8YFH

Structure of alpha-1,3-glucanase agn1

Summary for 8YFH

• Entry DOI: 10.2210/pdb8yfh/pdb
• Descriptor: Glucan endo-1,3-alpha-glucosidase agn1 (2 entities in total)
• Functional Keywords: glucanase, hydrolase
• Biological source: Schizosaccharomyces pombe DM3650
• Total number of polymer chains: 3
• Total formula weight: 133604.54

Authors

Horaguch, Y.,Yano, S.,Makabe, K. (deposition date: 2024-02-24, release date: 2025-02-26, Last modification date: 2026-03-11)

Primary citation

Horaguchi, Y.,Saitoh, H.,Konno, H.,Makabe, K.,Yano, S.
Crystal structure of GH71 alpha-1,3-glucanase Agn1p from Schizosaccharomyces pombe: an enzyme regulating cell division in fission yeast.
Biochem.Biophys.Res.Commun., 766:151907-151907, 2025

PubMed Abstract: Agn1p is a glycoside hydrolase family 71 α-1,3-glucanase from Schizosaccharomyces pombe. It is involved in cell division and releases nigero-pentaose from α-1,3-glucan as a primary hydrolysate. In this study, we used x-ray crystallography to determine the molecular structure of Agn1p, achieving a resolution of 1.80 Å for its free form and 2.10 Å for the substrate complex structure of an inactive mutant. We find that Agn1p comprises eight α-helices and sixteen β-strands, and these combined into a classical (α/β) TIM-barrel core domain and a β-sandwich accessory domain. The TIM-barrel had a deep cavity in the center. Next, to determine which amino acid residues are involved in the catalytic reaction, we conducted substitution experiments on Asp-69, Asp-237, and Glu-240, three residues located in the cavity, preparing the corresponding substitution mutants D69N, D237A, D237N, E240A and E240Q. We found that the far-UV CD spectra of the five substitution mutants were similar to those of wild-type Agn1p, but all five mutants lost α-1,3-glucan hydrolyzing activity. We also obtained the cocrystal of the D237N mutant and nigero-heptaose, and its structure was determined. Specifically, we observed the electron density for the hexamer or pentamer sugar portion of nigero-heptaose. Moreover, the substrates were located in the vicinity of Asp-69, Asp-237, and Glu-240. Overall, these results suggest that Agn1p contains a stable substrate binding site for the hexamer or pentamer sugar structure of nigero-oligosaccharide.

PubMed: 40306164
DOI: 10.1016/j.bbrc.2025.151907

Experimental method

X-RAY DIFFRACTION (1.8 Å)