Table 2. Structural alignment of the (α/β)8-barrel domain of AtAkαGal3 with rice α-galactosidase and T. maritima α-galactosidase and a sequence alignment between AtAkαGal3 and the raffinose/stachyose (Raf/Sta) synthases show the conserved, variable and potential hydrogen-bond interactions (distances within 3.5 Å) at the −1, +1, +2 and +3 subsites among these glycosidase families.
Bold labels indicate the key catalytic residues at the active site. Substrates and products: Gal, galactose; Gol, galactinol; Raf, raffinose; Sta, stachyose.
| Substrate/product | |||||||
|---|---|---|---|---|---|---|---|
| Gal | Gol | Raf | Sta | AtAkαGal3 residues 75–78, 201–531 (PDB entries 7exf, 7exg, 7exh, 7exj, 7exr, 7exq) | Rice α-galactosidase (GH27) residues 6–271 (PDB entry 1uas) | T. maritima α-galactosidase (GH36) residues 165–481 (PDB entry 6gvd) | Raf/Sta synthases (no structure, based on sequence) |
| +3 | Waters | Asp/Val | |||||
| +2 | +2 | Tyr449 | Trp | ||||
| Asp447(w) | Asp | ||||||
| Asp451(w) | Thr, (Arg)/Gln, (Arg, Glu) | ||||||
| +1 | +1 | +1 | Lys75 | Lys | |||
| Trp78 | Trp65 | Trp | |||||
| Asp446 | Trp164 (−1) | Trp | |||||
| Asp/1E | |||||||
| −1 | −1 | −1 | −1 | Asp243 | Asp51 | Asp220 | Asp |
| Asp244 | Asp52 | Asp221 | Asp | ||||
| Trp307 | Lys128 | Trp257 | Trp | ||||
| Lys381 | Lys325 | Lys | |||||
| Asp383 | Asp130 | Asp327 | Asp | ||||
| Arg443 | Arg181 | Arg383 | Arg | ||||
| Asp447 | Asp185 | Asp387 | Asp | ||||