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Difference between revisions of "Glycoside Hydrolase Family 107"
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With enzymes from the CAZY family [[GH29]] they form the clan GH-R. | With enzymes from the CAZY family [[GH29]] they form the clan GH-R. | ||
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== Kinetics and Mechanism == | == Kinetics and Mechanism == | ||
Content is to be added here. | Content is to be added here. | ||
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== Three-dimensional structures == | == Three-dimensional structures == | ||
| − | The crystal structures of ''Mariniflexile fucanivorans'' (PDB: [{{PDBlink}}6dns 6dns],[{{PDBlink}}6dms 6dms],[{{PDBlink}}6dlh 6dlh]) and ''Psychromonas sp.'' (PDB: [{{PDBlink}}6m8n 6m8n]). have been determined in 2018. | + | The crystal structures of ''Mariniflexile fucanivorans'' (PDB: [{{PDBlink}}6dns 6dns],[{{PDBlink}}6dms 6dms],[{{PDBlink}}6dlh 6dlh]) and ''Psychromonas sp.'' (PDB: [{{PDBlink}}6m8n 6m8n]). have been determined in 2018. The''Psychromonas sp.'' (PDB: [{{PDBlink}}6m8n 6m8n]) enzyme showed a single catalytic domain with a (β/α)<sub>8</sub> / TIM-barrel fold, while in the ''Mariniflexile fucanivorans'' enzyme, this catalytic domain is followed by three Ig-like domains that wrap around the catalytic one.<cite>Vickers2018</cite> |
== Family Firsts == | == Family Firsts == | ||
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== References == | == References == | ||
<biblio> | <biblio> | ||
| + | |||
| + | #Vickers2018 pmid=30282808 | ||
#Cantarel2009 pmid=18838391 | #Cantarel2009 pmid=18838391 | ||
| + | |||
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version]. | #DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version]. | ||
</biblio> | </biblio> | ||
[[Category:Glycoside Hydrolase Families|GH107]] | [[Category:Glycoside Hydrolase Families|GH107]] | ||
Revision as of 09:25, 12 December 2019
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: ^^^David Teze^^^
- Responsible Curator: ^^^Al Boraston^^^
| Glycoside Hydrolase Family GH107 | |
| Clan | GH-R |
| Mechanism | retaining |
| Active site residues | known |
| CAZy DB link | |
| https://www.cazy.org/GH107.html | |
Substrate specificities
The glycoside hydrolases of this family are endo-acting α-fucosidases active on sulfated fucans (or fucoidans) from brown algae.
All described GH107 family members are endo-1,4-fucanase of bacterial origin.
With enzymes from the CAZY family GH29 they form the clan GH-R.
Kinetics and Mechanism
Content is to be added here.
Catalytic Residues
The catalytic nucleophile is an aspartate, while the catalytic acid-base is a histidine. The later is unusual in GHs, and a divergence from GH29, but is likely necessary to avoid electronic repulsion with the substrate sulfate groups.
Three-dimensional structures
The crystal structures of Mariniflexile fucanivorans (PDB: 6dns,6dms,6dlh) and Psychromonas sp. (PDB: 6m8n). have been determined in 2018. ThePsychromonas sp. (PDB: 6m8n) enzyme showed a single catalytic domain with a (β/α)8 / TIM-barrel fold, while in the Mariniflexile fucanivorans enzyme, this catalytic domain is followed by three Ig-like domains that wrap around the catalytic one.[1]
Family Firsts
- First stereochemistry determination
- Content is to be added here.
- First catalytic nucleophile identification
- Content is to be added here.
- First general acid/base residue identification
- Content is to be added here.
- First 3-D structure
- Content is to be added here.
References
- Vickers C, Liu F, Abe K, Salama-Alber O, Jenkins M, Springate CMK, Burke JE, Withers SG, and Boraston AB. (2018). Endo-fucoidan hydrolases from glycoside hydrolase family 107 (GH107) display structural and mechanistic similarities to α-l-fucosidases from GH29. J Biol Chem. 2018;293(47):18296-18308. DOI:10.1074/jbc.RA118.005134 |
- 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 |
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Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. The Biochemist, vol. 30, no. 4., pp. 26-32. Download PDF version.