fig3

Figure 3. Sequence comparison within the structure-determined GH42 members. (A) The amino acid residues involved in ligand recognition in BiBga42A were aligned with eight structure-determined GH42 β-galactosidases using the ClustalW program^[44]. The residue numbers are based on BiBga42A. The sugar moieties interacting with the respective amino acid residues are indicated by their subsite positions. Asterisks indicate the residues from the neighboring subunit; (B) Structure-determined enzymes, i.e., eight β-galactosidases (blue) and one α-arabinopyranosidase (brown), and BiBga42A (bold black) were used for the tree construction. The Uniprot numbers, PDB IDs, and taxonomic names are shown. β-Galactosidase from B. adolescentis (PDB ID: 5VYM) was omitted from the analysis because the structure does not contain the catalytic domain. The maximum likelihood tree was constructed using MegaX based on the sequences aligned using ClustalW with default settings^[43]. The lowest amino acid identity detected among the members is 20% between B. lactis A0A2H4A2Z3 and B. bifidum E3EPA1, G. stearothermophilus F8TRX0, or Thermus sp. O69315, while the highest one is 76% between B. infantis B7GUD7 (BiBga42A) and B. bifidum E3EPA1 (BbgII). The sequences are: B. bifidum E3EPA1^[24], B. animalis subsp. lactis C6A6W5^[25], N. circulans subsp. alkalophilus A0A4D6T0U7^[26], G. stearothermophilus F8TRX0^[27], Rahnella sp. A0A0B4U8I5^[28], H. lacusprofundi B9LW28^[29], Marinomonas sp. A0A6P3CWF7^[30], T. thermophilus O69315^[23], and B. animalis subsp. lactis A0A2H4A2Z3^[31]. BiBga42A: a glycoside hydrolase family 42 β-galactosidase; GH: glycoside hydrolase.