Glycoside Hydrolase Family 50

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• Author: Mirjam Czjzek
• 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
https://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, 4]. Three enzymes, Aga50A and Aga50D from Saccharophagus degradans and Aga50B from Vibrio sp. have been reported to be pure exo-β-agarases [5].

Kinetics and Mechanism

That GH50 enzymes potentially utilize a retaining mechanism has only been inferred by analogy with clan GH-A enzymes. No mechanistic or kinetic analysis demonstrating the stereochemical outcome of the reaction have been reported for this family to date.

Catalytic Residues

Similarly, the catalytic residues in this family have not been directly identified, but may be inferred from superposition with other clan GH-A enzymes.

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/α)₈ barrel fold.

Family Firsts

Identification of first family member

This family was created in the CAZy Ddatabase following the work of Sugano 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. Lee DG, Park GT, Kim NY, Lee EJ, Jang MK, Shin YG, Park GS, Kim TM, Lee JH, Lee JH, Kim SJ, and Lee SH. (2006). Cloning, expression, and characterization of a glycoside hydrolase family 50 beta-agarase from a marine Agarivorans isolate. Biotechnol Lett. 2006;28(23):1925-32. DOI:10.1007/s10529-006-9171-y |
5. 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 |