Glycoside Hydrolase Family 136

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• Author: ^^^Chihaya Yamada^^^
• Responsible Curator: ^^^Shinya Fushinobu^^^

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Glycoside Hydrolase Family GH136
Clan	GH-N
Mechanism	retaining
Active site residues	Asp
CAZy DB link
https://www.cazy.org/GH136.html

Substrate specificities

This family of glycoside hydrolases contains lacto-N-biosidase, as demonstrated for LnbX from Bifidobacterium longum JCM 1217 [1]. LnbX liberates Galβ1-3GlcNAc(lacto-N-biose I, LNB) and lactose from lacto-N-tetraose, the main component of human milk oligosaccharides. It hydrolyzed the linkage GlcNAcβ1-3Gal in lacto-N-hexaose, lacto-N-fucopentaose I, and sialyllacto-N-tetraose a of human milk oligosaccharides as substrate of LnbX in the GH136. In addition, LnbX liberates Galβ1-3GalNAc (GNB) from the sugar chains of globo- and ganglio-series glycosphingolipids [2].

GH136 lacto-N-biosidase required neighboring chaperon gene for folding. Rarely, chaperone-like gene fused to lacto-N-biosidase gene in case of ErGH136_I and ErGH136_IIfrom Eubacterium ramulus [3].

Kinetics and Mechanism

LnbXc hydrolyzes the glycosidic linkage via a retaining mechanism involving a Grotthuss proton relay.

Catalytic Residues

The nucleophile is Asp418. The catalytic acid/base is Asp411 via water molecule.

Three-dimensional structures

Figure 1: Overall structure of LnbXc with LNB (cyan) and two Ca2+ ions (orange).

Figure 2: Overall structure of ErGH136 with LNB (yellow).

The X-ray crystal structure of the catalytic domain, LnbXc(31-625) revealed a right-handed β helix fold that is usually shared by polysaccharide active enzymes. Three forms, ligand free at 2.36 Å resolution (PDB ID 5GQC), LNB complex at 1.82 Å (PDB ID 5GQF), and GNB complex at 2.70 Å (PDB ID 5GQG) were determined [4]. The X-ray crystal structure of ErGH136 in complex with LNB (PDB ID 6KQT) revealed the N-terminal domain (ErLnb136I, from AA 7-224) consists of 8 α-helices (α1-α8)　and Y145 of the α6-α7 loop positioned near the active site [3].

Family Firsts

First stereochemistry determination

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First catalytic nucleophile identification

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First general acid/base residue identification

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First 3-D structure

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References

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