Glycoside Hydrolase Family 78

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Author:
Responsible Curator: ^^^Zui Fujimoto^^^

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.

Kinetics and Mechanism

GH78 enzymes hydrolyze glycosidic bonds through an acid base-assisted single displacement or inverting mechanism elucidated by proton NMR [1].

Bacillus sp. GL1 α-L-rhamnosidase B (BsRhaB) was a monomer with a molecular mass of about 100 kDa and was most active at pH 7.0 and 50°C against the gellan-degrading product (rhamnosyl-glucose) [2]. Aspergillus aculeatus two α-L-rhamnosidases (RhaA and RhaB) had molecular masses of 92 and 85 kDa, and were most active at pH 4.5 to 5, showed Km and Vmax values of 2.8 mM and 24 U/mg (RhaA) and 0.30 mM and 14 U/mg (RhaB) against p-nitrophenyl-α-L-rhamnopyranoside [3]. Aspergillus kawachii α-L-rhamnosidase had a molecular mass of 90 kDa and exhibited optimal activity at pH 4.0 and temperature of 50°C against p-nitrophenyl-α-L-rhamnopyranoside [4]. Streptomyces avermitilis α-L-rhamnosidase (SaRha78A) had a molecular mass of 113 kDa and exhibited optimal activity at pH 6.0 and temperature of 50°C against p-nitrophenyl-α-L-rhamnopyranoside [5].

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 [6]. 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) [7]. Then, crystal structure of the putative α-L-rhamnosidase BT1001 from Bacteroides thetaiotaomicron VPI-5482 was determined by Structural genom project [8]. Recently, crystal structure of Streptomyces avermitilis α-L-rhamnosidase (SaRha78A) in complex with L-rhamnose was reported [6].

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 [6].

Family Firsts

First stereochemistry determination: Clostridium stercorarium α-L-rhamnosidase (RamA), by ¹H-NMR [1].
First general base residue identification: Streptomyces avermitilis α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data [6].
First general acid residue identification: Streptomyces avermitilis α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data [6].
First 3-D structure: Bacillus sp. GL1 α-L-rhamnosidase B (BsRhaB) [7].

References

All Medline abstracts: PubMed