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Glycoside Hydrolases

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Overview

Glycoside hydrolases are enzymes that catalyze the hydrolysis of the glycosidic linkage of glycosides, leading to the formation of a sugar hemiacetal or hemiketal and the corresponding free aglycon. Glycoside hydrolases are also referred to as glycosidases. Glycoside hydrolases can catalyze the hydrolysis of O-, N- and S-linked glycosides.

GHs.gif

Classification

Glycoside hydrolases can be classified in many different ways. The following paragraphs list several different ways, the utility of which depends on the context in which the classification is made and used.

exo- and endo- refers to the ability of a glycoside hydrolase to cleave a substrate at the end (most frequently, but not always the non-reducing end) or within the middle of a chain. For example, most cellulases are endo-acting, whereas LacZ β-galactosidase from E. coli is exo-acting.

EC numbers are codes representing the Enzyme Commission number. This is a numerical classification scheme for enzymes, based on the chemical reactions they catalyze. Every EC number is associated with a recommended name for the respective enzyme. EC numbers do not specify enzymes, but enzyme-catalyzed reactions. If different enzymes (for instance from different organisms) catalyze the same reaction, then they receive the same EC number. A necessary consequence of the EC classification scheme is that codes can be applied only to enzymes for which a function has been biochemically identified. Additionally, certain enzymes can catalyze reactions that fall in more than one class. These enzymes must bear more than one EC number.

Retaining and inverting classification refers to the stereochemical outcome of the hydrolysis reaction catalyzed by the glycoside hydrolase. Retaining enzymes produce a product with the same stereochemistry as the glycoside substrate , and inverting enzymes give a product with the opposite stereochemistry to the glycoside substrate.

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, and in the case of the glycoside hydrolases, this has allowed their classification into more than 100 families. Each family (GH family) contains proteins that are related by sequence, and by corollary, fold. Sequence-based classification schemes allow classification of proteins for which no biochemical evidence may have been obtained. An obvious shortcoming of sequence-based classifications are that they can only be applied to enzymes for which sequence information is available. As such sequence based classification methods are rather different (and in many ways complimentary) to the EC method discussed above.

Mechanism

Sequence-based classification

Glycoside Hydrolase Firsts

First sterochemistry determination
Cite some reference here, with a short explanation [1].
First catalytic nucleophile identification
First general acid/base residue identification
First 3-D structure

References

  1. Comfort DA, Bobrov KS, Ivanen DR, Shabalin KA, Harris JM, Kulminskaya AA, Brumer H, and Kelly RM. (2007). Biochemical analysis of Thermotoga maritima GH36 alpha-galactosidase (TmGalA) confirms the mechanistic commonality of clan GH-D glycoside hydrolases. Biochemistry. 2007;46(11):3319-30. DOI:10.1021/bi061521n | PubMed ID:17323919 [1]