7bys | pdb_00007bys
Crystal structure of exo-beta-1,3-galactanase from Phanerochaete chrysosporium Pc1,3Gal43A apo form
Structural highlights
Publication Abstract from PubMedArabinogalactan 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-beta-1,3-galactanase is a glycoside hydrolase from the basidiomycete Phanerochaete chrysosporium (Pc1,3Gal43A), 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 Pc1,3Gal43A, which reveal a glycoside hydrolase family 43 subfamily 24 (GH43_sub24) catalytic domain together with a carbohydrate-binding module family (CBM) 35 binding domain. GH43_sub24 is known to lack the catalytic base Asp conserved among other GH43 subfamilies. Our structure in combination with kinetic analyses reveal that the tautomerized imidic acid group of Gln263 serves as the catalytic base residue instead. Pc1,3Gal43A 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 beta-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 beta-linked rather than alpha-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. Unique active site and subsite features in the arabinogalactan-degrading GH43 exo-beta-1,3-galactanase from Phanerochaete chrysosporium.,Matsuyama K, Kishine N, Fujimoto Z, Sunagawa N, Kotake T, Tsumuraya Y, Samejima M, Igarashi K, Kaneko S J Biol Chem. 2020 Oct 22. pii: RA120.016149. doi: 10.1074/jbc.RA120.016149. PMID:33093171[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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