Glycoside Hydrolase Family 13

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• Authors: ^^^Birte Svensson^^^ and ^^^Stefan Janecek^^^
• 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/GH13.html

Substrate specificities

Family GH13 is the major glycoside hydrolase family acting on substrates containing α-glucoside linkages. A number of reviews are concerned with α-amylases (Svensson 1994; Janecek 1997; Kuriki & Imanaka 1999; MacGregor et al. 2001; van der Maarel et al. 2002). GH13 contains hydrolases, transglycosidases and isomerases (MacGregor et al. 2001); noticeably animal amino acid transporters (Janecek et al. 1997), which have no glycosidase activity (Fort et al. 2007), are also GH13 members. The enzymes are found in a very wide range of organisms from all kingdoms. While known specificities are indicated by the enzyme named as listed below, for several of these numerous enzymes are characterized representing subspecificities defined by structural requirements for preferred substrates or the structure of the predominant product(s). Described enzymes include: α-amylase (EC 3.2.1.1); oligo-1,6-glucosidase (EC 3.2.1.10); α-glucosidase (EC 3.2.1.20); pullulanase (EC 3.2.1.41); cyclomaltodextrinase (EC 3.2.1.54); maltotetraose-forming α-amylase (EC 3.2.1.60); isoamylase (EC 3.2.1.68); glucodextranase (EC 3.2.1.70); trehalose-6-phosphate hydrolase (EC 3.2.1.93); maltohexaose-forming α-amylase (EC 3.2.1.98); maltotriose-forming α-amylase (EC 3.2.1.116); maltogenic amylase (EC 3.2.1.133); neopullulanase (EC 3.2.1.135); malto-oligosyltrehalose trehalohydrolase (EC 3.2.1.141); maltopentaose-forming α-amylase (EC 3.2.1.-); amylosucrase (EC 2.4.1.4); sucrose phosphorylase (EC 2.4.1.7); branching enzyme (EC 2.4.1.18); cyclomaltodextrin glucanotransferase (CGTase) (EC 2.4.1.19); 4-α-glucanotransferase (EC 2.4.1.25); isomaltulose synthase (EC 5.4.99.11); trehalose synthase (EC 5.4.99.16). As mentioned above, heavy-chains of heteromeric amino acid transporters belong to the GH13 (Janecek et al. 1997; Gabrisko & Janecek 2009). Among thousands of sequences and ~30 different enzymes specificities (Cantarel et al. 2009) many are closely related to each other, GH13 therefore has officially been subdivided into almost 40 subfamilies (Stam et al. 2006); several subfamilies, e.g., the oligo-1,6-glucosidase and neopullulanase subfamilies were described earlier (Oslancova & Janecek 2002). Noticeably a considerable number of GH13 members contain carbohydrate binding modules (CBMs) referred to as starch binding domains belonging to CBM20, 21, 25, 26, 34, 41, 45, 48, 53, and 58 (Svensson et al. 1989; Janecek & Sevcik 1999; Rodriguez-Sanoja et al. 2005; Machovic & Janecek 2006; Christiansen et al. 2009).

The GH13 enzymes have a wide range of different preferred substrates and products. For example, the α-amylases prefer polysaccharides of the α-1,4-glucan type, such as amylose and amylopectin, but are also able to attack the supramolecular structures represented by starch granules and glycogen particles. Besides they have some significant albeit slower turn-over of maltooligosaccharides of a certain degree of polymerization. These typical substrate profiles can be manipulated through protein engineering.

