IUBMB enzyme classifications

The complex nature and interconnectivity of plant cell wall polymers preclude straightforward enzymatic digestion. There are dozens of enzyme families involved in plant cell wall hydrolysis, including cellulases, hemicellu-lases, pectinases, and lignin-modifying enzymes. The Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) has classified cellulases and hemicellulases, like all enzymes, into different classes based on activity. Table 33.2 and Table 33.3, compiled from the IUBMB enzyme nomenclature database (http //www.chem.qmul.ac.uk/iubmb/ enzyme/), list the IUBMB enzyme classifications for cellulases and hemicellulases.153... 

The classification adopted by the Nomenclature Committee (NC) of the International Union of Biochemistry and Molecular Biology (IUBMB) divides peptidases into classes and subclasses according to the positional specificity in the cleavage of the peptide link of the substrate. The last publication of the complete printed version of the Enzyme Nomenclature was in 1992 [1][2], but a constantly updated version with supplements is available on the World Wide Web at http //www.chem.qmul.ac.uk/iubmb/enzyme/. Similarly, all available Protein Data Bank (PDB) entries classified as recommended by the NC-IUBMB can be found on the WWW at http //www.bio-chem.ucl.ac.uk/bsm/enzymes/. 

Moss, G. P., Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzyme-Catalysed Reactions. In URL http //www.chem.qmul.ac.uk/iubmb/enzyme/ 1992. 

Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB). Enzyme Nomenclature Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzyme-Catalysed Reactions. Published in Enzyme Nomenclature 1992 [Academic Press, San Diego, California, ISBN 0-12-227164-5 (hardback), 0-12-227165-3 (paperback)] with Supplement 1 (1993), Supplement 2 (1994), Supplement 3 (1995), Supplement 4 (1997), and Supplement 5 (in Eur.J. Biochem. 1994, 223, 1—5 Eur. J. Biochem. 1995, 232, 1—6 Eur.J. Biochem. 1996, 237, 1—5 Eur. J. Biochem. 1997, 250, 1—6, and Eur.J. Biochem. 1999, 264, 610—650, respectively) [Copyright lUBMB] and online at http //www.chem.qmuLac.uk/iubmb/enzyme/index.html). 

The widely accepted basis of all enzyme classifications are the recommendations of the Enzyme Committee (E.C.) of the International Union of Biochemistry and Molecular Biology (IUBMB)1491. Within this system, enzymatic activities are classified by a four-level hierarchy and each entry is described by a set of four numbers. The first number describes the top level and can be either 1 for oxidoreductases, 2 for transferases, 3 for hydrolases, 4 for lyases, 5 for isomerases or 6 for ligases. The meaning of the three lower hierarchy levels depends on the top level group. As an example, glycogen synthase is classified as 2.4.1.11 here, the 2 stands for transferases, the 4 for glycosyl-transferases, the 1 for hexosyl-transferases and the 11 for the particular subfamily. 

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 classic enzyme commission (EC) classification for GTs is on the basis of their donor and acceptor specihcity as well as the product formed. Currently, 295 entries are in this database (http //www.chem.qmul.ac.uk/iubmb/). The distinction between these enzymes is noted by their ability to catalyze the transfer of hexoses (EC 2.4.l.y, hexosyltransferases), pentoses (EC 2.4.2.y, pentosyltransferases), or other glycosyl groups (2.4.99.y, sialyltransferases). This classification is restricted to enzymes that are fully characterized, and it can be problematic for enzymes that act on several distinct acceptors but at different rates. It also does not take into account the origin of the enzyme or its three-dimensional stmcture. 

The ENZYME database1501, maintained by the Swiss Institute for Bioinformatics (SIB), provides a comprehensive list of all IUBMB classifications, together with associated information such as systematic and alternative enzyme names, cofactor requirements, and pointers to the corresponding entry in the SWISS-PROT database of protein sequences1511. In addition, there is a concise free-text description of the reaction catalyzed, together with a description of preferential substrates and products. Currently, the ENZYME database holds entries for approximately 3700 enzymes. 

A much more ambitious database that builds on the IUBMB classification is BRENDA, maintained by the Institute of Biochemistry at the University of Cologne. In addition to the data provided by the ENZYME database, the BRENDA curators have extracted a large body of information from the enzyme literature and incorporated it into the database. The database format strives to be readable by both humans and machines. The categories of data stored in BRENDA comprise the EC-number, systematic and recommended names, synonyms, CAS-registry numbers, the reaction catalyzed, a list of known substrates and products, the natural substrates, specific activities, KM values, pH and temperature optima, cofactor and ion requirements, inhibitors, sources, localization, purification schemes, molecular weight, subunit structure, posttranslational modifications, enzyme stability, database links, and last but not least an extensive bibliography. Currently, BRENDA holds entries for approximately 3500 different enzymes. 

According to the EC-System of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology IUBMB [2], the enzymes are classified in six main classes (Table l).To allow a refined classification, the main classes are subdivided into three orders of enzyme subclasses (EC X.a.b.c., e.g., EC 1.1.1.1 for alcohol dehydrogenase). The majority of the described enzymes belong to the EC classes 1,2 and 3. 

Additional information <1, 2> (this group of enzymes is under review by NC-IUBMB, recommendation for a nomenclature system based on acceptor amino acid specificity rather than on protein substrate. In accordance with this system protein-tyrosine kinases would belong to EC 2.7.1 l.X, <1,2> [1] The present data set is restricted to a literature review and does not contain a complete description of kinases. Classification system based on kinase domain phylogeny revealing families of enzymes with related substrate specificities, <1,2> [3]) [1, 3]... 

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