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, only coordinated by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction to take place [1]. Sequence alignment suggest that the enzymes of clades B and C do not bind zinc ions which could be related to the difference of substrate.

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 Zg4663. 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 |

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].