Sequence-based classification of glycoside hydrolases

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• Authors: ^^^Steve Withers^^^, ^^^Spencer Williams^^^
• Responsible Curator: ^^^Spencer Williams^^^

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Sequence-based classification

Sequence classification methods require knowledge of at least part of the amino acid sequence for an enzyme. Algorithmic methods are then used to compare sequences. Using a combination of comparison algorithms the glycoside hydrolases have been classified into more than 100 families [1]. This classification is permanently available through the Carbohydrate Active enZyme database [2]. Each family (GH family) contains proteins that are related by sequence, and by corollary, fold. An obvious shortcoming of sequence-based classifications is that they can only be applied to enzymes for which sequence information is available. On the other hand sequence-based classification schemes allow classification of proteins for which no biochemical evidence has been obtained such as the thousands of uncharacterized glycosidase-related sequences that originate from genome sequencing efforts worldwide. This allows a number of useful predictions to be made since it has long been noted that the catalytic machinery and molecular mechanism is conserved for the vast majority of the glycosidase families [3] as well as the geometry around the glycosidic bond (irrespective of naming conventions) [4]. As such sequence based classification methods are rather different (and in many ways complimentary) to the Enzyme Commission classification scheme, which assigns proteins to groups based on the nature of the reactions that they catalyze.

Classification into 'clans'

Classification of families into larger groups, termed 'clans', has been proposed [5]. A `clan' is a group of families that possess significant similarity in their tertiary structure, catalytic residues and mechanism. Thus knowledge of 3D structure and the functional assignment of catalytic residues is required for classification into clans. Families within clans are thought to have a common evolutionary ancestry. For an updated table of glycoside hydrolase clans see the CAZy Database [6].

References

<biblio>

1. 1 pmid=1747104

1. 2 Carbohydrate Active Enzymes database; URL http://www.cazy.org/

1. 3 pmid=1618761
2. 4 pmid=7624375

1. 5 pmid=8687420
2. 6 Carbohydrate Active Enzymes database, glycoside hydrolase classification; URL http://www.cazy.org/Glycoside-Hydrolases.html