Glycoside Hydrolase Family 50

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• Author:
• Responsible Curator: ^^^Mirjam Czjzek^^^

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Glycoside Hydrolase Family GH50
Clan	GH-A
Mechanism	probably retaining
Active site residues	inferred from clan GH-A as two Glu
CAZy DB link
http://www.cazy.org/GH50.html

Substrate specificities

To date, all characterized glycoside hydrolases of family 50 are β-agarases (EC 3.2.1.81) that cleave β-1,4 glycosidic bonds of agarose, releasing neoagaro-biose -tetraose and -hexaose [1, 2, 3]. Three enzymes, Aga50A and Aga50D from Saccharophagus degradans and Aga50B from Vibrio sp. have been reported to be pure exo-β-agarases [4].

Kinetics and Mechanism

Actually, a potential retaining mechanism of this glycoside hydrolase familly can only be inferred from analogy to clan GH-A enzymes http://www.cazy.org/GH50.html. No mechanistic or kintetic analysis demonstrating the stereochemical outcome of the reaction have been reported for this family to date.

Catalytic Residues

Unkown

Three-dimensional structures

Unknown; from analogy to clan GH-A enzymes it can be inferred that the 3D structure will be based on a (β/a)₈ barrel fold.

Family Firsts

Identification of first family member

The family was created in Cazy based on the work of XXXX et al. [1].

First stereochemistry determination

not determined yet.

First catalytic nucleophile identification

not determined yet.

First general acid/base residue identification

not determined yet.

First 3-D structure

not determined yet.

References

1. Sugano Y, Terada I, Arita M, Noma M, and Matsumoto T. (1993). Purification and characterization of a new agarase from a marine bacterium, Vibrio sp. strain JT0107. Appl Environ Microbiol. 1993;59(5):1549-54. DOI:10.1128/aem.59.5.1549-1554.1993 |
2. Sugano Y, Matsumoto T, and Noma M. (1994). Sequence analysis of the agaB gene encoding a new beta-agarase from Vibrio sp. strain JT0107. Biochim Biophys Acta. 1994;1218(1):105-8. DOI:10.1016/0167-4781(94)90109-0 |
3. Ohta Y, Hatada Y, Ito S, and Horikoshi K. (2005). High-level expression of a neoagarobiose-producing beta-agarase gene from Agarivorans sp. JAMB-A11 in Bacillus subtilis and enzymic properties of the recombinant enzyme. Biotechnol Appl Biochem. 2005;41(Pt 2):183-91. DOI:10.1042/BA20040083 |
4. Kim HT, Lee S, Lee D, Kim HS, Bang WG, Kim KH, and Choi IG. (2010). Overexpression and molecular characterization of Aga50D from Saccharophagus degradans 2-40: an exo-type beta-agarase producing neoagarobiose. Appl Microbiol Biotechnol. 2010;86(1):227-34. DOI:10.1007/s00253-009-2256-5 |
5. Sugano Y, Matsumoto T, and Noma M. (1994). Sequence analysis of the agaB gene encoding a new beta-agarase from Vibrio sp. strain JT0107. Biochim Biophys Acta. 1994;1218(1):105-8. DOI:10.1016/0167-4781(94)90109-0 |