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

Family GH78 glycoside hydrolases are found in bacteria and fungi. The characterized activity of this family is α-L-rhamnosidase (EC 3.2.1.40). α-L-Rhamnosidases catalyze the hydrolysis of α-L-rhamnosyl-linkages in L-rhamnose containing compounds, flavonoid glycosides such as naringin, hesperidin and rutin, polysaccharides such as rhamnogalacturonan and arabinogalactan-protein, or 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 acid base-assisted single displacement or inverting mechanism elucidated by proton NMR [3, 4].

α-L-rhamnosidases have molecular masses of 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

The crystallographic and mutagenesis studies of Streptomyces avermitilis α-L-rhamnosidase (SaRha78A) indicated that Glu895 appeared to be the catalytic general base, and Glu636 appeared to comprise the catalytic proton donor (acid) of the enzyme, activating a water molecule [9]. Glutamate is conserved for the catalytic general base in all characterized α-L-rhamnosidases.

Three-dimensional structures

The first crystal structure was determined for Bacillus sp. GL1 α-L-rhamnosidase B (BsRhaB) (PDB ID 2okx)[10]. Then, crystal structure of the putative α-L-rhamnosidase BT1001 from Bacteroides thetaiotaomicron VPI-5482 was determined by Structural genom project (PDB ID 3cih)[11]. Recently, crystal structure of Streptomyces avermitilis α-L-rhamnosidase (SaRha78A) in complex with L-rhamnose has been reported (PDB IDs 3w5m, 3w5n)[9].

α-L-Rhamnosidases have a modular structure. BsRhaB, BT1001, and SaRha78A show five-, four and six-module structures. The catalytic module of GH78 enzymes is an (α/α)₆-barrel. A fibronectin type 3 fold β-domain often appears in the N-terminus, and the Greek key β-domain exist just after the catalytic module comprising the C-terminus. Several β-domains are inserted between the N-terminal domain and the catalytic module. Streptomyces avermitilis α-L-rhamnosidase (SaRha78A) possesses one carbohydrate binding module (CBM67), which binds terminal L-rhamnose sugars in the presence of calcium ion [9].

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

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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

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 |
12. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, and Henrissat B. (2009). The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res. 2009;37(Database issue):D233-8. DOI:10.1093/nar/gkn663 |

13. Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). DOI: 10.1042/BJ20080382