Enzymes enzyme-catalyzed reactions, classes

The EC number contains four numerical elements each separated by points. For example, alcohol dehydrogenase is assigned the number EC 1.1.1.1. The first numerical element (the furthest one to the left) identifies which of the six main classes the enzyme belongs. For alcohol dehydrogenase, this class is the oxidoreductases. The second element identifies the subclass for EC 1.1.x.x, this refers to oxidoreductases acting on the CH—OH group of donors. The third element identifies the sub-sub-class for EC 1.1.1.x this refers to oxidoreductases that use NAD or NADP+ as the acceptor. The final sub-sub-sub-class is unique for that enzyme-catalyzed reaction. 

A class of compounds in which a positively charged atom from group V or VI of the periodic table (c.g., N, O, S, P, As, Se) is bonded to a carbon atom having an unshared pair of electrons. Whereas there is only one canonical form for nitrogen ylides (R3N —CR2 ), because of pTT-dTT bonding, two canonical forms can be written for phosphorus Le., R3P=CR2 R3P —CR2 ) and sulfur ylides (R2S=CR2 R3S —CR2 ). A number of enzyme-catalyzed reactions have been reported to utilize ylide-based chemistry. For example, the ylide form of the... 

Many enzymes catalyze reactions with two interacting substrates, and although the kinetics of these reactions are more complex than those of one-substrate reactions, they still obey Michaelis-Menten kinetics. Reactions of the type A + B <= P + Q usually fall within either of two classes with respect to kinetic behavior and mechanism of action. 

There is also a separate expert system for the combination with MultiCASE, which predicts the possible metabolites, formed of a compound. This system is known as META, which was developed to identify molecular sites susceptible to metabolic transformation. The metabolism dictionary associated with META is able to recognize 663 enzyme-catalyzed reaction rules, which have been categorized into 29 enzyme-reaction classes and 286 spontaneous reactions (Klopman and Rosenkranz 1994). 

Lipases are a special class of esterases that also catalyze the hydrolytic cleavage of ester bonds, but differ in their substrate spectrum. Lipases have the special capability to catalyze the hydrolysis of water-insoluble substrates such as fats and lipids. Like many other enzyme-catalyzed reactions, the ester hydrolysis is a reversible process, which allows using lipases and other esterases for the synthesis of esters. The use of lipases as catalysts in synthetic chemistry is described elsewhere in this chapter. 

Zha D, Wilensek S, Hermes M, Jaeger K-E, Reetz MT (2001) Complete reversal of enantioselectivity of an enzyme-catalyzed reaction by directed evolution. Chem Commun (Cambridge UK) 2664-2665 Zou JY, Hallberg BM, Bergfors T, Oesch F, Arand M, Mowbray SL, Jones TA (2000) Structure of Aspergillus niger epoxide hydrolase at 1.8 resolution Implications for the structure and function of the mammalian microsomal class of epoxide hydrolases. Structure (London) 8 111-122... 

In Section 3.2 we introduced the basic processes of advection, diffusion, and drift, by which material is transported in biophysical systems. In this chapter we focus on a specialized class of transport transport across biological membranes. Transport of a substance across a membrane may be driven by passive permeation, as described by Equation (3.60), or it may be facilitated by a carrier protein or transporter that is embedded in the membrane. Thus transport of substances across membranes mediated by transporters is termed carrier-mediated transport. The most basic way to think about carrier proteins or transporters is as enzymes that catalyze reactions that involve transport. 

A veiy important aspect of chemical kinetics is that dealing with the rates of enzyme-catalyzed reactions. Enzymes are a class of proteins that catalyze virtually all biochemical reactions. In this experiment we shall study the inversion of sucrose, as catalyzed by the enzyme invertase (/3-fractofuranidase) derived from yeast. The rate of the enzyme-catalyzed reaction will then be compared to that of the same reaction catalyzed by hydrogen ions. 

Present-day structures of proteins provide some hints on the role of gene duplications in evolution. Proteins commonly occur in families. These are structurally related enzymes catalyzing reactions of the same class with different substrate specificities. Examples are families of proteases or dehydrogenases. In addition to this, one observes interesting regularities in the structures of many globular proteins Substructures (so-called motifs) are often repeated exactly or with minor modifications only. Such repetitions were found in the same protein molecule as well as in different protein molecules. Both the modular structure of polymers as well as the existence of protein families can be explained by a gene duplication mechanism. 

Six classes of enzyme-catalyzed reaction are recognized in systematic nomenclature [61]. Their names and the type of chemical reaction catalyzed by each are indicated in Table 4.1. All enzymes have systematic names based on the above, but many are known by historically important trivial names e.g. trypsin, chymo-trypsin, pepsin, lysozyme, catalase. 

