Table 1.
Characteristics of docking trials of the N-terminal domain of four selected amylomaltasesa
| N-terminal domain | G2 | G3 | G4 | β-CD |
|---|---|---|---|---|
| E. coli | Vina Score: − 4.6 | Vina Score: − 5.1 | Vina Score: − 5.8 | Vina Score: − 5.0 |
| T81, T82, E83, Y108, T110 × 2 | T82, E83, E84, Y108, T110 × 2, R123 × 2 | T81 × 2, E83, Q87, Y108 × 2, H109, T110, T112 | N56 × 2, Y108, T110 × 2, R123 × 3 | |
| C. glutamicum | Vina Score: − 4.3 | Vina Score: − 4.6 | Vina Score: − 5.1 | Vina Score: − 4.7 |
| E102 × 2, L103 × 2, E104, W143 | E102 × 2, L103, E104 × 2, W143, H144 × 2, K145 × 3, G158 | E102, L103 × 2, E104, W143, H144, E156, G158 | W143, H144 × 2, K145 × 2, E156 × 3, G158 | |
| K. marisflavi | Vina Score: − 4.7 | Vina Score: − 5.9 | Vina Score: − 4.8 | Vina Score: − 4.3 |
| D97, E98, Y121, Y122 × 2 | P71, I96, D97, Y122 × 2, R130 × 3 | I96, D97, E98 × 3, Y121, R130 × 2, | E98 × 2, S99, G100 × 2, Y121, Q123 × 3, R130 | |
| P. thermopropionicum | Vina Score: − 3.7 | Vina Score: − 3.8 | Vina Score: − 4.6 | Vina Score: − 4.2 |
| L103, E104 × 3, Y146, Q148 | S78 × 2, K107 × 2, G141, L142 | S78, E104, N105 × 2, K107, L142, P143, W144 × 2 | K150 × 3, Q157, E159 |
aThe results of docking maltose (G2), maltotriose (G3), maltotetraose (G4) and β-cyclodextrin (β-CD) on the structure of the hypothesised CBM and putative novel SBD of four representative family GH77 amylomaltases. The structures of potential CBMs in amylomaltases from Escherichia coli (Weiss et al. 2015; PDB: 4S3Q) and Corynebacterium glutamicum (Joo et al. 2016; PDB: 5B68) were extracted from their structural coordinates, whereas the counterparts from Kushneria marisflavi (UniProt: A0A240US28) and Pelotomaculum thermopropionicum (UniProt: A5D1W1) were obtained by homology modelling using the fold recognition approach performed on the Phyre2 server (Kelley and Sternberg 2009). Vina Score means the binding energy (kJ/mol) for the individual complexes. The residues represent the residues with numbering from the N-terminus of a given amylomaltase involved in the hydrogen bond contact with the respective oligosaccharide; for some of the residues, there are more bond contacts (indicated by “ × 2” or “ × 3”). Note, not all of them belong to the five CSRs (Figs. 2 and 4). The complexes with maltose and β-CD are displayed in Fig. 5 for the two experimentally determined structures and in Fig. 6 for two modelled structures