The α-amylase family, , was defined in 1991 as family GH13 when the sequence-based classification of glycoside hydrolases was created (Henrissat 1991). The α-amylase family as an enzyme family, however, was established based on results of several independent findings focused on starch hydrolases and related enzymes (MacGregor & Svensson 1989; Jespersen et al. 1991, 1993; Takata et al. 1992). These enzymes were shown to exhibit sequence similarities and, at that time, a predicted (β/α)8-barrel (i.e. TIM-barrel) fold. The basic criteria for a protein to be a member of the α-amylase family were as follows (Takata et al. 1992): the enzyme should (i) act on the α-glucosidic linkages; (ii) hydrolyse or form by transglycosylation the α-glucosidic linkages; (iii) contain the four conserved sequence regions in its amino acid sequence; and (iv) possess the catalytic triad formed by the three residues corresponding to Asp206, Glu230 and Asp297 of Taka-amylase A (the α-amylase from Aspergillus oryzae). A dramatic increase of the number of GH13 members to several thousands (Cantarel et al. 2009) offered a greater variety in both substrate and product specificities and sequence diversity so that the above criteria had to be updated. For example, also enzymes active on α-1,1-, α-1,2-, α-1,3- and α-1,5-glucosidic linkages belong to the α-amylase family (MacGregor et al. 2001) and the four best known and well-accepted conserved sequence regions, defined first for eleven α-amylases (Nakajima et al. 1986), were completed by the additional three regions (Janecek 1992, 1994a) which can often help to assign the correct enzyme specificity of α-amylase family members (for a review, see Janecek 2002). Of note may be the enzyme neopullulanase (Kuriki et al. 1991) that was found to catalyze both the hydrolysis of α-1,4- and α-1,6-glucosidic bonds as well as the transglycosylation to form these two types of glucosidic bonds.

The α-amylase family represents a clan GH-H of three glycoside hydrolase families GH13, GH70 and GH77 (MacGregor et al. 2001), and should be distinguished from the second smaller α-amylase family GH57 (Janecek 2005). A remote homology to the family GH31 has also been discussed (Janecek et al. 2007).

The evolutionary relationships were described for the entire GH13 family (Jespersen et al. 1993; Janecek 1994b, 1997; Stam et al. 2006) and some closely related specificities, i.e. subfamilies (Park et al. 2000; Oslancova & Janecek 2002), as well as many examples of close evolutionary relatedness were reported for the individual groups of α-amylases, e.g., those from animals and actinomycetes (Janecek 1994a), plants and archaeons (Janecek et al. 1999; Jones et al. 1999), insects (Da Lage et al. 2004), and fungi (van der Kaaij et al. 2007; Hostinova et al. 2010).

Exogenous and endogenous inhibitory proteins have also been reported from microorganisms and plants (Bowman 1945) directed towards α-amylases (Svensson et al. 2004) and limit dextrinases (Macri et al. 1993; MacGregor et al. 2003; MacGregor 2004).

Family GH13 is the major glycoside hydrolase family acting on α-glucoside containing substrates. It has recently been subdivided into 35 subfamilies [1], currently 36 subfamilies are given in CAZy [2]. There has been a number of reviews concerned with α-amylases [3, 4, 5, 6]. GH13 contains hydrolases, transglycosidases and isomerases, noticeably amino acid transporters [7], which have no glycoside activity, are GH13 members. The enzymes are found in a very wide range of organisms from all kingdoms. While known specificities are indicated by the enzyme named as follows 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: α-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-α-glucosidase (EC 3.2.1.10); maltogenic amylase (EC 3.2.1.133); neopullulanase (EC 3.2.1.135); α-glucosidase (EC 3.2.1.20); maltotetraose-forming α-amylase (EC 3.2.1.60); isoamylase (EC 3.2.1.68); glucodextranase (EC 3.2.1.70); maltohexaose-forming α-amylase (EC 3.2.1.98); maltotriose-forming α-amylase (EC 3.2.1.116); branching enzyme (EC 2.4.1.18); trehalose synthase (EC 5.4.99.16); 4-α-glucanotransferase (EC 2.4.1.25); maltopentaose-forming α-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, 53, and 58 [8, 9, 10, 11, 12].

The different enzymes have a wide range of different preferred substrates and product. For example, the α-amylases prefer polysaccharides of the α-(1,4)-glucan type such as amylose and also amylopectin, but they do attack also the supramolecular structures represented by starch granules and glycogen particles and have some significant albeit slower turn-over of maltooligosaccharides of a certain degree of polymerization. These preferred substrate profiles can be manipulated through protein engineering.