The first applications of enzymes in bioanalytical chemistry can be dated back to the middle of nineteenth century, and they were also used for design of first biosensors. These enzymes, which have proved particularly useful in development of biosensors, are able to stabilize the transition state between substrate and its products at the active sites. Enzymes are classified regarding their functions, and the classes of enzymes are relevant to different types of biosensors. The increase in reaction rate that occurs in enzyme-catalyzed reactions may range from several up to e.g. 13 orders of magnitude observed for hydrolysis of urea in the presence of urease. Kinetic properties of enzymes are most commonly expressed by Michaelis constant Ku that corresponds to concentration of substrate required to achieve half of the maximum rate of enzyme-catalyzed reaction. When enzyme is saturated, the reaction rate depends only on the turnover number, i.e., number of substrate molecules reacting per second. 

Some of the natural extensions of this classical approach include the treatment of mechanisms with multiple intermediate complexes and near-equilibrium conditions (e.g., Peller and Alberty, 1959). Enzyme-catalyzed reactions that involve two substrates and two products are among the most common mechanisms found in biochemistry (about 90% of all enzymatic reactions according to Webb, 1963). It is not surprising, then, that this class of mechanisms also has received a great deal of attention (e.g., Dalziel, 1957,1969 Peller and Alberty, 1959 Bloomfield et al., 1962a,b Cleland, 1963a,b,c). This class includes mechanisms in which reactant molecules enter and exit a single pathway in fixed order and mechanisms with parallel pathways in which reactant molecules enter and exit in a random order (Cleland, 1970). 

Monooxvgenases. These enzymes are important in the detoxication of pyrethroid, carbamate, organophosphorus and other classes of insecticides (2). They are microsomal, membrane associated enzymes which catalyze reactions in which one atom from molecular oxygen is inserted into the insecticide and the second oxygen atom is reduced to form water. Catalysis depends on the close association of the heme-containing cytochrome P450 terminal oxidase with NADPH cytochrome C reductase for electron transport, and it also depends on availability of NADPH and oxygen. 

It is estimated that approximately one-third of all enzyme-catalyzed reactions require a metal ion or ions for catalytic activity. The functions of these metal ions can be placed in three broad categories (1) structural integrity (no specific catalytic function), (2) electron transfer reactions, and (3) electrophilic catalysis. The latter of these broad classes of function/structure will be the focus of this chapter, in which we will explore current data and theories of metalloenzyme catalysis. 

There are, however, clear stereomechanistic differences between these two classes of enzyme-catalyzed reactions. The Claisen-type condensations uniformly involve inversion of configuration at the a-carbon of the esteratic substrate, involving C-C bond formation at either the re or the si face of the ketonic or aldehydic substrate (Table VII) (196-211). Moreover, neither Schiff bases nor metal ions have been directly implicated in the catalytic mechanisms of these enzymes. Unlike the aldolases, these enzymes do not catalyze rapid enolization of the nucleophilic substrate in the absence of the second substrate. Inversion of configuration suggests that at least two catalytic groups, perhaps operating in concert, facilitate C-C bond formation. Physicochemical measurements on citrate synthase are consistent with this interpretation of inversion of configuration. 

The X-ray crystal structure of P. putida muconate lactonizing enzyme (cycloisomerase) was determined in 1987, and was found to contain an a/(i barrel fold, also found in triosephosphate isomerase and enolase. Remarkably, the structure of P. putida mandelate racemase, which catalyzes a mechanistically distinct reaction earlier in the same pathway, was found in 1990 to have a homologous structure, indicating that the structural fold of the enolase superfamily is able to support a range of enzyme-catalyzed reactions. The P. putida 3-carboxy- r, x-muconate lactonizing enzyme, in contrast, shares sequence similarity with a class II fumarase enzyme, and determination of its structure in 2004 has shown that it shares the same fold as the class II fumarase superfamily, hence these two catalysts of similar reactions have evolved from different ancestors. ... 

Superoxide dismutases are a class of enzymes that catalyze reactions similar to the one below ... 

Erie, D. 1981. Nonuniqueness of stable limit cycles in a class of enzyme catalyzed reactions./. Math. Anal. Applic. 82 386-91. 

Isomers that result from different arrangements of four different groups around the same carbon atom represent another class of stereoisomers called optical isomers. Optical isomers have the same physical and chemical properties, except in chemical reactions where chirality is important, such as enzyme-catalyzed reactions in biological systems. Human cells, for example, incorporate only L-amino acids into proteins. Only the L-form of ascorbic acid is active as vitamin C. The chirality of a drug molecule can also be important. For example, only one isomer of some drugs is effective and the other isomer can be harmful. 

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