Fig. 1.

Tertiary structures of representative family GH13 α-amylases. The structures from following subfamilies and origins are shown: a GH13_1, Aspergillus oryzae (PDB code: 2TAA; [31]); b GH13_5, Bacillus licheniformis (PDB code: 1BLI; [249]); c GH13_6, Hordeum vulgare—barley isozyme AMY-1 (PDB code: 1P6W; [129]); d GH13_37, uncultured bacterium AmyP (modeled structure; residues Leu6-Thr491) obtained from the Phyre server [245] based on the Flavobacterium sp. 92 GH13 cyclomaltodextrinase (PDB code: 3EDE; [205]) as template; e unclassified, A. haloplanktis (PDB code: 1G94; [12]); f unclassified, Halothermothrix orenii AmyB (PDB code: 3BC9; [70]); g unclassified, Bacteroides thetaiotaomicron (PDB code: 3K8L; [38]). The individual domains are colored as follows: catalytic (β/α)₈-barrel blue, domain B green, domain C red, N-terminal domain cyan; starch-binding domain of CBM58 family magenta. The GH13 catalytic triad, i.e., catalytic nucleophile—Asp (top), proton donor—Glu (left) and transition-state stabilizer—Asp (right)—is highlighted in the (β/α)₈-barrel domain in each structure in a similar position. Saccharide molecules are colored yellow to emphasize: c an additional surface binding site as “a pair of sugar tongs” with the side-chain of tyrosine (in black) involved in binding; e a heptasaccharide occupying the subsites from −4 to +3 as a transglycosylation product from acarbose (a pseudotetrasaccharide); and g a maltopentaose bound by the SBD of the family CBM58 inserted within the domain B. The structures were retrieved from the Protein Data Bank (PDB; [250]) and visualized with the program WebLabViewerLite (Molecular Simulations, Inc.)