Naming enzymes

Reactions can also be searched by enzymes, either by enzyme name or enzyme class (EC notation), both in specific or in generic form. Table 10.3-1 shows the results of searching for EC classes. 

The hepatitis B virus (HBV) genome is one of the smallest viral genomes (approximately 3,200 base pairs) and encodes only one viral enzyme, namely the HBV reverse transcriptase (RT). Like the HIV RT, the HBV RT is an error-prone enzyme lacking proofreading activity. In combination with a high virus production, this results in an HBV quasispecies. 

In many cases, the racemization of a substrate required for DKR is difficult As an example, the production of optically pure cc-amino acids, which are used as intermediates for pharmaceuticals, cosmetics, and as chiral synfhons in organic chemistry [31], may be discussed. One of the important methods of the synthesis of amino acids is the hydrolysis of the appropriate hydantoins. Racemic 5-substituted hydantoins 15 are easily available from aldehydes using a commonly known synthetic procedure (Scheme 5.10) [32]. In the next step, they are enantioselectively hydrolyzed by d- or L-specific hydantoinase and the resulting N-carbamoyl amino acids 16 are hydrolyzed to optically pure a-amino acid 17 by other enzymes, namely, L- or D-specific carbamoylase. This process was introduced in the 1970s for the production of L-amino acids 17 [33]. For many substrates, the racemization process is too slow and in order to increase its rate enzymes called racemases are used. In processes the three enzymes, racemase, hydantoinase, and carbamoylase, can be used simultaneously this enables the production of a-amino acids without isolation of intermediates and increases the yield and productivity. Unfortunately, the commercial application of this process is limited because it is based on L-selective hydantoin-hydrolyzing enzymes [34, 35]. For production of D-amino acid the enzymes of opposite stereoselectivity are required. A recent study indicates that the inversion of enantioselectivity of hydantoinase, the key enzyme in the... 

Restriction enzymes are named after the bacterium from which they are isolated. For example, EcoRI is from Escherichia coli, and BamEII is from Bacillus amyloliquefaciens (Table 40-2). The first three letters in the restriction enzyme name consist of the first letter of the genus (E) and the first two letters of the species (co). These may be followed by a strain designation (R) and a roman numeral (I) to indicate the order of discov-ery (eg, EcoRI, EcoRIE). Each enzyme recognizes and cleaves a specific double-stranded DNA sequence that is 4—7 bp long. These DNA cuts result in blunt ends (eg,... 

Enzymes are usually named in terms of the reaction that is catalyzed, commonly adding the suffix -ase to the name of the stoichiometrically converted reactant or substrate. For instance, an enzyme that catalyses the hydrolysis of urea is urease. Enzyme names can only be applied to single enzymes, especially those with termination -ase. For systems that involve the action of two or more enzymes the use of the term should be avoided and the word system should be included. 

Enzymes are named by a systematic set of rules that nobody follows. The only given is that enzyme names end in -ase and may have something in them that may say something about the type of reaction they catalyze—such as chymotrypsin, pepsin, and enterokinase (all proteases). 

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.

More recently, a novel type of halogenating enzyme, named hydroperoxide halolyase, which generates halogenated aldehydes, has been described in the marine diatom Stephanopyxis turris (Wichard and Pohnert 2006). In other microalgae, halogenation of organic compounds was shown to mainly involve methyl halide transferases (Moore et al. 1996 Manley 2002), and no vHPO has yet been identified on genomic data obtained from diatoms (Scala et al. 2002 Armbrust et al. 2004). Clearly, these emissions are not directly associated with an oxidative burst. 

A final word needs to be said about the supposedly unique features of enzymes, namely, their ability to produce enantiomerically pure products. This is not the place to speculate about the stereospecificity of enzymes, a problem that has been discussed elegantly by Comforth (15). It cannot be denied that the high (>99.9%) enantiomeric purity achieved by enzymes may be uniquely useful in the case of liquid products. However, when crystalline products are obtained in an asymmetric synthesis and the e.e. exceeds 80%, crystallization to enantiomeric purity without excessive loss of material is routinely achieved. 

Fig. 6.11. Peptide prodrugs (6.20, 6.21, and 6.22) for the intestine-selective delivery of 5-aminosalicylic acid (6.23). The prodrugs undergo selective activation by intestinal brush border enzymes, namely aminopeptidase A and/or carboxypeptidases [39].

Two cases have been selected here to illustrate the targeting of pathologically overexpressed enzymes, namely peptidases overexpressed in infected wounds and in tumors. 

The catalysis takes place in a specific region of the enzyme named the active site or catalytic cavity. This active site involves those amino acid residues (i.e., side chains) directly implicated in the mode of binding and the specificity of the substrate, as well as in the catalytic process itself. 

Both xenobiotics and endogenous substrates are primarily metabolized by a super-family of enzymes, named cytochrome F450s (CYP450s,... 

NADH (reduced nicotinamide adenine dinucleotide) is utilized in biological reductions to deliver hydride to an aldehyde or ketone carbonyl group (see Box 7.6). A proton from water is used to complete the process, and the product is thus an alcohol. The reaction is catalysed by an enzyme called a dehydrogenase. The reverse reaction may also be catalysed by the enzyme, namely the oxidation of an alcohol to an aldehyde or ketone. It is this reverse reaction that provides the dehydrogenase nomenclature. 

In addition to the enzyme name, we also usually give its EC number. The annotated enzyme list (pp.420ff) includes all of the enzymes mentioned in this book, classified according to the Enzyme Catalog system. 

In addition, at each step the four-figure EC number (see p. 88) for the enzyme responsible for a reaction is given in italics. The enzyme name and its systematic classification in the system used by the Enzyme Catalogue are available in the following annotated enzyme list (pp. 420-430), in which all of the enzymes mentioned in this book are listed according to their EC number. The book s index is helpful when looking for a specific enzyme in the text. 

Only the enzymes mentioned in this atlas are listed here, from among the more than 2000 enzymes known. The enzyme names are based on the iUBlVlB s of dal Enzyme nomenclature 1992. The additions shown in round brackets belong to the enzyme name, while prosthetic groups and other cofactors are enclosed in square brackets. Common names of enzyme groups are given in italics, and trivial names are shown in quotation marks. 

To avoid the undesirable effects of excess cholinergic stimulation, ACh is rapidly hydrolyzed after its release at the synapse by an enzyme named acetylcholinesterase AChE. A similar enzyme, butylcholinesterase BuChE also occurs. If the cholinesterase is inhibited, the ACh is not hydrolyzed so rapidly, and levels of ACh rise. 

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