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 characterized within this recently discovered family of glycoside hydrolases is that of α-1,3-L-(3,6-anhydro)-galactosidase [1, 2, 3, 4]. Nevertheless phylogenetic analyses (Figure 1) of this family together with activity tests for another member, Zg3597 (Clade C), show that the family GH117 most probably is polyspecific [1].

Kinetics and Mechanism

The stereochemical outcome of members of glycoside hydrolase family GH117 is still not determined experimentally. Nevertheless a mechanism based on the structure of an inactive mutant complexed to a neoagarobiose have been proposed [4] (Figure 2). In this unusual inverting catalytic mechanism an aspartic acid acting as the base and a histidine acting as the acid.

Two of the three 3D structures revealed the presence of a divalent cation, directly coordinated only by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction [1, 4]. Sequence alignments suggest that the enzymes of clades B and C do not bind zinc ions, which could be related to their difference in substrate specificity [1].

Catalytic Residues

From structural analysis and sequence alignments the catalytic residues have been predicted to be two 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 [5] and one from Zobellia 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]. AhgA adopts a five-bladed β-propeller fold and forms a 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) lacks the domain-swapping signature, in which the crucial residues are missing. This enzyme from R. baltica thus likely occurs as a monomer and may represent an ‘ancestral’ form of the GH117 family, which would be limited to the catalytic β-propeller domain [1].

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

Family Firsts

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

The first 3D structure was reported in 2011 for an α-1,3-L-(3,6-anhydro)-galactosidase (AhgA or Zg4663) from the marine bacteria Zobellia galactanivorans, 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 |
5. 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 |