8JHH

Glycoside hydrolase family 55 endo-beta-1,3-glucanase from Microdochium nivale

This is a non-PDB format compatible entry.

Summary for 8JHH

• Entry DOI: 10.2210/pdb8jhh/pdb
• Descriptor: MnLam55A, GLYCEROL (3 entities in total)
• Functional Keywords: endo-beta-1, 3-glucanase, glycoside hydrolase family 55, laminarinase, glycosidase, hydrolase
• Biological source: Microdochium nivale
• Total number of polymer chains: 2
• Total formula weight: 160940.55

Authors

Ota, T.,Saburi, W.,Yamashita, K.,Tagami, T.,Yu, J.,Komba, S.,Jewell, L.E.,Hsiang, T.,Imai, R.,Yao, M.,Mori, H. (deposition date: 2023-05-23, release date: 2024-04-03, Last modification date: 2024-11-13)

Primary citation

Ota, T.,Saburi, W.,Tagami, T.,Yu, J.,Komba, S.,Jewell, L.E.,Hsiang, T.,Imai, R.,Yao, M.,Mori, H.
Molecular mechanism for endo-type action of glycoside hydrolase family 55 endo-beta-1,3-glucanase on beta 1-3/1-6-glucan.
J.Biol.Chem., 299:105294-105294, 2023

PubMed Abstract: The glycoside hydrolase family 55 (GH55) includes inverting exo-β-1,3-glucosidases and endo-β-1,3-glucanases, acting on laminarin, which is a β1-3/1-6-glucan consisting of a β1-3/1-6-linked main chain and β1-6-linked branches. Despite their different modes of action toward laminarin, endo-β-1,3-glucanases share with exo-β-1,3-glucosidases conserved residues that form the dead-end structure of subsite -1. Here, we investigated the mechanism of endo-type action on laminarin by GH55 endo-β-1,3-glucanase MnLam55A, identified from Microdochium nivale. MnLam55A, like other endo-β-1,3-glucanases, degraded internal β-d-glucosidic linkages of laminarin, producing more reducing sugars than the sum of d-glucose and gentiooligosaccharides detected. β1-3-Glucans lacking β1-6-linkages in the main chain were not hydrolyzed. NMR analysis of the initial degradation of laminarin revealed that MnLam55A preferentially cleaved the nonreducing terminal β1-3-linkage of the laminarioligosaccharide moiety at the reducing end side of the main chain β1-6-linkage. MnLam55A liberates d-glucose from laminaritriose and longer laminarioligosaccharides, but k/K values to laminarioligosaccharides (≤4.21 s mM) were much lower than to laminarin (5920 s mM). These results indicate that β-glucan binding to the minus subsites of MnLam55A, including exclusive binding of the gentiobiosyl moiety to subsites -1 and -2, is required for high hydrolytic activity. A crystal structure of MnLam55A, determined at 2.4 Å resolution, showed that MnLam55A adopts an overall structure and catalytic site similar to those of exo-β-1,3-glucosidases. However, MnLam55A possesses an extended substrate-binding cleft that is expected to form the minus subsites. Sequence comparison suggested that other endo-type enzymes share the extended cleft. The specific hydrolysis of internal linkages in laminarin is presumably common to GH55 endo-β-1,3-glucanases.

PubMed: 37774972
DOI: 10.1016/j.jbc.2023.105294

Experimental method

X-RAY DIFFRACTION (2.4 Å)