Glycoside Hydrolase Family 128

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• Author: ^^^Yuichi Sakamoto^^^ and ^^^Camilla Santos^^^
• Responsible Curator: ^^^Mario Murakami^^^

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Glycoside Hydrolase Family GH128
Clan	GH-A
Mechanism	retaining
Active site residues	known
CAZy DB link
https://www.cazy.org/GH128.html

Substrate specificities

Glycoside hydrolase Family 128 comprises prokaryotic and eukaryotic enzymes that are active on β-1,3-glucans. Endo-β-1,3-glucanases that degrade the carbohydrate at higher rates are found in bacterial subgroups (I and II) such as those from Amycolatopsis mediterranei [1] and Pseudomonas viridiflava [1]. Fungal enzymes, which are likely involved in cell wall remodeling processes, are more diverse in terms of activity: endo-β-1,3-glucanases, represented by the enzyme from Lentinula edodes (subgroup IV) [1, 2]; exo-β-1,3-glucanases that release trisaccharides (Aureobsidium namibiae, subgroup VI) [1] and monosaccharides (Cryptococcus neoformans, subgroup V) [1] from the reducing ends; and exo-β-1,3-glucanases that release trisaccharides from the non-reducing ends of triple-helical β-1,3-glucans, represented by the enzyme from Blastomyces gilchristii (subgroup III) [1]. Some fungal members from this family are devoid of catalytic activity but conserve the capacity to bind short β-1,3-glucooligosaccharides (subgroup VII) such as those from Trichoderma gamsii [1] and a second GH128 member from Cryptococcus neoformans [1].

Kinetics and Mechanism

Family 128 enzymes are retaining enzymes, which operate by a classical Koshland retention mechanism as confirmed through ¹H-nuclear magnetic resonance spectroscopy with the retention of the anomeric configuration of enzymatic products [1].

Catalytic Residues

As a clan GH-A family, the two acidic catalytic residues are located at the C-terminal ends of the strands β7 and β4. Both nucleophile and acid/base are glutamates and their function were validated by site-directed mutagenesis [1]

Three-dimensional structures

The GH128 members exhibit a fold resembling an (α/β)₈-barrel in which the helix α2 and the strand β3 are strictly absent [1]. Some enzymes such as the endo-β-1,3-glucanase from Lentinula edodes and the exo-β-1,3-glucanase from Cryptococcus neoformans, also lack the helices α1 and α3, respectively [1].

Two distinct modes of substrate binding were observed in the GH128 family [1]. The most widespread mode, named as hydrophobic knuckle, involves a tryptophan residue that interacts with four glucoside moieties from -5 to -2 and is fully complementary to the typically curved conformation of β-1,3-glucan chains. The other mode, only observed in fungal members belonging to subgroups IV and VI, requires substrate conformational changes to allow the binding to the catalytic interface. In these fungal subgroups, the hydrophobic knuckle is absent and two aromatic residues, positioned at the -5 and -4 subsites, create a linearized cleft, which requires a 180° torsion in the glycosidic bond between the glycosyl moieties -2 and -3 in the β-1,3-glucan chain for binding. This mode of substrate recognition is called as “flattening” mechanism due to the unusual conformational, but also stereochemically favorable, adopted by the substrate. It is notable that such mode of substrate binding was not yet observed in other CAZy families active on β-1,3-glucans.

Clustering of GH128

Figure 1. Clustering of the GH128 family into seven subgroups. Adapted from [1].

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After creation of the GH128 family by Y. Sakamoto and colleagues [2], the group headed by M. Murakami carried out a task force to explore the functional and structural diversity of this family [1]. For this purpose, they employed phylogenetic and SSN analyses to segregate the family into putative isofunctional subgroups. The SSN analysis resulted in two well discretized clusters (subgroups VI and VII) and a third cluster that was further subdivided into five subgroups (I to V) based on SSN alignment scores and evolutionary closeness (Fig. 1). Them, they characterized, biochemically and structurally, one or more members of each subgroup: AmGH128_I, PvGH128_II, ScGH128_II, BgGH128_III, LeGH128_IV, CnGH128_V, AnGH128_VI, TgGH128_VII and CnGH128_VII. Subgroups I and II were found to be predominantly present in bacteria, and the subgroups III to VII are mostly found in fungi. Bacterial enzymes are faster, present the hydrophobic knuckle and attack the β-1,3-glucan in an endo mode of action, which is compatible with their biological function: nutrition and competition. Fungal β-1,3-glucanases are known to act on remodeling of their own cell walls. Therefore, these enzymes are slower, more diverse in terms of substrate recognition modes (flattening mechanism - subgroups IV and VI; hydrophobic knuckle - subgroups III, V and VII) and mode of action (exo-enzymes - subgroups III, V and VI; endo-enzymes - subgroup IV; oligosaccharide binding protein - subgroup VII). It was the first time that a glycoside hydrolase family was rationally studied based on SSN analysis. It is noteworthy to mention that a recent study led by Prof. H. Brumer applied a similar strategy to classify the polyspecific GH16 family into isofunctional subgroups using the available functional and structural data in the literature [3]. In addition, Brumer´s group made available an intuitive and robust program to perform SSN analyses, named as SSNpipe that is freely available from GitHub.

Family Firsts

First stereochemistry determination

Amycolatopsis mediterranei endo-β-1,3-glucanase (AmGH128_I) by ¹H-NMR [1].

First catalytic nucleophile identification

Amycolatopsis mediterranei endo-β-1,3-glucanase (AmGH128_I), by site-directed mutagenesis based on structural analysis [1].

First general acid/base residue identification

Amycolatopsis mediterranei endo-β-1,3-glucanase (AmGH128_I), by site-directed mutagenesis based on structural analysis [1].

First 3-D structure

Amycolatopsis mediterranei endo-β-1,3-glucanase (AmGH128_I) [1].

References

1. Santos CR, Costa PACR, Vieira PS, Gonzalez SET, Correa TLR, Lima EA, Mandelli F, Pirolla RAS, Domingues MN, Cabral L, Martins MP, Cordeiro RL, Junior AT, Souza BP, Prates ÉT, Gozzo FC, Persinoti GF, Skaf MS, and Murakami MT. (2020). Structural insights into β-1,3-glucan cleavage by a glycoside hydrolase family. Nat Chem Biol. 2020;16(8):920-929. DOI:10.1038/s41589-020-0554-5 |
2. Sakamoto Y, Nakade K, and Konno N. (2011). Endo-β-1,3-glucanase GLU1, from the fruiting body of Lentinula edodes, belongs to a new glycoside hydrolase family. Appl Environ Microbiol. 2011;77(23):8350-4. DOI:10.1128/AEM.05581-11 |
3. Viborg AH, Terrapon N, Lombard V, Michel G, Czjzek M, Henrissat B, and Brumer H. (2019). A subfamily roadmap of the evolutionarily diverse glycoside hydrolase family 16 (GH16). J Biol Chem. 2019;294(44):15973-15986. DOI:10.1074/jbc.RA119.010619 |