Kinetics and Mechanism

GH13 enzymes employ the retaining mechanism. This was first demonstrated by quantitative gas liquid chromatographic analysis of formation of α-maltose from different maltosides (Kimura & Chiba 1983) and further supported by the NMR analysis of the release of α-maltose from similar substrates (Isoda et al. 1992). It was also demonstrated for a number of different α-amylases that they follow the classical Koshland double-displacement mechanism. This has moreover been supported by covalent labelling using 4-deoxy-maltotriose-fluoride trapping the catalytic nucleophile (Uitdehaag et al. 1999), numerous three-dimensional structures, and site-directed mutational substitution of the catalytic site residues (Kelly et al. 2007; Yang et al. 2007). Some of the GH13 members use a multiple attack or processive mechanism (Robyt & French 1967; Mazur & Nakatani 1993; Kramhoft et al. 2005) involving several glycoside bond cleavages to be executed in the same enzyme-substrate encounter. In several cases the binding energies have been determined by using subsite mapping (Prodanov et al. 1984; Ajandouz et al. 1992; MacGregor et al. 1992; Kandra et al. 2006), which gives a subsite binding energy profile characteristic for individual enzymes. Several α-amylases have been reported to interact with polymeric substrates at surface sites situated as a certain distance of the active site (Bozonnet et al. 2007; Nielsen et al. 2008, 2009; Ragunath et al. 2008). Finally interaction with insoluble substrates, such as starch granules or glycogen can occur both at these sites (Tibbot et al. 2000; Nielsen et al. 2008, 2009;) as well as by the involvement of separate binding modules referred to as starch binding domains (Penninga et al. 1996; Rodriguez-Sanoja et al. 2000; Sumitani et al. 2000; Juge et al. 2006).

GH Family 13 enzymes are retaining as was first demonstrated by quantitative gas liquid chromatogrphic analysis of formation of a-maltose fro diferent maltosides (Kimura and Chiba, 1983) futher supported y NMR analysis of the release of a-maltose from similar substrates (isoda et al 1992) as demosntrated for a number of different a-amylasesref) and they follow the classical Koshland double-displacement mechanism (ref). This has been supported by covalent labeling using 4-deoxy-maltotriose-fluoride labelling the catalytic nucleophile (Uitdehaag et al., 1999), 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 α-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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The catalytic residues have been identified from early crystal structures (Matsuura et al. 1984; Buisson et al. 1987). In fact throughout the family GH13 only the catalytic triad plus an arginine residue are totally conserved; the catalytic site includes an aspartate as catalytic nucleophile, a glutamate as general acid/base, and an aspartate that participates critically in stabilizing the transition state (Uitdehaag et al. 1999). The fourth invariantly conserved GH13 residue, the arginine, is positioned two residues preceding the catalytic nucleophile (MacGregor et al. 2001). This conservation does not apply for the enzymatically inactive heavy-chains (rBAT proteins and 4F2hc antigens) of the amino acid transporters (Gabrisko & Janecek 2009). Numerous mutational analyses have been performed to confirm the essential roles of the three residues in catalysis, and normally the loss in activity is four-five orders of magnitude. The catalytic residues have been identified from early crystal structures (ref). In fact throughout the Family 13 only three residues are totally conserved (except for in the amino acid transporters) these include an Asp catalytic nucleophile, a Glu general acid/base, and a catalytic site residue which is an Asp that participates critically in stabilizing the transition state (ref). Numerous mutational analyses have been performed to confirm the essential roles of these three residues in catalysis, and normally the loss in activity is four-five orders of magnitude.

Three-dimensional structures

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Numerous GH13 subfamilies contain members for which a three-dimensional structure has been determined. In general, the GH13 members are multidomain proteins with catalytic (β/α)8-barrel (i.e. TIM-barrel) domain (called domain A) having a small domain B (usually varying in length and of irregular structure) (Janecek et al. 1997) inserted in the loop between the β3-strand and α3-helix of the barrel, and succeeded by the C-terminal antiparallel β-sandwich domain, called domain C. The catalytic site formed by the C-terminal extensions of strands β4, β5 and β7, carrying the catalytic triad of aspartate, glutamate and aspartate, respectively (Matsuura et al. 1984; Qian et al. 1993; Kadziola et al. 1994), but also other loops contribute to the overall architecture of the active site.

