Enzymes, classification description

The elucidation of so many structures has allowed a successful classification of protein structures [7,8] it has laid the basis for certain predictive methods [9,10], and it has given insight into the possible evolutionary origins of proteins [11-13]. Our understanding of biological function in terms of structure has not increased so fast. This has turned out to be a more difficult problem. In the case of enzymes, a description of several different states of the protein complexed with substrate, intermediates and products together with necessary co-factors and activators is required. Often these different states can only be achieved by co-crystallisation, and even then it may be difficult to trap the necessary conformation. To date, it is... 

A system based partly on historical names, partly on the substrate, and partly on the type of reaction catalyzed is far from satisfactory. In 1956, the International Union of Biochemistry set up a Commission on Enzymes to consider the classification and nomenclature of enzymes. The Commission presented a report in 1961 whose recommendations for naming and classifying enzymes were subsequently adopted (12). Enzymes are classified on the basis of the reactions they catalyze. Despite its apparent complexities, the system is precise and very descriptive, accommodating existing enzymes and serving as a systematic basis for the naming of new enzymes. AH enzymes are placed in one of the six principal classes. 

Enzymes involved in alkaloid transformations have been arbitrarily divided into two major classes or types of biotransformations. The classification used here is that which has evolved from early descriptions of mammalian detoxica-... 

There is still much to be learned about the structure and mechanism of action of this class of enzymes. Their mode of attack in terms of gross effects on substrates is now fairly well understood, especially in the cellulases, and this has resulted in a clearer classification of the purified components of the cellulase system. In order to explain the catalytic effects at a molecular level, it will be necessary first to obtain more information on the primary and, eventually, tertiary structures of the enzymes. The molecular mechanism, defined as a description of the number and structures of intermediates lying on the reaction path (6), then can be fully identified and from this the origin of the observed catalytic rate enhancements can be sought. 

Each PIR entry consists of Entry (entry ID), Title, Alternate names, Organism, Date, Accession (accession number), Reference, Function (description of protein function), Comment (e.g., enzyme specificity and reaction, etc.), Classification (superfamily), Keywords (e.g., dimer, alcohol metabolism, metalloprotein, etc.), Feature (lists of sequence positions for disulfide bonds, active site and binding site amino acid residues, etc.), Summary (number of amino acids and the molecular weight), and Sequence (in PIR format, Chapter 4). In addition, links to PDB, KEGG, BRENDA, WIT, alignments, and iProClass are provided. 

After the above survey on the general molecular structure of the different types of heme peroxidases, a more detailed analysis on the catalytic sites of some heme peroxidases of particular biotechnological interest produced by fungi is presented in Sects. 3.3-3.5. Previously, a description of the biotechnological interest of these enzymes, followed by a structural classification and evolutionary analysis of all the basidiomycete peroxidases, whose sequence is known to date, is presented in the two subsections included below. For a full evolutionary analysis of heme peroxidases, see Chap. 2. 

The International Union of Biochemistry (lUB) established a commission on enzyme nomenclature to adopt a systematic classification and nomenclature of all the existing and yet to be discovered enzymes. This system is based on the substrate and reaction specificity. Although, this International Union of Biochemistry system is complex, it is precise, descriptive and informative. 

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. 

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]... 

Nitrate reductase activity has been demonstrated in particulate fractions of Nostoc muscorum (Ortegaal., 1976), Anacystis nidulans (Manzanoet al., 1976) a.nd Anabaena cylindrica (Hattori, 1970). The enzyme is particulate and although it has been released by detergent treatment of acetone precipitates (Hattori, 1970), there has been no description of molecular characteristics. The association of the assimilatory nitrate reductase with membranes in the cyanobacterium appears to be a distinct divergence from the classification for bacterial nitrate reductases proposed by Pichinoty. 

Until very recently the naming of the individual enzymes has been entrusted largely to the discoverers. This resulted often in such descriptive names as zwisch-enferment or pH 5 enzyme. An international commission meanwhile has drafted specific rules for the classification and nomenclature of enzymes. The commission has established six main classes, which are further subdivided into sub-classes and sub-sub-classes, according to the nature of the reaction catalyzed and to the type of bond formed or severed. In Table IX several examples of each main class are listed to illustrate the system. 

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