Glycoside Hydrolase Family 13

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• Author: ^^^Birte Svensson^^^
• Responsible Curator: ^^^Birte Svensson^^^

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Glycoside Hydrolase Family GH13
Clan	GH-H
Mechanism	retaining
Active site residues	known
CAZy DB link
http://www.cazy.org/fam/GHnn.html

== Substrate specificities == Normal 0 21 false false false MicrosoftInternetExplorer4 CAZy Family 13 is the major glycoside hydrolase family acting on a-glucoside containing substrates. It has recently been subdivided into subfamilies (Stam et al., 2005). There has been a number of reviews concerned with a-amylases (ref). GH13 contains hydrolases, transglycosidases and isomerases, noticeably amino acid transporters, which have no glycoside activity, are GH13 members. The enzymes are found in a very wide range of organisms form all kingdoms. While known specificities are indicated by the enzyme named as follow below, for several of these enzymes numerous have been characterized to comprise subspecificities defined by structural requirements for preferred substrates or the structure of the predominant product(s). Known enzymes currently include; a-amylase (EC 3.2.1.1); pullulanase (EC 3.2.1.41); cyclomaltodextrin glucanotransferase (EC 2.4.1.19); cyclomaltodextrinase (EC 3.2.1.54); trehalose-6-phosphate hydrolase (EC 3.2.1.93); oligo-a-glucosidase (EC 3.2.1.10); maltogenic amylase (EC 3.2.1.133); neopullulanase (EC 3.2.1.135); a-glucosidase (EC 3.2.1.20); maltotetraose-forming a-amylase (EC 3.2.1.60); isoamylase (EC 3.2.1.68); glucodextranase (EC 3.2.1.70); maltohexaose-forming a-amylase (EC 3.2.1.98); maltotriose-forming a-amylase (EC 3.2.1.116); branching enzyme (EC 2.4.1.18); trehalose synthase (EC 5.4.99.16); 4-a-glucanotransferase (EC 2.4.1.25); maltopentaose-forming a-amylase (EC 3.2.1.-) ; amylosucrase (EC 2.4.1.4) ; sucrose phosphorylase (EC 2.4.1.7); malto-oligosyltrehalose trehalohydrolase (EC 3.2.1.141); isomaltulose synthase (EC 5.4.99.11); amino acid transporter. Interestingly several members of GH13 contains carbohydrate binding modules (CBMs) referred to as starch binding domains, and belonging to CBM20, 21, 25, 26, 34, 41, 45, 48, and 53 (refs).

The different enzymes have a wide range of different preferred substrates and product. E.g. the a-amylases prefer polysaccharides of the a(1,4)-glucan type such as amylase and also amylopectin, but they do attack also the supramolecular structures represented by starch granules and glycogen particles and have some significant. Albeit lower turn-over of maltooligosaccharides of a certain degree of polymerization. These preferred substrate profiles can be manipulated through protein engineering. Content is to be added here.

This is an example of how to make references to a journal article [1]. (See the References section below). Multiple references can go in the same place like this [1, 2]. You can even cite books using just the ISBN [3]. References that are not in PubMed can be typed in by hand [4].

Kinetics and Mechanism

    Normal   0   21         false   false   false                                 MicrosoftInternetExplorer4

GH Family 13 enzymes are retaining as was first demonstrated by a FILL IN (ref) and they follow the classical Koshland double-displacement mechanism (ref). This has been supported by covalent labeling using FILL IN (ref), numerous three-dimensional structures (ref), and site-directed mutational substitution of the catalytic site residues (ref).

Some of the Family 13 members use a multiple attack or processive mechanism (refs) involving several glycoside bond cleavages to be executed in the same enzyme-substrate encounter.

In several cases has the binding energies been determined using subsite mapping (refs) which give a typical subsite binding energy profile for individual enzymes (ref).

Several a-amylases have been reported to interact with polymeric substrates at surface sites situated as a certain distance of the active site (ref).

Finally interaction with insoluble substrates such as starch granules or glycogen can occur both at these sites (ref) as well as by the involvement of separate binding modules referred to as starch binding domains (ref).

Catalytic Residues

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Three-dimensional structures

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Family Firsts

First sterochemistry determination

Cite some reference here, with a short (1-2 sentence) explanation [1].

First catalytic nucleophile identification

Cite some reference here, with a short (1-2 sentence) explanation [4].

First general acid/base residue identification

Cite some reference here, with a short (1-2 sentence) explanation [2].

First 3-D structure

Cite some reference here, with a short (1-2 sentence) explanation [3].

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 |
2. He S and Withers SG. (1997). Assignment of sweet almond beta-glucosidase as a family 1 glycosidase and identification of its active site nucleophile. J Biol Chem. 1997;272(40):24864-7. DOI:10.1074/jbc.272.40.24864 |

4. Sinnott, M.L. (1990) Catalytic mechanisms of enzymic glycosyl transfer. Chem. Rev. 90, 1171-1202. DOI: 10.1021/cr00105a006