Journal:Acta Cryst D:S2059798318014900
From Proteopedia
Structure of the AmyC GH13 alpha-amylase from Alicyclobacillus sp, reveals accommodation of starch branching points in the alpha-amylase familyJon Agirre, Olga Moroz, Sebastian Meier, Jesper Brask, Astrid Munch, Tine Hoff, Carsten Andersen, Keith S. Wilsona and Gideon J. Davies [1] Molecular Tour The complex of α-amylase from Alicyclobacillus sp. 18711 (AliC) with acarbose was solved by molecular replacement, with two molecules of AliC in the asymmetric unit, at a resolution of 2.1 Å (6gxv). The fold, as expected, is a canonical with the A, B and C domains defined approximately as A, residues 4–104 and 210–397 (in deepskyblue), B, residues 105–209 (in yellow), and C, residues 398–484 (in white). A classical Ca2+–Na+–Ca2+ [2],[3] is found at the A/B-domain interface. The structure of AliC was determined in the presence of the (colored in green). As with many (retaining) α-amylase complexes, the acarbose is observed as a transglycosylated species, here a hexasaccharide which contains two of the acarviosin disaccharide motifs. The , -4 to +2, with the expected catalytic GH13 signature triad of Asp234 (nucleophile), Glu265 (acid/base) and all disposed for catalysis, here around the 2H3 half-chair of the unsaturated cyclohexitol moiety. AliC must also be able to accommodate branching in the +2 subsite, which is consistent with the .
A ‘branched-ligand’ AliC complex was obtained through co-crystallization, with crystals forming in a new space group. This form diffracted poorly and data could only be obtained to 2.95 Å resolution 6gya). Weak density in the -1 subsite, largely diffuse but greater than would be expected for discrete solvent, remained unmodelled. Density was clearer for a panose trisaccharide with an α-1,4-linked disaccharide in subsites +1 and +2 and, crucially, clear density for an α-1,6 branch accommodated in the +1 subsite, providing a structural context for the limit digest analysis of action on amylopectin starch. The (oligosaccharide colored in green). PDB references: Amylase in complex with acarbose, 6gxv; Amylase in complex with branched ligand, 6gya. References
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