Difference between revisions of "Glycoside Hydrolases"

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Glycoside hydrolases

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-* Authors: [[User:Withers|Stephen Withers]], [[User:SpencerWilliams|Spencer Williams]]
+#REDIRECT [[Glycoside hydrolases]]
-* Responsible Curator:  [[User:SpencerWilliams|Spencer Williams]]
-----
-== 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, and sometimes also as glycosyl hydrolases. Glycoside hydrolases can catalyze the hydrolysis of O-, N- and S-linked glycosides.
-[[Image:GHs.png|centre]]
-== 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.
-=== Endo/exo ===
-''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.
-[[Image:exo_endo.png|centre]]
-=== Enzyme Commission (EC) number ===
-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.
-=== Mechanistic classification ===
-Two reaction mechanisms are most commonly found for the retaining and inverting enzymes, as first outlined by Koshland and as described below.<cite>4</cite> However several interesting variations on these mechanisms have been found, and one fundamentally different mechanism, catalyzed by an NADH cofactor, has been discovered in recent years, as discussed below.
-[[Image:Retaining&Inverting.png|centre]]
-=== Sequence 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, 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. 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 orginate 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 <cite>4</cite> as well as the geometry around the glycosidic bond (irrespective of naming conventions) <cite>5</cite>. As such sequence based classification methods are rather different (and in many ways complimentary) to the EC method discussed above.
-== Mechanism ==
-Two reaction mechanisms are most commonly found for the retaining and inverting enzymes, as first outlined by Koshland and as described below <cite>2</cite>. However several interesting variations on these mechanisms have been found, and one fundamentally different mechanism, catalyzed by an NADH cofactor, has been discovered in recent years.
-===Inverting glycoside hydrolases===
-Hydrolysis of a glycoside with net inversion of anomeric configuration is generally achieved via a one step, single-displacement mechanism involving [[oxocarbenium ion]]-like [[transition state]]s, as shown  below. The reaction occurs with acid/base assistance from two amino acid side chains, normally glutamic or aspartic acids, that are typically located 6-11 A apart<cite>1</cite>.
-[[Image:Inverting glucosidase mechanism.png|centre]]
-===Retaining glycoside hydrolases===
-====Classical Koshland retaining mechanism====
-Hydrolysis with net retention of configuration is most commonly achieved via a two step, double-displacement mechanism involving a covalent glycosyl-enzyme [[intermediate]], as is shown in the figure below. Each step passes through an [[oxocarbenium ion]]-like [[transition state]]. Reaction occurs with acid/base and nucleophilic assistance provided by two amino acid side chains, typically glutamate or aspartate, located 5.5 A apart. In the first step (often called the glycosylation step), one residue plays the role of a nucleophile, attacking the anomeric centre to displace the aglycon and form a glycosyl enzyme intermediate. At the same time the other residue functions as an [[acid catalyst]] and protonates the glycosidic oxygen as the bond cleaves. In the second step (known as the deglycosylation step), the glycosyl enzyme is hydrolyzed by water, with the other residue now acting as a [[base catalyst]] deprotonating the water molecule as it attacks. The pKa value of the acid/base group cycles between high and low values during catalysis to optimize it for its role at each step of catalysis <cite>3</cite>. In the case of sialidases, the catalytic nucleophile is a tyrosine residue (see below). This mechanism was originally proposed by Dan Koshland, although at the time the identities of the residues was unclear <cite>2</cite>.
-[[Image:Retaining_glycosidase_mechanism_1.png|centre]]
-====Neighboring group participation====
