 6,7-Dimethyl-8-ribityllumazine, in turn, is formed in the penultimate step of the biosynthetic pathway from 5-amino-6-ribitylamino-4(3f/)-pyrimidinedione (3), an intermediate that is obtained from the product of GTP cyclohydrolase II by a sequence of deamination, side chain reduction, and dephosphorylation (Figure 3). The nature of the 4-carbon precursor required for the formation of 6,7-dimethyl-8-ribityllumazine (6) from 5-amino-6-ribitylamino-4(3f/)-pyrimidinedione (3) remained controversial for quite a long period, with working hypotheses including, but not limited to, tetroses, pentoses, and acetoin. 

Figure 2. The mevalonic acid biosynthetic pathway. The transformation of hy-droxymethyl-coenzyme A (HMG-CoA) to mevalonic acid is the first committed step of the pathway. The enzyme, HMG-CoA reductase, catalyzes this step and is inhibited by the compounds, mevinolin and compactin. Note that farnesyl-pyrophosphate (Farnesyl-PP), the substrate of the protein, farnesyltransferase, can be used to make cholesterol or elongated to make geranylgeranyl-pyrophosphate (Geranylgeranyl-PP). The later compound is the substrate for the protein, geranylgeranyltransferase, or is further elongated to make the long-chain isoprenoids, dolichols, ubiquinones, and isoprenoic acids.

Figure 4. Biosynthetic pathways of eicosanoid production. Unesterified arachidonic acid is oxygenated by cyclooxygenase or by 5-, 12-, or 15-lipoxygenases. Cyclooxygenase catalyzes the incorporation of two molecules of molecular oxygen into arachidonic acid and is the first committed step for the production of prostaglandins and thromboxanes. Alternatively, incorporation of one molecule of oxygen into the 5-position of arachidonic acid (as catalyzed by 5-lipoxygenase) is the first committed step in leukotriene biosynthesis.

Figure 5. Biosynthetic pathways for diacyl, plasmalogen and alkyl-ether molecular subclasses of phospholipids. Monoacyl dihydroxyacetone phosphate is the key branch-point intermediate whose utilization determines the phospholipid subclass distribution of newly synthesized phospholipids. Reduction of monoacyl dihydroxyacetone phosphate leads to the biosynthesis of diacyl phospholipids. Fatty alcohol exchange, catalyzed by alkyl dihydroxyacetone phosphate synthase, is the first committed step in the biosynthesis of alkyl-ether and plasmalogen subclasses of phospholipids.

The present information on the riboflavin biosynthetic pathway is summarized in Figure 1. Briefly, the pathway starts from GTP (1), which is converted into the first committed intermediate 2 by the hydrolytic release of pyrophosphate and of C-8 of the imidazole ring that are both catalyzed by a single enzyme, GTP cyclohydrolase II (reaction I). In Archaea and in fungi, that compound is transformed into 5-amino-6-ribitylamino-2,4(li/,3f/)-pyrimidinedione phosphate (5) by a reduction (reaction IV) that transforms the ribosyl side chain into the ribityl side chain (4) and by subsequent deamination (reaction V) of the pyrimidine ring yielding compound 5. In plants and in eubacteria (reactions II and III), these reaction steps occur in inverse order via the ribosylaminopyrimidine derivative 3. 

Squalene synthase is an enzyme catalyzing the formation of squalene from farnesyl diphosphate which is a committed step in the cholesterol biosynthetic pathway. Therefore, squalene synthase is considered a better target than HMG-CoA reductase because farnesyl pyrophosphate, a downstream product of HMG-CoA reductase, is needed for prenylation of proteins and for the biosyntheses of ubiquinone and dolichol (Fig. 2). Before squalestatins and zaragozic acids were discovered, a number of squalene synthase inhibitors were synthesized that showed respectable inhibitory potencies in vitro, but none were successful in animal testing [41]. It was the discovery of squalestatins and zaragozic acids that renewed interest in this biological target, and at picomolar potencies they were the most active inhibitors of squalene synthase. 

As purines are built on a ribose base (see Fig. 41.2), an activated form of ribose is used to initiate the purine biosynthetic pathway. 5-Phosphoribosyl-l-pyrophosphate (PRPP) is the activated source of the ribose moiety. It is synthesized from ATP and ribose 5 -phosphate (Fig. 41.3), which is produced from glucose through the pentose phosphate pathway (see Chapter 29). The enzyme that catalyzes this reaction, PRPP synthetase, is a regulated enzyme (see section 1I.A.5) however, this step is not the committed step of purine biosynthesis. PRPP has many other uses, which are described as the chapter progresses. 

In the first committed step of the purine biosynthetic pathway, PRPP reacts with glutamine to form phosphoribosylamine (Fig. 41.4). This reaction, which produces nitrogen 9 of the purine ring, is catalyzed by glutamine phosphoribosyl amido-transferase, a highly regulated enzyme. 

The committed step of purine synthesis is the formation of 5-phosphoribosyl 1-amine by glutamine phosphoribosyl amidotransferase. This enzyme is strongly inhibited by GMP and AMP (the end products of the purine biosynthetic pathway). The enzyme is also inhibited by the corresponding nucleoside di- and triphosphates, but under cellular conditions, these compounds probably do not play a central role in regulation. The active enzyme is a monomer of 133,000 daltons but is converted to an inactive dimer (270,000 daltons) by binding of the end products. 

A —> B. Control of the first step conserves the hrst compound. A, in the sequence and also saves metabolic energy by preventing subsequent reactions in the pathway. Compound G would likely inhibit the committed step. The end product of a biosynthetic pathway often controls the committed step. 

What is the committed step in purine biosynthesis and which of the following compounds are involved in the control of the purine biosynthetic pathway ... 

Feedback control. The binding of metaboUtes, i.e. substrates/products or effectors to enzymes is an important mode of regulation. Feedback inhibition (negative feedback control) is an important example, in which the first committed step in a biosynthetic pathway is inhibited by the ultimate end product of the pathway (Stadtman, 1966). Table 11.14 summarizes different modes of negative feedback controls that have been evolved to accommodate the regulation of divergent metabolic pathways. 

The first committed step in the biosynthetic pathway of the branched chain amino acids is catalyzed by the enzyme acetohydroxyacid synthase (AHAS, EC 2.2.1.6), which is also referred to as acetolactate synthase (ALS). As depicted in Fig. 2.1.1, the pathway leading to valine and leucine begins with the condensation of two molecules of pyruvate accompanied by loss of carbon dioxide to give (S)-2-acetolactate. A parallel reaction leading to isoleucine involves the condensation of pyruvate with 2-ketobutyrate to afford (S)-2-aceto-2-hydroxybutyrate after loss of carbon dioxide. Both reactions are catalyzed by AHAS, which requires the cofactors thiamin diphosphate (ThDP) and flavin adenine dinudeotide (FAD). A divalent metal ion, most commonly is also required. Several excellent reviews... 

The reaction catalyzed by acetyl-CoA carboxylase satisfies the accepted criteria for a regulatory step in a biosynthetic process [142-147]. This reaction occurs early in the pathway and is the first committed step, malonyl-CoA having no other apparent metabolic alternative. 

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