EC nomenclature for enzyme

EC nomenclature for enzymes A classification of ENZYMES according to the Enzyme Commission of the International Union of Biochemistry and Molecular Biology. Enzymes are allocated four numbers, the first of which defines the type of reaction catalyzed the next two define the substrates, and the fourth is a catalogue number. Categories of enzymes are EC 1, oxidoreduc-tases EC 2, transferases EC 3, hydrolases EC 4, lyases EC 5, isomerases EC 6, ligases (Synthetases). 

Enzymes are biological catalysts, all of which are proteins, except for a class of RNA-modifying catalysts known as ribozymes ribozymes are molecules of ribonucleic acid that catalyse reactions on the phosphodiester bond of other RNAs. The International Union of Biochemistry and Molecular Biology have developed a nomenclature for enzymes, the EC numbers each enzyme is described by a sequence of one of four numbers preceded by EC . The first number broadly classifies the enzyme based on its mechanism. 

To bring some consistency to the classification of enzymes, in 1964 the International Union of Biochemistry established an Enzyme Commission to develop a nomenclature for enzymes. Reactions were divided into six major groups numbered 1 through 6 (Table 8.3). These groups were subdivided and further subdivided, so that a four-digit number preceded by the letters EC for Enzyme Commission could precisely identify all enzymes. 

In the literature of PVA biodegradation, the orientation with respect to the enzymatic activities that are described is not clear-cut and sometimes even perplexing. This originates in the historical development of the field that gave rise to the nomenclature used today. Table 2 aims to give a clear denomination of the enzymes that are directly involved in the biodegradation of PVA, and that are cited in the literature so far. As an unambiguous denomination for enzyme activity, the Enzyme Commission number (EC number) is used. Every EC number is... 

This URL is an update of the IUBMB recommendations of names for enzymes. This site is the responsibility of the Nomenclature Committee of NC-IUBMB. This section gives balanced equations for enzyme-catalyzed reactions and certain references and information, arranged by EC number. Links are provided to BRENDA, EXPASY, GDT, KEGG, UM-BBD, ERGO, and PDP. 

Since the full enzyme name according to the EC nomenclature is rather long, the most commonly used enzymes have gotten abbreviations. For esterases and lipases there are certain rules in most cases, the first (two or three) letters characterize the source, the last the type of enzyme (E for esterase, L for lipases) (see Table 20-1). Alcohol dehydrogenases are treated similarly. 

Underneath the EC name, synonyms are given. The general reaction according EC nomenclature is denoted too. Afterwards, the product (enzyme) names are listed, one entry for each manufacturer per enzyme. If the product is sold under a brand name, this name is listed too. In one enzyme class, the entries are sorted by origin. 

NOS III e-NOS (for endothelial NOS) c-NOS (for constitutive or Ca -regulated NOS overlap with nomenclature for NOS I) ec-NOS or EC-NOS (for endothelial constitutive NOS) This isoform is constitutively expressed and its activity is regulated by Ca the prototypical enzyme is present in endothelial cells... 

Thus, the EC numbers provide unique identifiers for enzyme functions, and give us useful keyword entries in database searches (http //www.chem.qmw.ac.uk/iubmb/ enzyme/). Enzyme nomenclature/common names and properties are also available at ENZYME (http //www.expasy.org/enzyme) and BRENDA (http //www.brenda.uni-koeln. de). IntEhz (http //www.ebi.ac.uk/intenzy) is the integrated enzyme database and enzyme nomenclature. Table 11.1 lists some enzyme resource sites providing general information. 

Enzyme classification is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (lUBMB)", and it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided. EC classes define enzyme function based on the reaction, which is catalyzed by the enzyme. The classification scheme is hierarchical, with four levels. There are six broad categories of function at the top of this hierarchy and about 3500 specific reaction types at the bottom. EC classes are expressed... 

Biochemical nomenclature of enzymes [28] usually follotvs historical classifications that are different from the needs of synthetic organic chemists today. Whereas the common EC numbers are valuable for reference, in this overview an enzyme designation w ill be used that utilizes a three-letter code as reference to the natural substrate (from w hich usually stereochemistry is immediately obvious), follow ed by a single capital letter that indicates the conversion type (e.g., aldolases (A), synthases (S), isomerases (I), dehydrogenases (D), oxidases (O), kinases (K), (glycosyl)transferases (T), epimerases (E)etc.) [25]. 

