Glycoside Hydrolase Family 78

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• Author: Zui Fujimoto
• Responsible Curator: Zui Fujimoto

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Glycoside Hydrolase Family GH78
Clan	GH-M
Mechanism	inverting
Active site residues	known
CAZy DB link
https://www.cazy.org/GH78.html

Substrate specificities

Genes encoding family GH78 glycoside hydrolases are found in bacteria and fungi. The sole identified activity of enzymes of this family is hydrolysis of α-L-rhamnosides (EC 3.2.1.40). The GH78 α-L-rhamnosidases catalyze the hydrolysis of α-L-rhamnosyl-linkages in L-rhamnosides, including: flavonoid glycosides such as naringin, hesperidin and rutin; polysaccharides such as rhamnogalacturonan and arabinogalactan-protein and glycolipids. α-L-Rhamnosidases have been found to be one component of rhamnogalacturonan hydrolase [1], or naringinase [2].

Kinetics and Mechanism

GH78 enzymes hydrolyze glycosidic bonds through an inverting mechanism as elucidated by proton NMR [3, 4]. Typical GH78 α-L-rhamnosidases have molecular masses in the range 80-120 kDa, and are most active at pH 4.0 to 8 and temperature of 50°C against p-nitrophenyl-α-L-rhamnopyranoside [1, 5, 6, 7, 8].

Catalytic Residues

Crystallographic and mutagenesis studies of Streptomyces avermitilis α-L-rhamnosidase (SaRha78A), notably including an enzyme-product complex structure, suggested that Glu895 is the catalytic general base responsible for activating a water molecule, and that Glu636 is the catalytic general acid, assisting leaving-group departure [9]. All characterized α-L-rhamnosidases appear to contain a glutamate as the catalytic general base.

Three-dimensional structures

The first crystal structure of a GH78 member was determined for Bacillus sp. GL1 α-L-rhamnosidase B (BsRhaB) (PDB ID 2okx) [10]. Subsequently, the crystal structure of the putative α-L-rhamnosidase BT1001 from Bacteroides thetaiotaomicron VPI-5482 was determined by a structural genomics project (PDB ID 3cih) [11]. The crystal structure of Streptomyces avermitilis α-L-rhamnosidase (SaRha78A) in complex with the product L-rhamnose has revealed key active-site details (PDB IDs 3w5m, 3w5n) [9]. More recently, the crystal structure of a Klebsiella oxytoca α-rhamnosidase (KoRha) has been solved in complex L-rhamnose.

α-L-Rhamnosidases have a modular structure. BsRhaB, BT1001, and SaRha78A show five-, four and six-module structures. The catalytic domain of GH78 enzymes is an (α/α)₆-barrel. A fibronectin type-3 fold β-domain often appears at the N-terminus, and a C-terminal Greek key β-domain exists just after the catalytic domain. Several β-domains are also inserted between the N-terminal domain and the catalytic domain. Streptomyces avermitilis α-L-rhamnosidase (SaRha78A) possesses one carbohydrate binding module (CBM67), which binds terminal L-rhamnose sugars in the presence of a calcium ion [9]. On the other hand, KoRha has only two structual domains, one β-domain and one catalytic domain, forming a homodimer [12]. These two domains are common among all structure-determined enzymes.

Family Firsts

First stereochemistry determination

Aspergillus aculeatus α-L-rhamnosidase (RhaA), by ¹H-NMR [3].

First general base residue identification

Streptomyces avermitilis α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data [9].

First general acid residue identification

Streptomyces avermitilis α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data [9].

First 3-D structure

Bacillus sp. GL1 α-L-rhamnosidase B (BsRhaB) (PDB IDs 2okx) [10].

