7BYX

Crystal structure of exo-beta-1,3-galactanase from Phanerochaete chrysosporium Pc1,3Gal43A E208A with beta-1,3-galactotriose

Summary for 7BYX

• Entry DOI: 10.2210/pdb7byx/pdb
• Related: 7BYS 7BYT 7BYV
• Descriptor: Galactan 1,3-beta-galactosidase, 2-acetamido-2-deoxy-beta-D-glucopyranose, alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (11 entities in total)
• Functional Keywords: glycoside hydrolase family 43, exo-beta-1, 3-galactanase, arabinogalactan degrade, complex with beta-1, 3-galactotriose, hydrolase, carbohydrate binding module family 35
• Biological source: Phanerochaete chrysosporium (White-rot fungus)
• Total number of polymer chains: 4
• Total formula weight: 192232.16

Authors

Matsuyama, K.,Ishida, T.,Kishine, N.,Fujimoto, Z.,Igarashi, K.,Kaneko, S. (deposition date: 2020-04-24, release date: 2020-11-04, Last modification date: 2023-11-29)

Primary citation

Matsuyama, K.,Kishine, N.,Fujimoto, Z.,Sunagawa, N.,Kotake, T.,Tsumuraya, Y.,Samejima, M.,Igarashi, K.,Kaneko, S.
Unique active-site and subsite features in the arabinogalactan-degrading GH43 exo-beta-1,3-galactanase from Phanerochaete chrysosporium .
J.Biol.Chem., 295:18539-18552, 2020

PubMed Abstract: Arabinogalactan proteins (AGPs) are plant proteoglycans with functions in growth and development. However, these functions are largely unexplored, mainly because of the complexity of the sugar moieties. These carbohydrate sequences are generally analyzed with the aid of glycoside hydrolases. The exo-β-1,3-galactanase is a glycoside hydrolase from the basidiomycete (1,3Gal43A), which specifically cleaves AGPs. However, its structure is not known in relation to its mechanism bypassing side chains. In this study, we solved the apo and liganded structures of 1,3Gal43A, which reveal a glycoside hydrolase family 43 subfamily 24 (GH43_sub24) catalytic domain together with a carbohydrate-binding module family 35 (CBM35) binding domain. GH43_sub24 is known to lack the catalytic base Asp conserved among other GH43 subfamilies. Our structure in combination with kinetic analyses reveals that the tautomerized imidic acid group of Gln serves as the catalytic base residue instead. 1,3Gal43A has three subsites that continue from the bottom of the catalytic pocket to the solvent. Subsite -1 contains a space that can accommodate the C-6 methylol of Gal, enabling the enzyme to bypass the β-1,6-linked galactan side chains of AGPs. Furthermore, the galactan-binding domain in CBM35 has a different ligand interaction mechanism from other sugar-binding CBM35s, including those that bind galactomannan. Specifically, we noted a Gly → Trp substitution, which affects pyranose stacking, and an Asp → Asn substitution in the binding pocket, which recognizes β-linked rather than α-linked Gal residues. These findings should facilitate further structural analysis of AGPs and may also be helpful in engineering designer enzymes for efficient biomass utilization.

PubMed: 33093171
DOI: 10.1074/jbc.RA120.016149

Experimental method

X-RAY DIFFRACTION (2.3 Å)