A comprehensive list of all annotated transport proteins is freely available online on the TCDB website (http //www.tcdb.org). This Transporter Classification Database uses an International Union of Biochemistry and Molecular Biology (lUBMB) approved system of nomenclature for transport protein classification. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, except that it incorporates both functional and phylogenetic information (Saier et al., 2006 Saier et al., 2009). 

Another field in which nomenclature has grown up haphazardly is that of the enzymes of lipid metabolism. This has now been formalized to some extent under the Enzyme Commission (EC) nomenclature. The system is incomplete and not all lipid enzymes have EC names and numbers. Moreover, the system is very cumbersome for routine use and we have decided not to use it here. You will find a reference to this nomenclature in the reading list should you wish to learn about it. Enzymes that catalyse the biosynthesis of certain molecules are sometimes called synthetases or alternatively synthases. We shall standardize on the term synthetase in this book. 

According to the IUPAC-IUB Enzyme Nomenclature,11 pectinesterase belongs to the carboxyl ester hydrolases (EC 3.1.1.11) and has the systematic name pectin pectyl-hydrolase. The literature also contains the expressions pectin methylesterase, pectin demethoxylase, and pectin methoxylase for the same enzyme. The old name pectase,... 

One of the general principles of the Nomenclature Committee is that enzymes should be classified and named according to the reaction they catalyze. However, the overlapping specificities of and great similarities in the action of different peptidases render naming solely on the basis of function impossible [10]. For example, some enzymes can act as both endo- and exopeptidases. Thus, cathepsin H (EC 3.4.22.16) is not only an endopeptidase but also acts as an aminopeptidase (EC 3.4.11), and cathepsin B (EC 3.4.22.1) acts as an endopeptidase as well as a peptidyl-dipeptidase (EC 3.4.15). The actual classification of peptidases is, therefore, a compromise based not only on the reaction catalyzed but also on the chemical nature of the catalytic site, on physiological function, and on historical priority. 

NAD(P)+ as Anode Mediator. A majority of redox enzymes require the cation nicotinamide adenine dinucleotide, possibly phosphorylated (NAD(P)+) as a cofactor. Of the oxidoreductases listed in Enzyme Nomenclature, over 60% have NAD(P)+ as a reactant or product.For example, methanol can be oxidized to form formaldehyde by methanol dehydrogenase (MDH, EC 1.1.1.244) according to... 

Since its foundation in 1956 the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) has continually revised and updated the list of enzymes. Entries for new enzymes have been added, others have been deleted completely, or transferred to another EC number in the original class or to different EC classes, catalyzing other types of chemical reactions. The old numbers have not been allotted to new enzymes instead the place has been left vacant or cross-references given to the changes in nomenclature. 

These three biochemical reactions are catalyzed by hexokinase (EC 2.7.1.1), glucose-6-phosphate isomerase (EC 5.3.1.9), and 6-phosphofructokinase (EC 2.7.1.11), respectively. The EC numbers are from Enzyme Nomenclature (Webb, 1992). The first step is to write the conservation matrix for this reaction system at specified pH because that will show how to calculate the further transformed Gibbs energies of formation at specified [ATP] and [ADP]. 

During natural evolution, a broad variety of enzymes has been developed, which are classified according to the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB). Thus, for each type of characterized enzyme an EC (Enzyme Commission) number has been provided (see http // www.expasy.ch/enzyme/). For instance, all hydrolases have EC number 3 and further subdivisions are provided by three additional digits, e.g. all lipases (official name triacylglycerol lipases) have the EC number 3.1.1.3 and are thus distinguished from esterases (official name carboxyl esterases) having the EC number 3.1.1.1. This classification is based on the substrate (and cofactor) specificity of an enzyme only, however often very similar amino acid sequences and also related three-dimensional structures can be observed. 

The names of the examples of textile-relevant enzymes follow the nomenclature of Duclaux from 1898, characterising an enzyme by the end-syllable ase , added to the name of the snbstrate that is split, synthesised or otherwise catalysed. As with all catalysts, enzymes reduce the activation energy of a specific reaction. The discovery of large qnantities of new enzyme systems afforded a more differentiated nomenclatnre, realised in 1964 by the International Union of Pure and Applied Chemistry (lUPAC) and the International Union for Biochemistry (lUB). In the new enzyme classification (EC) the first nnmber refers to one of the six main gronps and the following numbers to subgroups, for example EC 3.4.S.6, where 3 stands for hydrolases. ... 

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