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Function and Structure Studies of GH Family 31 and 97 \Alpha

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Function and Structure Studies of GH Family 31 and 97 \Alpha 110610 (RV-17) Biosci. Biotechnol. Biochem., 75 (12), 110610-1–9, 2011 Award Review Function and Structure Studies of GH Family 31 and 97 -Glycosidases Masayuki OKUYAMA Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo 060-8589, Japan Online Publication, December 7, 2011 [doi:10.1271/bbb.110610] A huge number of glycoside hydrolases are classified an evolutionary relationship of proteins in the family, into the glycoside hydrolase family (GH family) based from which it is often possible to extract information on on their amino-acid sequence similarity. The glycoside function and structure.3) Classification in a GH family hydrolases acting on -glucosidic linkage are in GH has, accordingly, become indispensable for research on family 4, 13, 15, 31, 63, 97, and 122. This review deals glycoside hydrolases. Glycoside hydrolases are also mainly with findings on GH family 31 and 97 enzymes. divided into two mechanistic classes, inverting and Research on two GH family 31 enzymes is described: retaining enzymes: with inversion or net retention of clarification of the substrate recognition of Escherichia anomeric configuration during the catalytic reaction.4) coli -xylosidase, and glycosynthase derived from Schiz- The stereochemical outcome is generally conserved in a osaccharomyces pombe -glucosidase. GH family 97 is GH family. The inverting mechanism proceeds via a an aberrant GH family, containing inverting and simple single displacement. Two functional groups, retainingAdvance glycoside hydrolases. The inverting View enzyme usually carboxyl groups, act as general acid and general in GH family 97 displays significant similarity to base catalysts. The general acid catalyst donates a proton retaining -glycosidases, including GH family 97 retain- to the departure aglycon, and the general base catalyst ing -glycosidase, but the inverting enzyme has no simultaneously deprotonates the incoming water mole- catalytic nucleophile residue. It appears that a catalytic cule, which attacks the anomeric carbon (Fig. 1A). Most nucleophile has been eliminated during the molecular retaining glycosidases occur though a double-displace- evolution in the same way as a man-made nucleophile ment mechanism with two functional groups, which mutant enzyme, which catalyzes the inverting reaction, serve catalytic nucleophilic and catalytic acid/base. as in glycosynthase and chemical rescue. Although these functional groups mostly exist as carboxyl groups, sialidases use a phenolic hydroxyl Key words: glycoside hydrolase family 31; glycoside group of tyrosineProofs as a catalytic nucleophile.5) The hydrolase family 97; -xylosidase; -glyco- double-displace mechanism goes through two stages, synthase; divergence of catalytic residue glycosylation and deglycosylation (Fig. 1B). At the glycosylation step, the general acid/base catalyst proto- Carbohydrates are the most abundant organic mole- nates the glycosidic oxygen with bond cleavage, while cules in nature. It is traditionally thought that carbohy- the nucleophilic catalyst attacks the anomeric carbon drates are a significant fraction of the energy in the diet, from the opposite side of the glycosidic linkage and a storage form of energy, and structural components forms a covalent glycosyl-enzyme intermediate. At the such as cell walls of many organisms, the exoskeleton of deglycosylation step, the incoming water deprotonated insects, and the fibrous cellulose of plants. However, by the acid/base catalyst breaks down the intermediate carbohydrates, involved in glycoproteins and glycoli- by attacking the anomeric carbon from the opposite side pids, are now known to have essential roles in biological of the covalent bond of the intermediate. These inverting processes, including the mediation of some forms of and retaining mechanisms involve oxacarbenium-ion- intercellular communication. Glycoside hydrolases cat- like transition states. Recently, several interesting varia- alyze the hydrolysis of glycosidic linkages in such tions on the retaining mechanisms that go through a carbohydrates as glycosides, oligosaccharides, glycans, different transition state have been identified. Enzymes and glycoconjugates to obtain energy and to modify the that hydrolyze substrates containing an N-acetyl group at carbohydrates. the C2-position occasionally adopt the substrate-assisted A huge number of glycoside hydrolases have been mechanism, which goes through an oxazoline inter- discovered, and these are classified into glycoside mediate.6) These enzymes have no catalytic nucleophile hydrolase families (GH families) based on their residue, but the 2-acetamido group of the substrate acts amino-acid sequence