Database CAZy

In the absence of structural data for many interesting glycosidases, comparison of their sequences has revealed important structural relationships and similarities of catalytic properties. The database CAZy (Carbohydrate-Active EnZymes) is a sequence-based collection of currently around 100 GH families (currently GH 1 to GH 117, with around 15 families deleted), which are further grouped in 14 clans. It provides family-typical structural and mechanistic details and has become an invaluable tool in GH research.98... 

In this section, enzymes in the EC 2.4. class are presented that catalyze valuable and interesting reactions in the field of polymer chemistry. The Enzyme Commission (EC) classification scheme organizes enzymes according to their biochemical function in living systems. Enzymes can, however, also catalyze the reverse reaction, which is very often used in biocatalytic synthesis. Therefore, newer classification systems were developed based on the three-dimensional structure and function of the enzyme, the property of the enzyme, the biotransformation the enzyme catalyzes etc. [88-93]. The Carbohydrate-Active enZYmes Database (CAZy), which is currently the best database/classification system for carbohydrate-active enzymes uses an amino-acid-sequence-based classification and would classify some of the enzymes presented in the following as hydrolases rather than transferases (e.g. branching enzyme, sucrases, and amylomaltase) [91]. Nevertheless, we present these enzymes here because they are transferases according to the EC classification. 

Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B (2009) The carbohydrate-active enZymes database (CAZy) an expert resource for glycogenomics. Nucleic Acids Res 37 D233-D238... 

Cantarel, BE Coutinho, PM Rancurel, C Bernard, T Lombard, V Henrissat, B. The Carbohydrate-Active EnZymes database (CAZy) an expert resource for Glycogenomics. Nucleic Acids Research. 2009, 37. 

CAZy, Carbohydrate-active enzymes, (2006) online database http //www.cazy. org 21.10.2006. 

Cavitation number, 11 746 Cavity-filling process, 10 11-13 Cavity optics, 14 669-672 Cavity sinking, 9 601 CAZy database, 10 261 C-Bourdon tube, 20 648 CBr3 compounds, 19 358 C-C bond forming reactions,... 

P. M. Coutinho, B. Henrissat, in Recent Advances in Carbohydrate Bioengineering (Eds. H.). H.). Gilbert, G. Davies, B. Henrissat, B. Svensson), The Royal Society of Chemistry, Cambridge, 1999, p. 3 P. M. Coutinho, B. Henrissat, Carbohydrate Active Enzymes database http //afmb.cnrs-mrs.ff/CAZY/ 1999. 

Illustrations with organic structural formulae have been used widely. In depicting sugar rings. Mills formulae have been used if the conformation is not known with confidence, otherwise conformational structures are drawn. Ribbon diagrams of various carbohydrate-active proteins with known structures are available from protein databases. Their reproduction in this book would have increased its cost and, at a time when all beginning researchers have Web access, only marginally increased its usefulness. If the reader wants to know what, say, a GH6 cellulase looks like, he or she should go to CAZy, the wonderful resource for the whole scientific community started by Bernard Henrissat and maintained by him and Pedro Coutinho, and click on the links in the 3D column. The protein can then be viewed in various downloadable viewers. 

A -glycosylation sites in human proteins and 0-P-GlcNAc/phosphorylation sites respectively. CAZY (http //afmb.cnr-mrs.lr/CAZY/) is a comprehensive database for carbohydrate active enzymes (CAZYmes). CAZYmes are classified into seqnence-derived fanulies (Davis and Henrissat, 2002). They are modular, consisting of one or more catalytic domains in harness with many noncatalytic modules, which often posses a carbohydrate binding functionality. Active-site residues, molecular mechanisms and 3D structures are all conserved within families. 

The CAZy classification scheme complements the EC system by providing a protein sequence based framework within which the tremendous wealth of biochemical, mechanistic, and structural information on these enzymes can be united. In particular, the CAZy classification highlights evolutionary relationships between CAZymes, which in turn allow structural and functional relationships to be delineated within and between families. For example, although structural representatives exist for nearly three fourths of the more than 110 GH families, these consist of comparatively few three-dimensional fold types (13,29,30). In turn, catalytic activity can be related to enzyme structure within CAZy Whereas EC 3.2.1.21 describes all enzymes which have converged to become yS-glucosidases, the CAZy database highlights that this activity has been found in enzymes from three separate Families (GHl, GH3, and GH9), each with distinct three-dimensional protein folds employing one of two different catalytic mechanisms (29). 

As with glycoside hydrolases, the polysaccharide lyases (PL) have long been classified into sequence-related protein families (129) in the CAZy database (28). Presently, more than 20 PL families are listed in CAZy, and, because of significant recent attention, at least one three-dimensional structural representative is known for approximately one half of these (reviewed in Refe. (126,127), and (130) see also http //www.cazy.org/fam/acc PL.html). Not surprisingly, these endo-acting enzymes possess cleft-shaped active sites (126), akin to the polysaccharide erac/o-glycosidases vide supra). Characteristically, polysaccharide lyases bind their polyanionic substrates through basic amino acid residues and/or Ca++ ion complexation. Indeed, the activity of nearly all known pectate lyases strictly requires Ca++, which in some cases may directly affect the catalysis (126). 

Carbohydrates constitute one the of most complex structures occurring in nature (with nucleic acids and proteins) due to i) the monosaccharide diversity, ii) the type of linkage and iii) the nature of carbohydrate-linked molecules. As a result, GHs present a wide range of activities, which have necessitated the creation of a specific classification more explicit than the lUB Enzyme Nomenclature. In 1998, the Carbohydrate-Active Enzymes (CAZy) database was created, gathering glycosidases in famiUes based on amino-acid sequence and protein structures similarities. ... 

A peptide sequence based classification of this diverse group of over 65 000 enzymes divided into over 89 families is found within the CAZy (Carbohydrate-Active enZYmes) database [25, 36]. The group with the highest synthetic potential and impact for the synthesis of glycoconjugates are the Leloir-GTs and are therefore in the focus of this chapter. 

Known SiaTs have been classified into six glycosyltransferase (GT) famiUes in the Carbohydrate-Active enZyme (CAZy) database according to their protein sequence... 

Research on the galactosyltransferases over the last four decades has resulted in a wealth of information that is now easily accessible in various databases. The reader is encouraged to explore three databases in particular 1) Entrez 2) ExPASy and 3) CAZY. As detailed below, these databases contain information regarding nucleotide sequence, protein sequence and enzyme properties such as reaction catalyzed. Km, metal ion requirements, inhibitors, etc. 

More than 300 proteins are currently classified in the CAZy database, including glycoside hydrolases (GHs), glicosyltransferases (GTs), polysaccharide lyases (PLs) and carbohydrate esterases (CEs). Usually, CAZymes present a modular structure, nearly 7% of the enzymes having at least one carbohydrate-binding module [13]. CBMs are also classified... 

---