The first crystals for barley α-amylase were reported in the mid-forties, however the first crystal structures were those of TAKA-amylase A (Matsuura et al. 1984; Brzozowski & Davies 1997) and porcine pancreatic α-amylase (Buisson et al. 1987; Qian et al. 1993). This was followed by structures of other α-amylases from bacteria (Machius et al. 1995; Aghajari et al. 1998; Brzozowski et al. 2000) and from higher plants (Kadziola et al. 1994; Robert et al. 2003); the industrially important cyclodextrin glucanotransferase (Hofmann et al. 1989; Lawson et al. 1994; Leemhuis et al. 2003) and the closely related maltogenic α-amylase (Dauter et al. 1999). Later on the structures of the amylopectin debranching isoamylase (Katsuya et al. 1998) and the related pullulanase (Mikami et al. 2006) and limit dextrinase (Vester-Christensen et al. 2010) were determined. Furthermore the oligo-1,6-glucosidase (Kizaki et al. 1993) and the related dextran glucosidase (Hondoh et al. 2008), as well as maltogenic amylase (Kim et al. 1999), cyclomaltodextrinase (Lee et al. 2002) and neopullulanase (Hondoh et al. 2003) - nearly indistinguishable from each other - together with the neopullulanase-like “α-amylases” TVA I (Kamitori et al. 2002) and TVA II (Kamitori et al. 1999), and the amylosucrase (Skov et al. 2001), sucrose phosphorylase (Sprogoe et al. 2004), sucrose hydrolase (Kim et al. 2008) and sucrose isomerase (Zhang et al. 2003; Ravaud et al. 2007), were solved. Finally structures have been solved of glycogen branching (Abad et al. 2002) and debranching (Woo et al. 2008) enzymes.

Among the solved structures are numerous site-directed-mutant and ligand-complexed forms. However, although there are structures available for most of the GH13 specificities, some still remain to be determined. Noticeably crystal structures are available of several α-amylase/proteinaceous inhibitor complexes (for reviews, see Svensson et al. 2004; Payan 2004).

Numerous GH13 subfamilies contain members for which a three-dimensional structure has been determined. The first crystal are reported for barley α-amylase were reported in the mid-forties, however the first crystal structures were of porcine pancreatic and α-amylase and TAKA-amylase (ref). This was followed by structures of other α-amylases from bacteria and from higher plants (refs) and the industrially important cyclodextrin glucanotransferase (ref). Later on the amylopectin debranching isoamylase and the related pullulanases were structure determined (ref). More recently amylosucrase (ref), an exo-dextranase (ref) and also a dextrinsucrase (ref) was solved. Among the solved structures are numerous site-directed mutant and numerous ligand complexed forms. There are structurals available for many of these specificities, but some still remain to be determined.

Family Firsts

First sterochemistry determination

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α-Maltose was released from different α-maltosides by B. subtilis saccharifying α-amylase, Taka-amylase A, and porcine pancreas α-amylase, as determined by quantitative gas liquid chromatography (Kimura & Chiba 1983). This was as well demonstrated by NMR analysis of the anomeric configuration of the released product (Isoda et al. 1992). α-Maltose was released from different α-maltosides by B. subtilis saccharifying α-amylase, Taka-amylase A, and porcine pancreas α-amylase, as determined by quantitative gas liquid chromatography [13]. This was as well demonstrated by NMR analysis of the anomeric configuration of the released product [14].

First catalytic nucleophile

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A glycosidic covalent bond was formed in the intermediate of the mechanism between the catalytic nucleophile (D229) of Bacillus circulans 251 CGTase and a maltotriosyl moiety (Uitdehaag et al. 1999). Mutational analysis of human pancreatic α-amylase provided strong support for D197 being the catalytic nucleophile as demonstrated by kinetics analysis (Rydberg et al. 2002). A b-glycosidic covalent bond was formed in the intermediate of mechanism between the catalytic nucleophile (D229) of Bacillus circulans 251 CGTase and a maltotriosyl moiety [15]. Mutational analysis of human pancreatic α-amylase provided strong support for D197 being the catalytic nucleophile as demonstrated by kinetics analysis [16].

First general acid/base

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Mutational analysis of human pancreatic α-amylase using enzymatic kinetics and structural analysis provided strong support for E233 playing the role of the catalytic acid/base (Rydberg et al. 2002). Mutatitional analysis of human pancreatic α-amylase using enzymatic kinetics and structural analysis provided strong support for E233 playing the role of the catalytic acid/base [16].

First 3-D structure

The first high-resolution three-dimensional structure was determined for Taka-amylase A (Matsuura et al. 1984).

The first high-resolution three-dimensional structure was determined for Taka-amylase A [17].

Proteinaceous inhibitors Exogenous and endogenous inhibitory protein have been reported from microorganisms and plants (ref) directed towards α-amylases (ref) and limit dextrinases (ref).

References

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