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Protein-Carbohydrate Interactions Leading to Hydrolysis and Transglycosylation in Plant Glycoside Hydrolase Family 1 Enzymes

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Protein-Carbohydrate Interactions Leading to Hydrolysis and Transglycosylation in Plant Glycoside Hydrolase Family 1 Enzymes J. Appl. Glycosci., 59, 51‒62 (2012) doi: 10.5458/jag.jag.JAG-2011_022 ©2012 The Japanese Society of Applied Glycoscience Review Protein-carbohydrate Interactions Leading to Hydrolysis and Transglycosylation in Plant Glycoside Hydrolase Family 1 Enzymes (Received December 7, 2011; Accepted January 30, 2012) (J-STAGE Advance Published Date: February 11, 2012) James R. Ketudat Cairns,1,＊ Salila Pengthaisong,1 Sukanya Luang,1 Sompong Sansenya, 1 Anupong Tankrathok1 and Jisnuson Svasti2 1Schools of Biochemistry and Chemistry, Institute of Science, Suranaree University of Technology (Muang District, Nakhon Ratchasima 30000, Thailand) 2Department of Biochemistry and Centre for Protein Structure and Engineering, Faculty of Science, Mahidol University (Phayathai, Bangkok 10400, Thailand) Abstract: Glycoside hydrolase family 1 (GH1) includes enzymes with a wide range of specifi cities in terms of reactions, substrates and products, with plant GH1 enzymes covering a particularly wide range of hy- drolases and transglycosylases. In plants, in addition to β-D-glucosidases, β-D-mannosidases, disacchari- dases, thioglucosidases and hydroxyisourate hydrolase, GH1 has recently been found to include galactosyl and glucosyl transferases that utilize galactolipid and acyl glucose donors, respectively. The amino acids binding to the nonreducing monosaccharide residue of glycosides and oligosaccharides in subsite －1 are largely conserved in GH1 glycoside hydrolases, despite their different glycon specifi cities, and residues outside this subsite contribute to sugar specifi city. The conserved subsite －1 residues form extensive hy- drogen bonding and aromatic stacking interactions to the glycon to distort it toward the transition state, so they must make different interactions with different sugars. Aglycon specifi city is largely determined by interactions with the cleft leading into the active site, but different enzymes appear to interact with their substrates via different residues. The most extended aglycon binding interactions that have been studied extensively are those for cellooligosaccharides. Rice Os3BGlu7 (BGlu1) β-D-glucosidase, which binds cel- looligosaccharides residues in subsites +1 to +4 primarily by water-mediated hydrogen bonds and a few aromatic-sugar stacking interactions, appears to show remarkable plasticity in this binding. Although mutations that change the mechanism of the hydrolases, such as glycosynthases and thioglycoligases cre- ate transglycosylases, the structural basis for natural transglycosylase vs. glycoside hydrolase activities in GH1 enzymes remains to be determined. Key words: glycoside hydrolase, transglycosylase, β-glucosidase, enzyme specifi city, glycosides, oligosac- charides Glycoside hydrolases (GH, glycosidases) have been grouped into families related by sequence similarity and ＊Corresponding author (Tel +66‒44‒22‒4304, Fax +66‒44‒22‒4185, larger clans that show structural and mechanistic similari- Email: [email protected]). ty,1‒3) as catalogued in the Carbohydrate-Active enZYmes Abbreviations: AA5GT, anthocyanin 5-O-glucosyltransferase; AA7GT, (CAZy) website (http://www.cazy.org).4) GH family 1 (GH1) anthocyanin 7-O-glucosyltransferase; CAZY, Carbohydrate-Active en- zymes; DGDG, digalactosyl diacylglyceride; DIBOA, 2,4-dihydroxy-1,4- is one of these families with diverse functional properties, benzoxazin-3-one; DIMBOA, 2,4-dihydroxy-7-methoxy-1,4-benzoxazin- which belongs to GH Clan A.5,6) GH1 includes retaining 3-one; DIMBOA-Glc, 2-O-β-D-glucopyranosyl-4-hydroxy-7-methoxy-1, glycosidases from archaea, eubacteria and eukaryotes, with 4-benzoxazin-3-one; DP, degree of polymerization; GGGT, galactolipid: a wide range of substrate and reaction specifi cities, as well galactolipid galactosyl transferase; GH, glycoside hydrolase; GH1, as proteins with other biological and enzymatic functions. glycoside hydrolase family 1; GT; glycosyltransferases; HIUH, purine hydrolase hydroxyisourate hydrolase; HvBII, Hordeum vulgare β-D- These include broad spectrum β-D-glycosidases, as well as glucosidase isoenzyme βII; MGDG; monogalactosyl diacylglyceride; β-D-6-phosphoglycosidases (EC 3.2.1.85 and EC 3.2.1.86), NMR, nuclear magnetic resonance; Os3BGlu6, Oryza sativa β-D-glucosidases (EC 3.2.1.21), β-D-galactosidases (EC β-glucosidase isoenzyme Os3BGlu6; Os3BGlu7, O. sativa β-glucosidase 3.2.1.23) and β-D-mannosidases (EC 3.2.1.25) in archaea isoenzyme Os3BGlu7; Os4BGlu12, O. sativa β-glucosidase isoenzyme Os4BGlu12; Os9BGlu31, O. sativa β-transglucosylase isoenzyme Os- and eubacteria, insect myrosinases (β-D-thioglucosidases, 9BGlu31; Os7BGlu26, O. sativa