-Enzymes of glycoside hydrolase families [[Glycoside Hydrolase Family 18|18]], [[Glycoside Hydrolase Family 20|20]], [[Glycoside Hydrolase Family 56|56]], [[Glycoside Hydrolase Family 84|84]], and [[Glycoside Hydrolase Family 85|85]] hydrolyse substrates containing an ''N''-acetyl (acetamido) or ''N''-glycolyl group at the 2-position. These enzymes have no catalytic nucleophile: rather they utilize a mechanism in which the 2-acetamido group acts as an intramolecular nucleophile. Neighboring group participation by the 2-acdetamido group leads to formation of an oxazoline (or more strictly an oxazolinium ion) intermediate. This mechanism was deduced from X-ray structures of complexes of chitinases with natural inhibitors <cite>6</cite>, from the potent inhibition afforded by a stable thiazoline analogue of the oxazoline <cite>8</cite><cite>7</cite>, and from detailed mechanistic analyses using substrates of modified reactivity <cite>9</cite>. Typically, a stabilizing residue (a carboxylate) stabilizes the charge development in the [[transition state]]. Not all enzymes that cleave substrates possessing a 2-acetamido group utilize a neighboring groups participation mechanism; enzyme of glycoside hydrolase families [[Glycoside Hydrolase Family 3|3]], [[Glycoside Hydrolase Family 22|22]] and [[Glycoside Hydrolase Family 85|85]] utilize a classical retaining mechanism with an enzymic nucleophile. Other hexosaminidases such as those of [[Glycoside Hydrolase Family 19]] utilize an inverting mechanism.
-[[Image:Hex_neighboring_mechanism.png|centre]]
-====Exogenous bases: Myrosinases====
-Glycoside hydrolases termed myrosinases catalyze the hydrolysis of anionic thioglycosides (glucosinolates) found in plants. They are found in [[Glycoside Hydrolase Family 1]]. In these enzymes the usual acid/base glutamic acid found in other members of this family is replaced by a glutamine. This likely reduces charge repulsion between the anionic aglycon sulfate. The unusual aglycon is a sufficiently good leaving group to be able to cleave in the first glycosylation step to form the glycosyl enzyme intermediate without the requirement of an acid catalyst. However, since a base catalyst is required for the second step (hydrolysis or deglycosylation) these enzymes require an alternative basic group. This is provided by the co-enzyme L-ascorbate <cite>10</cite>.
-[[Image:myrosinase.png|centre]]
-====Alternative nucleophiles====
-Enzymes termed sialidases (also neuraminidases) hydrolyze glycosides of sialic acids. Closely related enzymes termed trans-sialidases catalyze the transglycosylation of sialisides. The sialidases and trans-sialidases of glycoside hydrolase families [[Glycoside Hydrolase Family 33|33]] and [[Glycoside Hydrolase Family 34|34]] utilize a tyrosine as a catalytic nucleophile, which is activated by an adjacent base residue. A rationale for this unusual difference is that the use of a negatively charged carboxylate as a nucelophile will be disfavoured as the anomeric centre is itself negatively charged, and thus charge repulsion interferes. A tyrosine residue is a neutral nucleophile, but requires a general base to enhance its nucleophilicity. This mechanism was implied from X-ray structures, and was supported by experiments involving trapping of the intermediate with fluorosugars followed by peptide mapping and then crystallography<cite>11</cite><cite>12</cite>, as well as via mechanistic studies on mutants <cite>13</cite>.
-[[Image:sialidase_mechanism.png|center]]
-====NAD-dependent hydrolysis====
-The glycoside hydrolases of family [[Glycoside Hydrolase Family 4|4]] and [[Glycoside Hydrolase Family 109|109]] use a mechanism that requires an NAD cofactor, which remains tightly bound throughout catalysis. The mechanism proceeds via anionic [[transition state]]s with elimination and redox steps rather than the classical mechanisms proceeding through [[oxocarbenium ion]]-like transition states. As shown below for a 6-phospho-beta-glucosidase, the mechanism involves an initial oxidation of the 3-hydroxyl of the substrate by the enzyme-bound NAD cofactor. This increases the acidity of the C2 proton such that an E1<sub>cb</sub> elimination can occur with assistance from an enzymatic base. The alpha-beta unsaturated intermediate formed then undergoes addition of water at the anomeric centre and finally the ketone at C3 is reduced to generate the free sugar product. Thus, even though glycosidic bond cleavage occurred via an elimination mechanism, the overall reaction is hydrolysis. This mechanism was elucidated through a combination of stereochemical studies by NMR, kinetic isotope effects, linear free energy relationships, X-ray crystallography and UV/Vis spectrophotometry <cite>14 15</cite>.
-[[Image:Family_4_mechanism.png|center]]
-== References ==
-<biblio>
-#1 pmid=7712292
-#2 Koshland, D. (1953) ''Biol. Rev.'' 28, 416.
-#3 pmid=8756457
-#4 pmid=1618761
-#5 pmid=7624375
-#6 pmid=7495789
-#7 pmid=11124970
-#8 Knapp, S., Vocadlo, D., Gao, Z. N., Kirk, B., Lou, J. P., and Withers, S. G. (1996) ''Journal of the American Chemical Society 118'', 6804-6805.
-#9 pmid=16171396
-#10 pmid=10978344
-#11 pmid=15130470
-#12 pmid=12812490
-#13 pmid=14580216
-#14 pmid=15237973
-#15 pmid=15341727
-</biblio>
-[[Category:Definitions and explanations]]

Difference between revisions of "Glycoside Hydrolases"

Latest revision as of 02:00, 29 September 2009

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