Enzyme family classification

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 next paragraphs try to interpret frequently occurring classes of conservation patterns , meaning the set of totally invariant or at least highly conserved positions in a family alignment. 1Tie conservation patterns of enzyme families are different from those of non-catalytic proteins and can be used for enzyme identification and classification. 

It has to be said that all of the mentioned complications should be considered exceptions rather than the rule. Overall, an analysis of conservation patterns has been and will continue to be a valuable tool in the identification and classification of new enzyme families. 

In addition to the above mentioned databases that try to cover the entire world of enzymes, there are a number of more topical databases focusing on particular enzyme families. The MEROPS database, maintained at the Babraham Institute in Cambridge, provides a catalog and a structure-based classification scheme for all proteolytic enzymes 58. In addition to the classification, the database also provides a digest of published information on the peptidases as well as dadograms and multiple sequence alignments of the peptidase families. 

As has been described in Sect. 5.3, the conservation patterns of enzymes are often indicative of the particular family they belong to and can be used for their classification. However, the iterative searches and multiple alignment methods used for their establishment require a certain bioinformatic infrastructure as well as some experience with these issues. If the goal of the analysis is not the detection of novel enzyme families, but rather the classification of a novel sequence into one of the already existing enzyme families, there are a number of protein domain and motif databases that will be useful in this respect[60 61. These databases do not store the sequences themselves but rather work with descriptors of protein families and protein domains. These descriptors can consist of the Profiles or Hidden Markov Models mentioned above, but other types are also being used. With a particular... 

The occurrence of Mo or W in Nature is, with the exeeption of nitrogenase, always accompanied by a unique pyranopterin dithiolene chelating ligand typically referred to as molybdopterin and this is always coordinated to the metal at the active site. The combination of Mo (or W) with either one or two bidentate molybdopterin ligands in addition to combinations of terminal oxido or sulfido ligands and amino acid side chains leads to an orderly classification of this enzyme family into three sub-groupsthe xanthine oxidase, sulfite oxidase and DMSO reductase families (Scheme 5.1). The eponymous enzyme in each case is historically the first one isolated and studied within its family. 

The enzymatic depolymerization of chitin by chitinases has been investigated for a few decades. Chitinases, a class of glycosyl hydrolyases, have been found in a variety of organisms ranging from bacteria to animals. Chitinases belong to two major families of carbohydrate enzymes, family 18 and family 19, based on the amino acid sequences (CAZY http //www.cazy.org). Both families of enzymes differ in their amino acid sequences, three-dimensional structures, and catalytic mechanisms (Fukamizo 2000). Prior to the family classification, plant chitinases are divided into five classes on the basis of their primary structures. Classes 1,11, and IV chitinases are included in family 19, whereas classes III and V belong to family 18. 

The amino acid sequence gives an identity to the protein and provides fundamental information on the nature of the protein, such as structure, mechanism of action, evolutionary origin, and classification into enzyme families. This primary information also serves as a guide for gene search, molecular cloning, and manipulation of genes in recombinant DNA technology. 

The evolutionary classification has a rational basis, since, to date, the catalytic mechanisms for most peptidases have been established, and the elucidation of their amino acid sequences is progressing rapidly. This classification has the major advantage of fitting well with the catalytic types, but allows no prediction about the types of reaction being catalyzed. For example, some families contain endo- and exopeptidases, e.g., SB-S8, SC-S9 and CA-Cl. Other families exhibit a single type of specificity, e.g., all families in clan MB are endopeptidases, family MC-M14 is almost exclusively composed of carboxypeptidases, and family MF-M17 is composed of aminopeptidases. Furthermore, the same enzyme specificity can sometimes be found in more than one family, e.g., D-Ala-D-Ala carboxypeptidases are found in four different families (SE-S11, SE-S12, SE-S13, and MD-M15). 

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