CAZypedia needs your help!
We have many unassigned pages in need of Authors and Responsible Curators. See a page that's out-of-date and just needs a touch-up? - You are also welcome to become a CAZypedian. Here's how.
Scientists at all career stages, including students, are welcome to contribute.
Learn more about CAZypedia's misson here and in this article.
Totally new to the CAZy classification? Read this first.
Difference between revisions of "Glycoside Hydrolase Family 50"
Jump to navigation
Jump to search
Harry Brumer (talk | contribs) m (Text replacement - "\^\^\^(.*)\^\^\^" to "$1") |
|||
| (8 intermediate revisions by 3 users not shown) | |||
| Line 1: | Line 1: | ||
<!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --> | <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --> | ||
| − | {{ | + | {{CuratorApproved}} |
| − | * [[Author]]: | + | * [[Author]]: [[User:Mirjam Czjzek|Mirjam Czjzek]] |
| − | * [[Responsible Curator]]: | + | * [[Responsible Curator]]: [[User:Mirjam Czjzek|Mirjam Czjzek]] |
---- | ---- | ||
| Line 18: | Line 18: | ||
|- | |- | ||
|'''Active site residues''' | |'''Active site residues''' | ||
| − | |inferred from clan GH-A as two Glu | + | |inferred from clan [http://www.cazy.org/Glycoside-Hydrolases.html GH-A]<br>as two Glu |
|- | |- | ||
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link''' | |{{Hl2}} colspan="2" align="center" |'''CAZy DB link''' | ||
| Line 26: | Line 26: | ||
</div> | </div> | ||
<!-- This is the end of the table --> | <!-- This is the end of the table --> | ||
| − | |||
== Substrate specificities == | == Substrate specificities == | ||
| − | To date, all characterized [[glycoside hydrolases]] of family 50 are β-agarases (EC [{{EClink}}3.2.1.81 3.2.1.81]) that cleave β-1,4 glycosidic bonds of agarose, releasing neoagaro-biose -tetraose and -hexaose <cite> | + | To date, all characterized [[glycoside hydrolases]] of family 50 are β-agarases (EC [{{EClink}}3.2.1.81 3.2.1.81]) that cleave β-1,4 glycosidic bonds of agarose, releasing neoagaro-biose -tetraose and -hexaose <cite>Sugano1993 Sugano1994 Ohta2005 Lee2006</cite>. Three enzymes, Aga50A and Aga50D from ''Saccharophagus degradans'' and Aga50B from ''Vibrio sp.'' have been reported to be pure exo-β-agarases <cite>Kim2010</cite>. |
| − | |||
== Kinetics and Mechanism == | == Kinetics and Mechanism == | ||
| − | + | That GH50 enzymes potentially utilize a retaining mechanism has only been inferred by analogy with clan [http://www.cazy.org/Glycoside-Hydrolases.html 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 == | == Catalytic Residues == | ||
| − | + | Similarly, the catalytic residues in this family have not been directly identified, but may be inferred from superposition with other clan [http://www.cazy.org/Glycoside-Hydrolases.html GH-A] enzymes. | |
| − | |||
== Three-dimensional structures == | == Three-dimensional structures == | ||
| − | + | Unknown; from analogy to clan [http://www.cazy.org/Glycoside-Hydrolases.html GH-A] enzymes it can be inferred that the 3D structure will be based on a (β/α)<sub>8</sub> barrel fold. | |
| − | |||
== Family Firsts == | == Family Firsts == | ||
| − | ;First stereochemistry determination: | + | ;Identification of first family member: This family was created in the [{{CAZyDBlink}}GH50.html CAZy Ddatabase] following the work of Sugano et al. <cite>Sugano1993</cite>. |
| − | ;First catalytic nucleophile identification: | + | ;First stereochemistry determination: not determined yet. |
| − | ;First general acid/base residue identification: | + | ;First catalytic nucleophile identification: not determined yet. |
| − | ;First 3-D structure: | + | ;First general acid/base residue identification: not determined yet. |
| + | ;First 3-D structure: not determined yet. | ||
== References == | == References == | ||
<biblio> | <biblio> | ||
| − | # | + | #Sugano1993 pmid=8517750 |
| − | # | + | #Sugano1994 pmid=8193156 |
| − | # | + | #Ohta2005 pmid=15307821 |
| − | # | + | #Lee2006 pmid=17028783 |
| − | + | #Kim2010 pmid=19802606 | |
</biblio> | </biblio> | ||
[[Category:Glycoside Hydrolase Families|GH050]] | [[Category:Glycoside Hydrolase Families|GH050]] | ||
Latest revision as of 13:14, 18 December 2021
This page has been approved by the Responsible Curator as essentially complete. CAZypedia is a living document, so further improvement of this page is still possible. If you would like to suggest an addition or correction, please contact the page's Responsible Curator directly by e-mail.
| 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
- 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 |
- 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 |
- 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 |
- 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 |
- 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 |