Glycoside Hydrolase Family 78

This page is currently under construction. This means that the Responsible Curator has deemed that the page's content is not quite up to CAZypedia's standards for full public consumption. All information should be considered to be under revision and may be subject to major changes.

• 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.

α-L-Rhamnosidases have been found to be one components 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) [10]. Then, crystal structure of the putative α-L-rhamnosidase BT1001 from Bacteroides thetaiotaomicron VPI-5482 was determined by Structural genom project [11]. Recently, crystal structure of Streptomyces avermitilis α-L-rhamnosidase (SaRha78A) in complex with L-rhamnose was reported [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) [10].

References

Error fetching PMID 7972516:
Error fetching PMID 9464254:
Error fetching PMID 10415111:
Error fetching PMID 10632887:
Error fetching PMID 11319105:
Error fetching PMID 17936784:
Error fetching PMID 23486481:
Error fetching PMID 16211523:
Error fetching PMID 18633609:
Error fetching PMID 23291751:

2. Young, N.M., Johnston R.A.Z. and Richards, J.C. (1989) Purification of the α-L-rhamnosidase of Penicillium decumbens and characterisation of two glycopeptide components. Carbohydr. Res. [

   http://dx.doi.org/10.1016/0008-6215(89)85045-1 DOI: 10.1016/0008-6215(89)85045-1]

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