References

1. Mutter M, Beldman G, Schols HA, and Voragen AG. (1994). Rhamnogalacturonan alpha-L-rhamnopyranohydrolase. A novel enzyme specific for the terminal nonreducing rhamnosyl unit in rhamnogalacturonan regions of pectin. Plant Physiol. 1994;106(1):241-50. DOI:10.1104/pp.106.1.241 |

2. Young, NM, Johnston RAZ, and Richards, JC. Purification of the α-L-rhamnosidase of Penicillium decumbens and characterisation of two glycopeptide components. Carbohydr. Res. 1989 Aug;191(1):53-62. DOI: 10.1016/0008-6215(89)85045-1

3. Pitson SM, Mutter M, van den Broek LA, Voragen AG, and Beldman G. (1998). Stereochemical course of hydrolysis catalysed by alpha-L-rhamnosyl and alpha-D-galacturonosyl hydrolases from Aspergillus aculeatus. Biochem Biophys Res Commun. 1998;242(3):552-9. DOI:10.1006/bbrc.1997.8009 |
4. Zverlov VV, Hertel C, Bronnenmeier K, Hroch A, Kellermann J, and Schwarz WH. (2000). The thermostable alpha-L-rhamnosidase RamA of Clostridium stercorarium: biochemical characterization and primary structure of a bacterial alpha-L-rhamnoside hydrolase, a new type of inverting glycoside hydrolase. Mol Microbiol. 2000;35(1):173-9. DOI:10.1046/j.1365-2958.2000.01691.x |
5. Hashimoto W, Nankai H, Sato N, Kawai S, and Murata K. (1999). Characterization of alpha-L-rhamnosidase of Bacillus sp. GL1 responsible for the complete depolymerization of gellan. Arch Biochem Biophys. 1999;368(1):56-60. DOI:10.1006/abbi.1999.1279 |
6. Manzanares P, van den Broeck HC, de Graaff LH, and Visser J. (2001). Purification and characterization of two different alpha-L-rhamnosidases, RhaA and RhaB, from Aspergillus aculeatus. Appl Environ Microbiol. 2001;67(5):2230-4. DOI:10.1128/AEM.67.5.2230-2234.2001 |
7. Koseki T, Mese Y, Nishibori N, Masaki K, Fujii T, Handa T, Yamane Y, Shiono Y, Murayama T, and Iefuji H. (2008). Characterization of an alpha-L-rhamnosidase from Aspergillus kawachii and its gene. Appl Microbiol Biotechnol. 2008;80(6):1007-13. DOI:10.1007/s00253-008-1599-7 |
8. Ichinose H, Fujimoto Z, and Kaneko S. (2013). Characterization of an α-L-Rhamnosidase from Streptomyces avermitilis. Biosci Biotechnol Biochem. 2013;77(1):213-6. DOI:10.1271/bbb.120735 |
9. Fujimoto Z, Jackson A, Michikawa M, Maehara T, Momma M, Henrissat B, Gilbert HJ, and Kaneko S. (2013). The structure of a Streptomyces avermitilis α-L-rhamnosidase reveals a novel carbohydrate-binding module CBM67 within the six-domain arrangement. J Biol Chem. 2013;288(17):12376-85. DOI:10.1074/jbc.M113.460097 |
10. Cui Z, Maruyama Y, Mikami B, Hashimoto W, and Murata K. (2007). Crystal structure of glycoside hydrolase family 78 alpha-L-Rhamnosidase from Bacillus sp. GL1. J Mol Biol. 2007;374(2):384-98. DOI:10.1016/j.jmb.2007.09.003 |
11. Bonanno JB, Almo SC, Bresnick A, Chance MR, Fiser A, Swaminathan S, Jiang J, Studier FW, Shapiro L, Lima CD, Gaasterland TM, Sali A, Bain K, Feil I, Gao X, Lorimer D, Ramos A, Sauder JM, Wasserman SR, Emtage S, D'Amico KL, and Burley SK. (2005). New York-Structural GenomiX Research Consortium (NYSGXRC): a large scale center for the protein structure initiative. J Struct Funct Genomics. 2005;6(2-3):225-32. DOI:10.1007/s10969-005-6827-0 |
12. O'Neill EC, Stevenson CE, Paterson MJ, Rejzek M, Chauvin AL, Lawson DM, and Field RA. (2015). Crystal structure of a novel two domain GH78 family α-rhamnosidase from Klebsiella oxytoca with rhamnose bound. Proteins. 2015;83(9):1742-9. DOI:10.1002/prot.24807 |