β-glucosidase isoenzyme Os7BGlu26; EC 3.2.1.147), digestive β-glycosidases, cytoplasmic Os3BGlu8, O. sativa β-glucosidase isoenzyme Os8BGlu8; pNP, para- β-D-glucosidase and the Klotho signaling protein and its nitrophenol; QM/MM, quantum mechanics/molecular mechanics; relatives in animals, and hydroxyisourate hydrolase (EC SbDhr1, Sorghum bicolor dhurrinase isoenzyme 1; SFR2, Sensitive-to- 3.5.2.17), as well as β-D-glycosidases with various specifi c- Freezing-2; ZmGlu1, Zea mays β-glucosidase isoenzyme Glu1; 7) UDP-glucose, uridine diphosphate-α-D-glucose; XET, xyloglucan endo- ities in plants. transferases. Although GH1 proteins from all domains and phyla of 52 J. Appl. Glycosci., Vol. 59, No. 2 (2012) living organisms have fascinating and potentially useful Activities of plant glycoside hydrolase family 1 enzymes. activities, it is in plants that these proteins have expanded the While archaea, bacteria and fungi tend to have one to a most to acquire a great variety of catalytic activities and this few GH1 genes and humans (Homo sapiens) have fi ve GH1 review will focus on the plant GH1 enzymes. Bacterial and genes, plants have many more.4,7) Arabidopsis (Arabidopsis animal enzymes will be mentioned when they have been thaliana) has 48 GH1 genes, while 40 GH1 genes have been used to demonstrate catalytic mechanisms, while the basis of identifi ed in rice genome databases, 34 of which are thought substrate binding and reaction specifi city will primarily be to encode translated rice proteins.8,9) With the exception of illustrated with plant enzymes, particularly those from rice Sensitive-to-Freezing-2 (SFR2) and its orthologues, plant (Oryza sativa). First, we will describe the types of activities GH1 enzymes fall into a relatively closely related phyloge- found in plants, then the catalytic mechanism and substrate netic cluster within GH1, as shown in Fig. 1. binding of GH1, and fi nally the engineering of GH1 enzymes As noted above, GH1 members have a wide variety of to produce transglycosylase activities and the recently activities, some of which may not even involve glycoside discovered naturally occurring plant GH1 transglycosylases. hydrolase activities, although the plant GH1 members that The roles of carbohydrate binding in these activities will be have been described to date are all hydrolases or transferas- emphasized. es. The GH1 glycosidases in plants include β-D-glucosidases, Fig. 1. Phylogenetic tree of plant and other glycoside hydrolase family 1 proteins. The tree was produced from GH1 sequences, including all rice and Arabidopsis genes with sequences including the catalytic amino acids in the genomic databases named as in Xu et al.8); Opassiri et al.,9) as well as all available GH1 sequences of the moss Phycomitrella patens ssp. patens, plant GH1 with known 3D structures and plant sequences previously compared in references 8 and 9 (designated by genus and species initials and Genbank accession), and a selection of archaeal, bacterial, animal and fungal sequences. The tree was generated by the neighbor-joining meth- od79) with MEGA580) after protein sequence alignment by MUSCLE.81) The phylogenetic clusters that include both rice and Arabidopsis sequences (At/Os1‒8) and the Brassicales-specifi c clusters (At I and II) are labeled as designated by Opassiri et al.9) The analysis of animal, fungal, archaeal and fungal sequences is not extensive, but includes those with known 3D structural models and those with high similarity to SFR2. The analysis involved 146 amino acid sequences. All positions with less than 95% site coverage were eliminated. There were a total of 372 positions in the fi nal dataset. Percent reproducibility in 1,000 bootstrap trees are listed on branches with >50% reproducibility, while branches with <50% reproducibility are not marked. It may be noted that in this analysis, clusters At/Os1, At/Os2 and At/Os4 form a reliably clustered group, as do At/Os7, At I, At II and the monocot plastid β-glucosidases. At/Os8, consisting of SFR2 galactosyl transferase homologues, clusters with bacterial and archaeal β-galactosidases/β-glycosidases and is distant from other plant, animal, fungal and certain bacterial and archaeal β-glucosidases. Ketudat Cairns et al.: Plant Glycoside Hydrolase Family 1 Specifi city 53 β-D-mannosidases, more general β-glycosidases, β-D- feruloyl glucose, p-coumaroyl glucose, vanillyl glucose and thioglucosidases and disaccharidases.10‒12) Many of the similar glucose esters, as was seen for the anthocyanidin β-D-glucosidases in fact have higher activities toward 3-O-glucoside glucosyl transferases, but Os9BGlu31 β-D-fucoside, but due to the paucity of β-D-fucosides in recognizes a different set of acceptor substrates. nature, are presumed to act primarily as β-D-glucosidases.7) Many of these enzymes also have lesser activities toward Catalytic mechanism of family 1 glycoside hydrolases. para-nitrophenyl (pNP)-β-D-galactoside,
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