Glycoside Hydrolase Family 117

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

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Glycoside Hydrolase Family GH117
Clan	None
Mechanism	Not known
Active site residues	Not known
CAZy DB link
https://www.cazy.org/GH117.html

Substrate specificities

Figure 1: Phylogeny of GH117 family. From [1].

The only activity so far identified in this recently discovered family of glycoside hydrolases is that α-1,3-L-(3,6-anhydro)-galactosidase [1, 2, 3]. Nevertheless phylogenetic analysis (figure 1) of this family and activity test on Zg3597 (Clade C) show that the family GH117 is polyspecific [1].

Kinetics and Mechanism

Mechanism of glycoside hydrolase family 117 is still unknown. But structural analyse revealed the presence of a zinc ion close to the active site which could be involved in the reaction mechanism [1].

Catalytic Residues

From structural analysis and sequences alignment the catalytic residues have been predicted to be two out of the three acidic residues Asp-97, Asp-252 and Glu-310 (Zg4663 numbering) [1].

Three-dimensional structures

At the moment two members of GH117 family have been crystallized. Both are enzymes from marine bacteria, one from Saccharophagus degradans [4] and one from Zobelia galactanivorans [1]. A crystal structure has only been reported for the α-1,3-L-(3,6-anhydro)-galactosidase (AhgA, Zg4663) from Z. galactanivorans (PDB: 3P2N) [1]. Zg4663 adopting the five-bladed β-propeller fold and form dimer via domain-swapping of the N-terminal HTH (Helix-Turn-Helix) domain (Figure 2) [1]. Interestingly, previous sequences reported from Vibrio sp. JT0107 and Bacillus sp. MK03 contain the conserved domain-swapping signature SxAxxR in the HTH domain. Consistently, these proteins were reported to form multimers (a dimer and an octamer respectively), based on calibrated gel filtration estimations [2, 3]. In contrast, RB13146 (Clade B) misses the domain-swapping signature, and the crucial residues are missing. This protein from R. baltica is thus likely a monomer and may represent an ‘ancestral’ form of the GH117 family which would be limited to the β-propeller, catalytic domain [1].

Figure 2: Structure of the dimer of AhgA. From [1].

Family Firsts

First stereochemistry determination

Cite some reference here, with a short (1-2 sentence) explanation [5].

First catalytic nucleophile identification

Cite some reference here, with a short (1-2 sentence) explanation [6].

First general acid/base residue identification

Cite some reference here, with a short (1-2 sentence) explanation [7].

First 3-D structure

Zg4663, α-1,3-L-(3,6-anhydro)-galactosidase (AhgA), PDB: 3P2N [1].

References

1. Rebuffet E, Groisillier A, Thompson A, Jeudy A, Barbeyron T, Czjzek M, and Michel G. (2011). Discovery and structural characterization of a novel glycosidase family of marine origin. Environ Microbiol. 2011;13(5):1253-70. DOI:10.1111/j.1462-2920.2011.02426.x |
2. Sugano Y, Kodama H, Terada I, Yamazaki Y, and Noma M. (1994). Purification and characterization of a novel enzyme, alpha-neoagarooligosaccharide hydrolase (alpha-NAOS hydrolase), from a marine bacterium, Vibrio sp. strain JT0107. J Bacteriol. 1994;176(22):6812-8. DOI:10.1128/jb.176.22.6812-6818.1994 |
3. Suzuki H, Sawai Y, Suzuki T, and Kawai K. (2002). Purification and characterization of an extracellular alpha-neoagarooligosaccharide hydrolase from Bacillus sp. MK03. J Biosci Bioeng. 2002;93(5):456-63. DOI:10.1016/s1389-1723(02)80092-5 |
4. Lee S, Lee JY, Ha SC, Jung J, Shin DH, Kim KH, and Choi IG. (2009). Crystallization and preliminary X-ray analysis of neoagarobiose hydrolase from Saccharophagus degradans 2-40. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009;65(Pt 12):1299-301. DOI:10.1107/S174430910904603X |

6. Sinnott, M.L. (1990) Catalytic mechanisms of enzymic glycosyl transfer. Chem. Rev. 90, 1171-1202. DOI: 10.1021/cr00105a006

7. He S and Withers SG. (1997). Assignment of sweet almond beta-glucosidase as a family 1 glycosidase and identification of its active site nucleophile. J Biol Chem. 1997;272(40):24864-7. DOI:10.1074/jbc.272.40.24864 |
8. Robert V. Stick and Spencer J. Williams. (2009) Carbohydrates. Elsevier Science.

This is an example of how to make references to a journal article [5]. (See the References section below). Multiple references can go in the same place like this [5, 7]. You can even cite books using just the ISBN [8]. References that are not in PubMed can be typed in by hand [6].