International Union of Biochemistry and Molecular Biology

International Union of Biochemistry and Molecular Biology, Biochemical Nomenclature and Related Documents, 2nd ed., Pordand Press, London, 1992. 

International Union of Biochemistry and Molecular Biology Nomenclature Committee, 1992. Enzyme Nomenclature. New York Academic Press. A reference volume and glossary on die official classification and nomenclature of enzymes. 

Since the early 1970s a panel convened by the International Union of Pure and Applied Chemistry and the International Union of Biochemistry and Molecular Biology has been working to formulate recommendations for carbohydrate nomenclature that meet developing needs of research and electronic data handling, while retaining links to the established literature base on carbohydrates. The realization of these endeavors is presented here in the final document Nomenclature of Carbohydrates, which provides a definitive reference for current researchers, both in the text version and in the version accessible on the World Wide Web (http //www.chem.qmw.ac.uk/iupac/2carb/), where amendments and revisions are maintained. 

The responsibility for enzyme nomenclature is supported by the Nomenclature Committee of the International Union of Biochemistry (IUB now the International Union of Biochemistry and Molecular Biology, IUBMB) and the International Union of Pure and Applied Chemistry (IUPAC). These committees collect information about changes and additions to enzyme nomenclature13"15. 

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/. 

Webb EC, editor. Enzyme nomenclature 1992. San Diego International Union of Biochemistry and Molecular Biology/Academic Press, 1992. 

The ENZYME nomenclature database, a repository of information based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB), currently contains 4435 enzyme entries (Release 38.0, September 2005). Of these, 545 entries are superseded, resulting in a final list of 3,890 enzymes, 224 sub-subclasses, and 65 subclasses. 

Enzymes, the hammer, the saw, the glue, briefly the tools of biocatalysis are by the Enzyme Commission, International Union of Biochemistry and Molecular Biology, which is a subdivision of the Federation of Biochemistry, divided into 6 classes according to the chemical reactions they catalyse (lUBMB, 1992). The six classes are ... 

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. 

We have tried throughout this book to use the enzyme name most commonly used by working biochemists and to point out cases in which an enzyme has more than one widely used name. For current information on enzyme nomenclature, refer to the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (www.chem.qmw.ac.uk/iubmb/nomenclature/). 

The International Union of Biochemistry and Molecular Biology (IUBMB) developed a system of nomenclature in which enzymes are divided into six major classes (Figure 5.1), each with numerous subgroups. The suffix -ase is attached to a fairly complete description of the chemical reaction catalyzed, for example D-glyceraldehyde 3-phosphate NAD oxidoreductase. The IUBMB names are unambiguous and informative, but are sometimes too cumbersome to be of general use. 

International Union of Biochemistry and Molecular Biology, Biochemical Nomenclature and Related Documents, 2nd Edition, Portland Press. London, UK, 1992. Richer, J.-C., K Panico, and W.H. Powell Guide to the Use of IUPAC Nomenclature of Organic Compounds, Blackwell, Oxford and London, UK, 1994. 

The International Union of Biochemistry and Molecular Biology recommends that the term peptidase be used synonymously with the term peptide hydrolase (IUBMB, 1992). Thus, in this unit the term peptidase is used in reference to any enzyme that catalyzes the hydrolysis of peptide bonds, without distinguishing between exo- and endopeptidase activities. Peptidases may be assayed using native or modified proteins, peptides, or synthetic substrates. In this unit, the focus is on assays based on the hydrolysis of common, commercially available, protein substrates. Thus, the assays are not intended to be selective for a given peptidase they are designed to provide estimates of overall peptidase activity. Other units in this publication focus on synthetic or model substrates, which can be designed for the measurement of specific endo- and/or exopeptidase activities. 

Most biochemical databases request the user to enter keywords to search/retrieve information concerning biomolecules (unless the identifiers of the compounds are known). The keyword is normally the IUBMB (International Union of Biochemistry and Molecular Biology) name or common name of the compound. In particular, the linkage and conformational designations of oligomeric compounds needs to be specified. The IUBMB nomenclature for biochemical compounds can be accessed from the IUBMB site at http //www.chem.qmw.ac.uk/iubmb/. Some useful databases for biochemical compounds are listed in Table 5.3. 

In addition to the metabolic databases listed above, some of the enzyme databases described in the previous chapter (Chapter 6) also serve as useful metabolic resources. All of the enzyme and metabolic databases make use of EC (Enzyme Commission) numbers which are available at the International Union of Biochemistry and Molecular Biology (IUBMB) site (http //www.chem.qmw.ac.uk/ iubmb/enzyme/). 

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