Glycoside Hydrolase Family 173

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• Authors: Clelton Aparecido dos Santos and Gabriela Felix Persinoti
• Responsible Curator: Mario Murakami

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Glycoside Hydrolase Family GH173
Clan	GH-A
Mechanism	retaining (inferred)
Active site residues	known (inferred)
CAZy DB link
https://www.cazy.org/GH173.html

Substrate specificities

The GH173 family comprises so far members with β-galactosidase activity [1]. The founding member of the GH173 family named herein as CapGH173 (PBMDCECB_44807), was identified in a metagenome-assembled genome (Bacteroidales bacterium MAG42) recovered from capybara gut microbiota, which potentially represents a novel genus from the UBA932 family. The enzyme CapGH173 was found in a Polysaccharide Utilization Loci (PUL) that includes enzymes from the families GH2 and GH78, yet the target carbohydrate remains unclear. GH173 members often exhibit a modular architecture including a GH36 domain. Substrate kinetics characterization of CapGH173 was demonstrated on synthetic substrate p-nitrophenyl-β-D-galactopyranoside (pNP-β-D-Gal). Phylogenetic analysis showed that this family belongs to the GH-A clan, being remotely related to the families GH30 and GH5 [1].

Kinetics and Mechanism

GH173 members are inferred to be retaining enzymes [1].

Catalytic Residues

The residues E305 and E207 (sequence numbering based on the founding member, CapGH173) was inferred to correspond to the nucleophile and acid/base, respectively, based on the structural analysis of AlphaFold models [1].

Three-dimensional structures

Protein modeling and threading performed using AlphaFold and PDBsum, respectively, suggest that CapGH173 consists of an (α/β)₈-barrel structure, which is an archetypal scaffold of the clan GH-A. According to structural predictions, CapGH173 exhibits a two-domain architecture including an appended β-sandwich domain, which is a similar structural organization found in the GH30 family. Except for the residues defining the clan GH-A, sequence alignment with GH5 and GH30 members revealed very low sequence conservation, below the criterium for significant similarity detection (using an e-value < 0.05), demonstrating that although the domains in the tertiary structure can be similar, the sequences between these families are remarkably diverse [1].  

Family Firsts

First stereochemistry determination

CapGH173 is inferred to operate by a retaining mechanism.

First catalytic nucleophile identification

E305 (inferred).

First general acid/base residue identification

E207 (inferred).

First 3-D structure

Currently no experimental structure is available for GH173 members.

References

1. Cabral L, Persinoti GF, Paixão DAA, Martins MP, Morais MAB, Chinaglia M, Domingues MN, Sforca ML, Pirolla RAS, Generoso WC, Santos CA, Maciel LF, Terrapon N, Lombard V, Henrissat B, and Murakami MT. (2022). Gut microbiome of the largest living rodent harbors unprecedented enzymatic systems to degrade plant polysaccharides. Nat Commun. 2022;13(1):629. DOI:10.1038/s41467-022-28310-y |