Crystal structure of endo-β-1,6-galactanase from Streptomyces avermitilis

Endo-β-1,6-galactanases hydrolyze β-1,6-linked galactosyl linkages in galactans, yielding β-1,6-linked galacto-oligosaccharides, predominantly galactobiose. Here, we report to our knowledge the first crystal structure of an endo-β-1,6-galactanase, together with its β-1,6-galactobiose-bound complex, revealing the structural basis for substrate recognition by this enzyme. Endo-β-1,6-galactanase from Streptomyces avermitilis (Sa16Gal30A) is a member of glycoside hydrolase family 30 (GH30) subfamily 5. Sa16Gal30A consists of two structural domains: a catalytic (β/α)₈-barrel domain and an appended β-sandwich domain. The β-1,6-galactobiose complex structure revealed two β-1,6-galactobiose molecules bound within the catalytic domain: one at the catalytic site and another at the distinct surface site distal to the catalytic center. This structure represents the first reported structure of a GH30 subfamily 5 enzyme and provides structural insights into the molecular basis of β-1,6-galactan recognition within the catalytic cleft. Sa16Gal30A possesses three extended regions, loops 2, 4 and 8, in the catalytic domain compared with enzymes from other GH30 subfamilies, and these loops appear to modulate substrate specificity towards β-1,6-galactan by shaping the architecture of the catalytic cleft. In addition, a secondary β-1,6-galactan-binding site was identified at a distal location, which may function as a distal subsite, thereby facilitating the efficient hydrolysis of long β-1,6-galactan chains.