Database CAZy Carbohydrate-Active

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... 

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

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. 

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. 

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. 

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. 

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. ... 

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

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. 

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