24TE
Crystal structure of GH30 Streptomyces avermitilis endo-beta-1,6-galactanase complexed with Gal-beta1,6-Gal
Summary for 24TE
| Entry DOI | 10.2210/pdb24te/pdb |
| Descriptor | Secreted endo-beta-1,6-galactanase, beta-D-galactopyranose-(1-6)-beta-D-galactopyranose, SULFATE ION, ... (6 entities in total) |
| Functional Keywords | glycoside hydrolase family 30, hydrolase |
| Biological source | Streptomyces avermitilis MA-4680 = NBRC 14893 |
| Total number of polymer chains | 1 |
| Total formula weight | 53457.77 |
| Authors | |
| Primary citation | Fujimoto, Z.,Kishine, N.,Kotake, T.,Kaneko, S. Crystal structure of endo-beta-1,6-galactanase from Streptomyces avermitilis. Acta Crystallogr D Struct Biol, 82:962-971, 2026 Cited by PubMed Abstract: 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)-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. PubMed: 42478457DOI: 10.1107/S2059798326006133 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2 Å) |
Structure validation
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