Glycoside Hydrolase Family 107

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• Author: ^^^David Teze^^^
• Responsible Curator: ^^^Al Boraston^^^

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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, and together with enzymes from the CAZY family GH29, they form the clan GH-R. Members of the GH107 family were first described in 2006.[1]

Kinetics and Mechanism

The mechanism was proven to be retaining by observation of the formation of an alpha-linked mercaptoethanol by transglycosylation.[2] It should then follow a classical Koshland double-displacement mechanism similarly to GH29.

Figure 1: Mechanism of GH107 family. According to [2].

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. These two residues have been identified by structural superimposition with GH29 enzymes, and are conserved within the few members of the GH107 family. The catalytic His has been confirmed by the lack of activity of th H294Q mutant of Mariniflexile fucanivorans, despite its structure was maintained.[2] The catalytic aspartate was also proposed to be one of the catalytic residue on sequence analysis alone, in a simultaneous paper.[3]

Three-dimensional structures

The crystal structures of Mariniflexile fucanivorans (PDB: 6dns,6dms,6dlh) and Psychromonas sp. (PDB: 6m8n) have been determined in 2018.[2] 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.[2]

Family Firsts

First stereochemistry determination

Content is to be added here.

First catalytic nucleophile identification

The catalytic nucleophile has been identified as a catalytic residue by two simultaneous studies, in the Autumn of 2018.[2][3]

First general acid/base residue identification

The catalytic histidine has been identified in 2018.[2]

First 3-D structure

The crystal structures of Mariniflexile fucanivorans (PDB: 6dns,6dms,6dlh) and Psychromonas sp. (PDB: 6m8n) have been released at the same time, in 2018.[2]

References

1. Colin S, Deniaud E, Jam M, Descamps V, Chevolot Y, Kervarec N, Yvin JC, Barbeyron T, Michel G, and Kloareg B. (2006). Cloning and biochemical characterization of the fucanase FcnA: definition of a novel glycoside hydrolase family specific for sulfated fucans. Glycobiology. 2006;16(11):1021-32. DOI:10.1093/glycob/cwl029 |
2. 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 |
3. Schultz-Johansen M, Cueff M, Hardouin K, Jam M, Larocque R, Glaring MA, Hervé C, Czjzek M, and Stougaard P. (2018). Discovery and screening of novel metagenome-derived GH107 enzymes targeting sulfated fucans from brown algae. FEBS J. 2018;285(22):4281-4295. DOI:10.1111/febs.14662 |
4. 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 |

5. 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.