similarity.1,2) Currently more than as an intramolecular nucleophile. Glycoside hydrolases 100 GH families are recognized. They are available that employ the aforementioned mechanisms catalyze through the website, Carbohydrate Active enZymes single or double substitution reactions. On the other (http://www.cazy.org/). Classifying glycoside hydrolases hand, the catalytic mechanism of GH family 4 and 109 is important because it indicates a common ancestor and glycoside hydrolases is distinctly different and includes This review was written in response to the author’s receipt of the Japan Society for Bioscience, Biotechnology, and Agrochemistry Award for the Encouragement of Young Scientists in 2010. Correspondence: Fax: +81-11-706-2808; E-mail: [email protected] 110610-2 M. OKUYAMA a b Advance View Fig. 1. General Mechanism of Inverting Glycosidases (a) and General Mechanism of Retaining Glycosidases (b). elimination and redox steps.7,8) This mechanism requires amylosucrase, oligo-1,6-glucosidase, and sucrose iso- NADþ, divalent metal cations, and reducing conditions, merase as well as -glucosidase. Although their catalytic and proceeds via anionic transition states. Bacillus activities are diverse, the tertiary structure and catalytic subtilis 6-phospho- -glucosidase (GlvA), a member of residues are conserved in this family.11) The enzymes GH family 4, also hydrolyzes 6-phospho -glucosides possess a ð=Þ8Proofsbarrel fold as a catalytic domain and containing an activated leaving group with inversion.9) conserve catalytically significant residues at the rim of This unique specificity has been explained by a differ- the -barrel. The family employs the double-displace- ence in essential catalytic residues in GH family 4 ment mechanism to catalyze the reaction and preserves enzymes as compared with the typical glycosidases the catalytic nucleophile and the acid/base residues at that employ the standard oxocarbenium ion mecha- the ends of -strands 4 and 5 respectively. GH family 15 nism.9) While typical enzymes have essential catalytic includes glucan 1,4- -glucosidase, so-called glucoamy- residues around the scissile bond, GH family 4 enzymes lase. The glucoamylase hydrolyzes terminal (1!4)- bear functional residues around positions, C2 and C3. linked -glucose residues from the non-reducing ends of The loose interaction of GlvA around the scissile bond the chains with release of -glucose; that is, the is responsible for GlvA being able to hydrolyze - glucoamylase is an inverting enzyme. The most of glycosides. glucoamylases are multi-domain enzymes consisting of Glycoside hydrolases acting on -glucose residues of a catalytic domain and a starch-binding domain.12) The the non-reducing end, so-called -glucosidases and catalytic domain folds as a ð=Þ6-barrel, while the glucoamylases, are found in GH family 4, 13, 15, 31, starch-binding domain folds as an antiparallel -barrel. 63, 97, and 122. Additionally, in a broad sense, GH A funnel-shaped active site is formed by long loops family 37 and 65 , -trehalases are also included in this connecting the -helices. There has been considerable category (Table 1). Among them, GH family 31 and 97 research on the structure-function relationships of enzymes are featured in this review. A brief introduction glucoamylase, involving the substrate-binding and cata- to other -glycosidases is provided below. As mentioned lytic mechanisms.11) GH family 63 contains processing above, GH family 4 enzymes display the unusual -glucosidase I that hydrolyzes terminal (1!2)-linked mechanism to hydrolyze the -glucosidic linkage with -glucose residues of the N-glycan precursor of glyco- retention. The tertiary structure of GH family 4 enzymes proteins with inversion of the anomeric form. Recently, shows no similarity to that of any known glycoside a tertiary structure of a homolog of the processing hydrolases, but bears a resemblance to those of NAD- enzyme derived from E. coli (YgjK) was described.13) dependent dehydrogenases, such as lactate dehydrogen- The structure is composed of a -sandwich domain and ase and malate dehydrogenase.8,10) GH family 13 is one a catalytic domain. The catalytic domain displays an of the largest GH families, containing -amylase, ð=Þ6 barrel fold similar to those of clan GH-L, pullulanase, cyclodextrin glucanotransferase (CGTase), including GH family 15 glucoamylase and GH family 65 branching enzyme, neopullulanase, trehalose synthase, maltose phosphorylase. GH family 122 contains only Studies of GH 31 and 97 -Glycosidases 110610-3 Table 1. Glycoside Hydrolase Families Containing the Enzyme Acting on -Glucoside Glycoside Catalytic hydrolase Fold Clan Known activities mechanism family Family 4 Retaining NAD(P)-binding — maltose-6-phosphate glucosidase, -glucosidase, -galactosidase Rossmann-fold 6-phospho- -glucosidase, -glucuronidase Family
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