Enzymes, abbreviations, substrates

Fibrinolytics. Figure 3 Plasminogen activation (a) Kinetics of plasminogen activation by uPA (urokinase-type) and tPA (tissue-type) plasminogen activators. Effect of fibrin (b) Ternary complex formation between enzyme (tPA), substrate (Pg) and cofactor (F) Abbreviations plasmin (P), fibrin (F), plasminogen (Pg). Plasmin, formed in time, is expressed in arbitrary units. 

Figure 5.4. Abbreviated scheme for biosynthesis of major flavonoid subclasses, showing the primary enzymes and substrates leading to different subclasses. Bold-faced, uppercase abbreviations refer to enzyme names, whereas substrate names are presented in lowercase letters. PAL, phenylalanine ammonia lyase C4H, cinnamate 4-hydroxylase 4CL, 4-coumarate CoA ligase CHS, chalcone synthase CHI, chalcone isomerase CHR, chalcone reductase IPS, isoflavone synthase F3H, flavonone 3-hydroxylase F3 H, flavonoid 3 -hydroxylase F3 5 H, flavonoid 3 5 -hydroxylase FNSI/II, flavone synthase DFR, dihydroflavonol 4-reductase FLS, flavonol synthase ANS, anthocyanidin synthase LAR, leucoanthocyanidin reductase ANR, anthocyanidin reductase UFGT, UDP-glucose flavonoid 3-O-glucosyltransferase. R3 = H or OH. R5 = H or OH. Glc = glucose. Please refer to text for more information.

The first reaction in the direction of the protoberberines is the formation of the berberine bridge (Fig. 2), catalyzed by the berberine bridge enzyme (abbreviated BBE), which specifically only accepts (S)-reticuline and not the (R)-enantiomer as substrate (ref. 23). As a next step a methylation at C-9 follows to form (S)-tetrahydrocolumbamine catalyzed by a methyltransferase with a much higher substrate specificity than the methyltransferases described before (ref. 24). In the genus Berberis (S)-tetrahydrocolumbamine is then oxidized by an enzyme called (S)-tetrahydroprotoberberine oxidase (abbreviated STOX) (ref. 25) and finally the methylene dioxy bridge is formed by the so called berberine synthase (ref. 26). 

Phosphatidylinositol (abbreviated Ptdlns, or PI) is a minor class of phospholipids composed of glycerol, fatty acids and inositol. Pis are found in the cytosolic side of eukaryotic cell membranes. They are substrates fora large number of enzymes which are involved in cell signalling. 

The Enzymes II (E-IIs) of the phosphoenolpyruvate (P-enolpyruvate)-dependent phosphotransferase system (PTS) are carbohydrate transporters found only in prokaryotes. They not only transport hexoses and hexitols, but also pentitols and disaccharides. The PTS substrates are listed in Table I. The abbreviations used (as superscripts) throughout the text for these substrates are as follows Bgl, jS-gluco-side Cel, cellobiose Fru, fructose Glc, glucose Gut, glucitol Lac, lactose Man, mannose Mtl, mannitol Nag, iV-acetylglucosamine Scr, sucrose Sor, sorbose Xtl, xylitol. 

In a sequential reaction, all the substrates must be bound to the enzyme before any release of product can occur. Sequential systems can be either ordered or random. In an ordered sequential reaction, substrates must bind to the enzyme in a particular order, whereas in a random sequential system, substrates may bind to the enzyme in any order. In reaction schemes, substrates are usually abbreviated as A, B, C, and D in the order that they bind to the enzyme, whereas products are abbreviated as P, Q, R, and S in the order that they leave the enzyme. Sequential binding of substrates is a consequence of their orientation within the enzyme active site. 

Figure 2. Free energy profile for converting di hydroxy acetone phosphate, the substrate (abbreviated S) and glyceraldehyde 3-phosphate, the product (abbreviated P), with intermediate formation of the enedi-olate (abbreviated Z). Catalysis occurs either by a free carboxyl group (levels connected by dotted lines) or by triose-phosphate isomerase (levels connected by dashed lines). The vertical arrows show the limits of those states that are less well defined as a result of uncertainty in the experimental data. The transition state marked "e" refers to the exchange of protons between the solvent and the enzyme-bound enediol intermediate (EZ). Reproduced with permission of the authors and the American Chemical Society.

Reversible competitive inhibition is also common. This impairment of an enzyme is due to the fact that the inhibitor (drug or poison or even natural material) looks like the normal substrate for the enzyme. Using the abbreviations E, S and I for enzyme, substrate and inhibitor, respectively,... 

Fatty acid synthesis begins when the substrates, acetyl-CoA and malonyl-CoA, are transferred onto the protein by malonyl-CoA acetyl-CoA-ACP transacylase (MAT, steps 1 and 2 in fig. 18.12a). The numbers in parentheses below the abbreviation of the enzyme in this figure refer to the reactions shown in fig. 18.12. (Whereas E. coli has separate enzymes that catalyze the transfer of acetyl- and malonyl-CoA to ACP, both reactions are catalyzed by the same enzymatic activity (MAT) on the animal fatty acid synthase.) Subsequently, /3-ketobutyryl-ACP and CO2 are formed in a condensation reaction catalyzed by /3-ketoacyl-ACP synthase (KS, step 3 in fig. 18.12a). 

Various lipases and esterases have been used for the enantioselective esterification of alcohols and hydrolysis of esters. For example, Burkholderia cepacia lipases (PS, Amano Enzyme Inc.) and Candida antarctica lipase (CAL, Novozymes) have been widely used for its wide substrate specificities, high activities and chemo, regio and enantioselectivities. Fundamentals and some selected applications are shown in this section. The origins and abbreviations of lipases introduced here are as follows. 

The reactants of enzyme-catalyzed reactions are termed substrates and each enzyme is quite specific in character, acting on a particular substrate or substrates to produce a particular product or products. The names of enzymes usually indicate the substrate involved. For example, hydrogen peroxide oxidoreductase is an enzyme that uses hydrogen peroxide as its substrate to carry out the oxidation of organic substrates. Such formal names are often abbreviated such as in the contraction of hydrogen peroxide oxidoreductase to peroxidase. However, in the interest of avoiding... 

Fig. 5.9. Proposed scheme for the intramitochondrial metabolism of malate by Hymenolepis diminuta. Abbreviations ME, malic enzyme F, fumarase T, transhydrogenase FR, fumarate reductase ETS, electron transport system. Once within the matrix compartment, malate oxidation, as catalysed by malic enzyme, results in NADPH formation. Via the activity of fumarase, malate also is converted to fumarate in the matrix compartment. NADPH then serves as a substrate for the inner-membrane-associated transhydrogenase and transhydrogenation between NADPH and matrix NAD is a scalar reaction associated with the matrix side of the inner membrane. Matrix NADH so formed reduces the electron transport system via a site on the matrix side of the inner membrane permitting fumarate reductase activity. The reduction of fumarate to succinate results in succinate accumulation within the matrix compartment. (After McKelvey Fioravanti, 1985.)...

Glutathione metabolic pathway The genes for which expression was studied in fibroblast cultures from skin biopsies are shown in black box (no difference between controls and patients) or in dark grey box (lower expression in patents compared to controls). These genes code for the enzymes shown in unhighlighted text. Substrates and products are in light grey box. Abbreviations are as in the text... 

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